diff options
Diffstat (limited to 'sourcecodes')
132 files changed, 335 insertions, 8749 deletions
diff --git a/sourcecodes/data/Backupfiles/evidencemodified b/sourcecodes/data/Backupfiles/evidencemodified deleted file mode 100644 index 9b3f7563..00000000 --- a/sourcecodes/data/Backupfiles/evidencemodified +++ /dev/null Binary files differdiff --git a/sourcecodes/data/Backupfiles/initialstructure b/sourcecodes/data/Backupfiles/initialstructure deleted file mode 100644 index 9ecf1bc7..00000000 --- a/sourcecodes/data/Backupfiles/initialstructure +++ /dev/null Binary files differdiff --git a/sourcecodes/data/Backupfiles/newintervention b/sourcecodes/data/Backupfiles/newintervention deleted file mode 100644 index d818a943..00000000 --- a/sourcecodes/data/Backupfiles/newintervention +++ /dev/null Binary files differdiff --git a/sourcecodes/data/Backupfiles/temp_evidence_file b/sourcecodes/data/Backupfiles/temp_evidence_file deleted file mode 100644 index b687ceaf..00000000 --- a/sourcecodes/data/Backupfiles/temp_evidence_file +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified \ No newline at end of file diff --git a/sourcecodes/data/Backupfiles/temp_intervention_file b/sourcecodes/data/Backupfiles/temp_intervention_file deleted file mode 100644 index cdf5ce0f..00000000 --- a/sourcecodes/data/Backupfiles/temp_intervention_file +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/newintervention \ No newline at end of file diff --git a/sourcecodes/data/Backupfiles/temp_shell_file_initial_structure b/sourcecodes/data/Backupfiles/temp_shell_file_initial_structure deleted file mode 100644 index 5d1c323d..00000000 --- a/sourcecodes/data/Backupfiles/temp_shell_file_initial_structure +++ /dev/null @@ -1,36 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure \ No newline at end of file diff --git a/sourcecodes/data/example1/Bqxrun_initialstructure.sh b/sourcecodes/data/example1/Bqxrun_initialstructure.sh deleted file mode 100644 index a8a8ebe0..00000000 --- a/sourcecodes/data/example1/Bqxrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Bqx -fi -exit diff --git a/sourcecodes/data/example2/hQGrun_initialstructure.sh b/sourcecodes/data/example2/hQGrun_initialstructure.sh deleted file mode 100644 index 7d4cbfea..00000000 --- a/sourcecodes/data/example2/hQGrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure hQG -fi -exit diff --git a/sourcecodes/data/example_chl/bWRrun_evidencemodified.sh b/sourcecodes/data/example_chl/bWRrun_evidencemodified.sh deleted file mode 100644 index 763a268b..00000000 --- a/sourcecodes/data/example_chl/bWRrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified bWR -fi -exit diff --git a/sourcecodes/data/example_chl/bWRrun_initialstructure.sh b/sourcecodes/data/example_chl/bWRrun_initialstructure.sh deleted file mode 100644 index 3725f758..00000000 --- a/sourcecodes/data/example_chl/bWRrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure bWR -fi -exit diff --git a/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh b/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh deleted file mode 100644 index 5a228612..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified cuL -fi -exit diff --git a/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh b/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh deleted file mode 100644 index 1d0835a4..00000000 --- a/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure cuL -fi -exit diff --git a/sourcecodes/data/example_sci/Llurun_evidencemodified.sh b/sourcecodes/data/example_sci/Llurun_evidencemodified.sh deleted file mode 100644 index ee0dde13..00000000 --- a/sourcecodes/data/example_sci/Llurun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified Llu -fi -exit diff --git a/sourcecodes/data/example_sci/Llurun_initialstructure.sh b/sourcecodes/data/example_sci/Llurun_initialstructure.sh deleted file mode 100644 index adde14dd..00000000 --- a/sourcecodes/data/example_sci/Llurun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Llu -fi -exit diff --git a/sourcecodes/data/example_sci_bk/Lluban.txt b/sourcecodes/data/example_sci_bk/Lluban.txt deleted file mode 100644 index 38108f00..00000000 --- a/sourcecodes/data/example_sci_bk/Lluban.txt +++ /dev/null @@ -1,15 +0,0 @@ -From To -Gene1 Genotype -Gene2 Genotype -Gene3 Genotype -Phenotype Genotype -Gene1 Genotype -Gene2 Genotype -Gene3 Genotype -Phenotype Gene1 -Phenotype Gene2 -Phenotype Gene3 -Phenotype Genotype -Phenotype Gene1 -Phenotype Gene2 -Phenotype Gene3 diff --git a/sourcecodes/data/example_sci_bk/Llucontinuous_input.txt b/sourcecodes/data/example_sci_bk/Llucontinuous_input.txt deleted file mode 100644 index 79295d7e..00000000 --- a/sourcecodes/data/example_sci_bk/Llucontinuous_input.txt +++ /dev/null @@ -1,503 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -2 1 1 1 1 -2 -1.0008 -0.44837 0.21808 -1.196 -1 -0.29368 -0.53043 -1.0893 -0.10136 -2 0.70835 0.72886 -0.18098 -0.42907 -1 0.63703 0.86428 1.7013 0.1425 -1 -1.2402 -0.69712 -1.7002 -0.71634 -1 -1.1952 0.27155 -0.79413 -1.0965 -2 0.62914 0.94265 1.8385 0.6135 -1 -1.91 -2.379 -3.1094 -1.0924 -2 -0.83436 -0.90968 -1.3598 1.335 -1 0.15685 0.4766 1.2891 -1.3309 -2 0.7047 1.0623 1.9811 1.2821 -1 0.59747 -0.023123 0.88555 -0.8844 -1 -1.0557 -1.5548 -1.3016 -0.77687 -2 1.5206 2.0289 0.90366 1.8089 -1 0.65525 -0.47226 -1.1824 0.41863 -2 -0.39262 0.382 -0.64829 0.40947 -2 0.14966 0.22972 0.33797 0.69647 -1 -1.8836 -0.68534 -0.99941 -0.78961 -1 0.48181 0.01241 1.2145 0.16835 -2 1.4673 2.0438 2.4674 2.5234 -1 -1.3242 -0.80218 -1.6446 -0.31044 -1 -1.2471 -2.0351 -1.0296 -1.937 -1 0.23695 -0.01724 -0.32851 -0.16484 -1 -0.13986 -0.6065 -0.8491 -0.95538 -2 0.90888 1.0365 2.7222 1.3507 -1 -0.30556 -1.1546 -0.86033 -2.2006 -2 0.5391 0.99532 0.96947 1.1575 -2 1.1235 0.37982 0.64439 0.94362 -2 1.7073 1.9303 2.8018 1.9158 -1 -0.20553 -0.074104 -0.50073 -1.0697 -1 -0.27415 0.23076 -0.27564 -0.11286 -1 -1.304 -1.1213 -0.71793 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-0.45147 -2 1.3618 1.6805 1.2152 2.1905 -2 -0.36075 1.0698 0.38569 2.5707 -1 -0.55325 -0.17572 -1.0232 -1.134 -2 0.9795 1.3777 0.26495 0.23258 -1 -0.92872 -1.2233 -2.1998 -1.9011 -1 0.47029 -0.06201 -0.34515 -0.57857 -1 -2.6597 -1.5144 -3.0038 -1.949 -2 -0.064474 -0.25394 -0.34794 0.76334 -2 0.52259 0.76325 0.93484 0.060827 -1 0.89037 0.68007 0.50459 -0.88464 -2 1.0031 1.3853 1.7313 0.75303 -2 0.6954 1.3692 0.19298 1.6174 -2 -0.14026 1.1774 0.39386 -0.25913 -2 -1.7796 -1.2709 -2.5775 -0.36996 -2 0.41557 1.9905 1.839 1.1327 -1 0.53878 -0.71974 -0.65395 -0.62597 -2 0.22326 1.3888 0.17221 1.2265 -1 -0.12667 -1.1336 -0.67 -3.6161 -2 1.0183 1.5883 2.2784 1.7509 -1 -2.0415 -2.2483 -2.8307 -3.1148 -2 -1.1513 -0.08575 -0.62876 2.164 -1 0.1961 0.075096 1.9551 0.039445 -2 -0.96925 0.12921 -1.2741 1.8371 -1 0.34137 0.086468 1.4716 0.55236 -1 -0.20756 -0.74846 0.65256 -0.7032 -2 1.1736 1.0214 1.258 1.0002 -2 0.48081 1.3275 0.54443 1.2194 -2 -0.45146 0.38298 0.64902 0.90395 -1 0.75519 -1.0627 -0.35778 -1.7689 -1 -1.4308 -1.0998 -1.0094 -0.66361 -1 -0.097019 0.18029 -9.0423e-07 0.59444 -2 1.3769 2.4872 3.2855 0.98727 -2 0.79201 0.76361 0.88459 3.119 -2 2.5125 2.4776 4.6119 3.966 -1 0.57129 -0.93689 -0.20516 -0.42323 -1 -0.91517 -0.25445 -1.3515 -0.99354 -1 0.17456 -0.98904 -0.49643 -0.8997 -1 -2.2724 -1.6869 -3.8034 -2.0882 -2 -1.8188 -0.57721 -2.4386 0.058963 -2 -0.19227 0.038901 -0.85065 0.6644 -1 -1.5517 -0.57182 -0.9874 -1.4081 -2 -0.47999 0.49667 0.27351 0.6261 -2 0.45041 0.48469 0.55808 2.0659 -1 -1.1302 -1.255 -2.7206 -1.2712 -1 -0.60672 -1.1008 -2.6889 -1.0078 -1 -1.0508 -0.99612 -1.555 -1.0463 -2 0.14434 0.97791 1.2498 1.7391 -2 0.21333 1.6686 1.219 1.8919 -2 -0.35461 -0.64694 -1.3312 -0.10481 -1 -2.0611 -2.1245 -3.6067 -1.6584 -2 -0.3534 0.45962 -0.39991 0.45667 -1 -0.37564 -0.63085 -1.2641 -1.3292 -1 0.30023 -0.20283 0.041852 -0.17139 -2 0.25089 1.0204 1.8084 1.0493 -1 -0.44041 -1.1143 -0.59224 -0.84288 -2 -0.11392 0.5681 -0.054604 0.88897 -1 0.41829 -1.042 -0.0042274 -1.9512 -2 1.4863 2.9227 3.0012 3.1253 -1 -0.60588 -1.1196 -1.4647 -0.92268 -1 -0.10497 -0.74629 -1.8353 -0.35425 -1 -1.2499 -0.83335 -2.4047 -1.4657 -1 -0.51414 -1.4602 -0.54649 -1.0475 -1 0.56956 0.79545 0.86494 -0.59471 -1 -0.64964 -0.78543 -1.9412 -2.2114 -2 1.0044 0.56431 1.2968 1.3807 -1 -1.1924 -0.69401 -0.72828 -1.7252 -2 0.15739 1.0449 0.3742 1.4303 -2 0.49582 1.4353 1.1652 1.5814 - diff --git a/sourcecodes/data/example_sci_bk/Llugraphviz.txt b/sourcecodes/data/example_sci_bk/Llugraphviz.txt deleted file mode 100644 index 88bbd3ba..00000000 --- a/sourcecodes/data/example_sci_bk/Llugraphviz.txt +++ /dev/null @@ -1,10 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Genotype -> Gene3; -Genotype -> Gene1; -Gene3 -> Phenotype; -Gene2 -> Gene3; -Gene2 -> Phenotype; -Gene1 -> Gene2; -} \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluk.txt b/sourcecodes/data/example_sci_bk/Lluk.txt deleted file mode 100644 index 83b33d23..00000000 --- a/sourcecodes/data/example_sci_bk/Lluk.txt +++ /dev/null @@ -1 +0,0 @@ -1000 diff --git a/sourcecodes/data/example_sci_bk/Llumap.txt b/sourcecodes/data/example_sci_bk/Llumap.txt deleted file mode 100644 index 958281d5..00000000 --- a/sourcecodes/data/example_sci_bk/Llumap.txt +++ /dev/null @@ -1,5 +0,0 @@ -Genotype 2 0.500305 1.514000 -Gene3 1 1.027261 -0.015284 -Gene2 1 1.160583 0.138097 -Phenotype 1 1.554104 0.069005 -Gene1 1 1.515414 0.174451 diff --git a/sourcecodes/data/example_sci_bk/Llumapdata.txt b/sourcecodes/data/example_sci_bk/Llumapdata.txt deleted file mode 100644 index d684ea06..00000000 --- a/sourcecodes/data/example_sci_bk/Llumapdata.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype Gene1 Gene2 Gene3 Phenotype diff --git a/sourcecodes/data/example_sci_bk/Lluname.txt b/sourcecodes/data/example_sci_bk/Lluname.txt deleted file mode 100644 index f3a1f5bf..00000000 --- a/sourcecodes/data/example_sci_bk/Lluname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 diff --git a/sourcecodes/data/example_sci_bk/Llunet_figure.txt b/sourcecodes/data/example_sci_bk/Llunet_figure.txt deleted file mode 100644 index bdc07cbd..00000000 --- a/sourcecodes/data/example_sci_bk/Llunet_figure.txt +++ /dev/null @@ -1,433 +0,0 @@ -5 -1200 1200 -Genotype 0 0 -Gene1 120 200 -Gene2 0 400 -Gene3 120 600 -Phenotype 0 800 -Genotype 2 -250 150 -0 -2 2 4 -1 0.4860 -2 0.5140 -Gene1 1 -250 150 -1 1 -1 3 --3.5013 0.0009 --3.4313 0.0012 --3.3613 0.0015 --3.2912 0.0019 --3.2212 0.0024 --3.1512 0.0030 --3.0811 0.0037 --3.0111 0.0046 --2.9411 0.0056 --2.8710 0.0069 --2.8010 0.0083 --2.7310 0.0101 --2.6609 0.0121 --2.5909 0.0145 --2.5209 0.0174 --2.4508 0.0206 --2.3808 0.0243 --2.3108 0.0286 --2.2407 0.0335 --2.1707 0.0389 --2.1007 0.0451 --2.0306 0.0520 --1.9606 0.0597 --1.8906 0.0682 --1.8205 0.0775 --1.7505 0.0876 --1.6805 0.0986 --1.6104 0.1105 --1.5404 0.1231 --1.4704 0.1366 --1.4003 0.1508 --1.3303 0.1657 --1.2603 0.1811 --1.1902 0.1971 --1.1202 0.2134 --1.0502 0.2300 --0.9801 0.2467 --0.9101 0.2633 --0.8401 0.2797 --0.7700 0.2956 --0.7000 0.3110 --0.6300 0.3256 --0.5599 0.3392 --0.4899 0.3517 --0.4199 0.3629 --0.3498 0.3726 --0.2798 0.3808 --0.2098 0.3873 --0.1397 0.3920 --0.0697 0.3948 -0.0003 0.3958 -0.0704 0.3948 -0.1404 0.3920 -0.2104 0.3872 -0.2805 0.3807 -0.3505 0.3726 -0.4205 0.3628 -0.4906 0.3516 -0.5606 0.3391 -0.6306 0.3254 -0.7007 0.3108 -0.7707 0.2955 -0.8407 0.2795 -0.9108 0.2631 -0.9808 0.2465 -1.0508 0.2299 -1.1209 0.2133 -1.1909 0.1969 -1.2609 0.1810 -1.3310 0.1655 -1.4010 0.1507 -1.4710 0.1365 -1.5411 0.1230 -1.6111 0.1103 -1.6811 0.0985 -1.7512 0.0875 -1.8212 0.0774 -1.8912 0.0681 -1.9613 0.0596 -2.0313 0.0520 -2.1013 0.0451 -2.1714 0.0389 -2.2414 0.0334 -2.3114 0.0286 -2.3815 0.0243 -2.4515 0.0206 -2.5215 0.0173 -2.5916 0.0145 -2.6616 0.0121 -2.7316 0.0101 -2.8017 0.0083 -2.8717 0.0068 -2.9417 0.0056 -3.0118 0.0046 -3.0818 0.0037 -3.1518 0.0030 -3.2219 0.0024 -3.2919 0.0019 -3.3619 0.0015 -3.4320 0.0012 -3.5020 0.0009 -Gene2 1 -250 150 -1 2 -2 4 5 --3.5862 0.0008 --3.5124 0.0010 --3.4385 0.0013 --3.3647 0.0016 --3.2909 0.0020 --3.2171 0.0026 --3.1432 0.0032 --3.0694 0.0041 --2.9956 0.0050 --2.9218 0.0062 --2.8479 0.0077 --2.7741 0.0094 --2.7003 0.0114 --2.6264 0.0138 --2.5526 0.0166 --2.4788 0.0199 --2.4050 0.0237 --2.3311 0.0281 --2.2573 0.0331 --2.1835 0.0388 --2.1097 0.0453 --2.0358 0.0526 --1.9620 0.0607 --1.8882 0.0696 --1.8143 0.0795 --1.7405 0.0903 --1.6667 0.1021 --1.5929 0.1147 --1.5190 0.1282 --1.4452 0.1426 --1.3714 0.1578 --1.2976 0.1736 --1.2237 0.1900 --1.1499 0.2069 --1.0761 0.2241 --1.0022 0.2414 --0.9284 0.2587 --0.8546 0.2758 --0.7808 0.2924 --0.7069 0.3084 --0.6331 0.3236 --0.5593 0.3377 --0.4855 0.3506 --0.4116 0.3621 --0.3378 0.3719 --0.2640 0.3800 --0.1901 0.3863 --0.1163 0.3905 --0.0425 0.3927 -0.0313 0.3929 -0.1052 0.3910 -0.1790 0.3870 -0.2528 0.3811 -0.3266 0.3732 -0.4005 0.3636 -0.4743 0.3524 -0.5481 0.3397 -0.6220 0.3258 -0.6958 0.3108 -0.7696 0.2949 -0.8434 0.2783 -0.9173 0.2613 -0.9911 0.2440 -1.0649 0.2267 -1.1387 0.2095 -1.2126 0.1925 -1.2864 0.1760 -1.3602 0.1601 -1.4341 0.1449 -1.5079 0.1304 -1.5817 0.1167 -1.6555 0.1039 -1.7294 0.0920 -1.8032 0.0811 -1.8770 0.0711 -1.9508 0.0620 -2.0247 0.0537 -2.0985 0.0464 -2.1723 0.0398 -2.2462 0.0340 -2.3200 0.0288 -2.3938 0.0243 -2.4676 0.0205 -2.5415 0.0171 -2.6153 0.0142 -2.6891 0.0117 -2.7629 0.0097 -2.8368 0.0079 -2.9106 0.0064 -2.9844 0.0052 -3.0583 0.0042 -3.1321 0.0034 -3.2059 0.0027 -3.2797 0.0021 -3.3536 0.0017 -3.4274 0.0013 -3.5012 0.0010 -3.5750 0.0008 -3.6489 0.0006 -3.7227 0.0005 -3.7965 0.0004 -Gene3 1 -250 150 -2 1 3 -1 5 --4.3571 0.0001 --4.2762 0.0001 --4.1954 0.0001 --4.1145 0.0001 --4.0336 0.0002 --3.9527 0.0002 --3.8719 0.0003 --3.7910 0.0004 --3.7101 0.0006 --3.6293 0.0008 --3.5484 0.0010 --3.4675 0.0013 --3.3866 0.0018 --3.3058 0.0023 --3.2249 0.0029 --3.1440 0.0037 --3.0632 0.0047 --2.9823 0.0059 --2.9014 0.0074 --2.8205 0.0092 --2.7397 0.0113 --2.6588 0.0139 --2.5779 0.0170 --2.4971 0.0206 --2.4162 0.0248 --2.3353 0.0297 --2.2544 0.0354 --2.1736 0.0419 --2.0927 0.0493 --2.0118 0.0576 --1.9310 0.0669 --1.8501 0.0773 --1.7692 0.0887 --1.6883 0.1012 --1.6075 0.1147 --1.5266 0.1292 --1.4457 0.1447 --1.3648 0.1610 --1.2840 0.1781 --1.2031 0.1958 --1.1222 0.2139 --1.0414 0.2323 --0.9605 0.2507 --0.8796 0.2688 --0.7987 0.2866 --0.7179 0.3036 --0.6370 0.3197 --0.5561 0.3345 --0.4753 0.3479 --0.3944 0.3597 --0.3135 0.3695 --0.2326 0.3773 --0.1518 0.3828 --0.0709 0.3861 -0.0100 0.3870 -0.0908 0.3855 -0.1717 0.3817 -0.2526 0.3756 -0.3335 0.3673 -0.4143 0.3570 -0.4952 0.3449 -0.5761 0.3311 -0.6569 0.3160 -0.7378 0.2996 -0.8187 0.2824 -0.8996 0.2645 -0.9804 0.2463 -1.0613 0.2279 -1.1422 0.2095 -1.2230 0.1915 -1.3039 0.1740 -1.3848 0.1570 -1.4657 0.1409 -1.5465 0.1256 -1.6274 0.1114 -1.7083 0.0981 -1.7891 0.0859 -1.8700 0.0747 -1.9509 0.0646 -2.0318 0.0555 -2.1126 0.0474 -2.1935 0.0402 -2.2744 0.0340 -2.3552 0.0285 -2.4361 0.0237 -2.5170 0.0197 -2.5979 0.0162 -2.6787 0.0132 -2.7596 0.0108 -2.8405 0.0087 -2.9213 0.0070 -3.0022 0.0056 -3.0831 0.0044 -3.1640 0.0035 -3.2448 0.0027 -3.3257 0.0021 -3.4066 0.0016 -3.4874 0.0013 -3.5683 0.0010 -3.6492 0.0007 -3.7301 0.0006 -Phenotype 1 -250 150 -2 3 4 -0 --3.5574 0.0010 --3.4806 0.0013 --3.4037 0.0016 --3.3268 0.0021 --3.2499 0.0026 --3.1731 0.0033 --3.0962 0.0042 --3.0193 0.0052 --2.9425 0.0065 --2.8656 0.0080 --2.7887 0.0098 --2.7118 0.0120 --2.6350 0.0146 --2.5581 0.0176 --2.4812 0.0212 --2.4044 0.0253 --2.3275 0.0300 --2.2506 0.0354 --2.1737 0.0416 --2.0969 0.0486 --2.0200 0.0564 --1.9431 0.0651 --1.8663 0.0748 --1.7894 0.0854 --1.7125 0.0970 --1.6356 0.1096 --1.5588 0.1230 --1.4819 0.1374 --1.4050 0.1526 --1.3282 0.1685 --1.2513 0.1850 --1.1744 0.2021 --1.0975 0.2195 --1.0207 0.2370 --0.9438 0.2545 --0.8669 0.2718 --0.7901 0.2887 --0.7132 0.3049 --0.6363 0.3202 --0.5594 0.3344 --0.4826 0.3473 --0.4057 0.3587 --0.3288 0.3684 --0.2520 0.3763 --0.1751 0.3822 --0.0982 0.3860 --0.0213 0.3877 -0.0555 0.3872 -0.1324 0.3846 -0.2093 0.3798 -0.2861 0.3731 -0.3630 0.3644 -0.4399 0.3539 -0.5168 0.3418 -0.5936 0.3283 -0.6705 0.3136 -0.7474 0.2979 -0.8242 0.2813 -0.9011 0.2643 -0.9780 0.2468 -1.0549 0.2293 -1.1317 0.2118 -1.2086 0.1945 -1.2855 0.1777 -1.3623 0.1614 -1.4392 0.1458 -1.5161 0.1310 -1.5930 0.1170 -1.6698 0.1039 -1.7467 0.0918 -1.8236 0.0806 -1.9004 0.0704 -1.9773 0.0612 -2.0542 0.0529 -2.1311 0.0454 -2.2079 0.0388 -2.2848 0.0329 -2.3617 0.0278 -2.4385 0.0234 -2.5154 0.0195 -2.5923 0.0162 -2.6692 0.0134 -2.7460 0.0110 -2.8229 0.0090 -2.8998 0.0073 -2.9766 0.0059 -3.0535 0.0047 -3.1304 0.0038 -3.2073 0.0030 -3.2841 0.0024 -3.3610 0.0019 -3.4379 0.0015 -3.5147 0.0011 -3.5916 0.0009 -3.6685 0.0007 -3.7454 0.0005 -3.8222 0.0004 -3.8991 0.0003 -3.9760 0.0002 -4.0528 0.0002 -4.1297 0.0001 diff --git a/sourcecodes/data/example_sci_bk/Llunet_figure_new.txt b/sourcecodes/data/example_sci_bk/Llunet_figure_new.txt deleted file mode 100644 index 7e6f0d97..00000000 --- a/sourcecodes/data/example_sci_bk/Llunet_figure_new.txt +++ /dev/null @@ -1,433 +0,0 @@ -1 -5 -1200 1200 -Genotype 0 0 -Gene1 120 200 -Gene2 0 400 -Gene3 120 600 -Phenotype 0 800 -Genotype 2 -250 150 -0 -2 2 4 -1.0000 1.0000 -Gene1 1 -250 150 -1 1 -1 3 --3.5013 0.0000 --3.4313 0.0000 --3.3613 0.0000 --3.2912 0.0000 --3.2212 0.0000 --3.1512 0.0000 --3.0811 0.0000 --3.0111 0.0000 --2.9411 0.0000 --2.8710 0.0000 --2.8010 0.0000 --2.7310 0.0000 --2.6609 0.0000 --2.5909 0.0000 --2.5209 0.0001 --2.4508 0.0002 --2.3808 0.0004 --2.3108 0.0007 --2.2407 0.0014 --2.1707 0.0026 --2.1007 0.0046 --2.0306 0.0079 --1.9606 0.0133 --1.8906 0.0217 --1.8205 0.0344 --1.7505 0.0529 --1.6805 0.0791 --1.6104 0.1147 --1.5404 0.1615 --1.4704 0.2207 --1.4003 0.2928 --1.3303 0.3771 --1.2603 0.4715 --1.1902 0.5723 --1.1202 0.6743 --1.0502 0.7713 --0.9801 0.8564 --0.9101 0.9232 --0.8401 0.9660 --0.7700 0.9813 --0.7000 0.9676 --0.6300 0.9263 --0.5599 0.8608 --0.4899 0.7765 --0.4199 0.6800 --0.3498 0.5781 --0.2798 0.4771 --0.2098 0.3822 --0.1397 0.2973 --0.0697 0.2244 -0.0003 0.1645 -0.0704 0.1170 -0.1404 0.0808 -0.2104 0.0542 -0.2805 0.0353 -0.3505 0.0223 -0.4205 0.0137 -0.4906 0.0081 -0.5606 0.0047 -0.6306 0.0026 -0.7007 0.0014 -0.7707 0.0008 -0.8407 0.0004 -0.9108 0.0002 -0.9808 0.0001 -1.0508 0.0000 -1.1209 0.0000 -1.1909 0.0000 -1.2609 0.0000 -1.3310 0.0000 -1.4010 0.0000 -1.4710 0.0000 -1.5411 0.0000 -1.6111 0.0000 -1.6811 0.0000 -1.7512 0.0000 -1.8212 0.0000 -1.8912 0.0000 -1.9613 0.0000 -2.0313 0.0000 -2.1013 0.0000 -2.1714 0.0000 -2.2414 0.0000 -2.3114 0.0000 -2.3815 0.0000 -2.4515 0.0000 -2.5215 0.0000 -2.5916 0.0000 -2.6616 0.0000 -2.7316 0.0000 -2.8017 0.0000 -2.8717 0.0000 -2.9417 0.0000 -3.0118 0.0000 -3.0818 0.0000 -3.1518 0.0000 -3.2219 0.0000 -3.2919 0.0000 -3.3619 0.0000 -3.4320 0.0000 -3.5020 0.0000 -Gene2 1 -250 150 -1 2 -2 4 5 --3.5862 0.0000 --3.5124 0.0000 --3.4385 0.0000 --3.3647 0.0000 --3.2909 0.0000 --3.2171 0.0001 --3.1432 0.0001 --3.0694 0.0002 --2.9956 0.0003 --2.9218 0.0005 --2.8479 0.0008 --2.7741 0.0012 --2.7003 0.0018 --2.6264 0.0028 --2.5526 0.0041 --2.4788 0.0060 --2.4050 0.0087 --2.3311 0.0124 --2.2573 0.0175 --2.1835 0.0242 --2.1097 0.0329 --2.0358 0.0441 --1.9620 0.0583 --1.8882 0.0759 --1.8143 0.0974 --1.7405 0.1230 --1.6667 0.1530 --1.5929 0.1874 --1.5190 0.2262 --1.4452 0.2689 --1.3714 0.3148 --1.2976 0.3631 --1.2237 0.4126 --1.1499 0.4617 --1.0761 0.5089 --1.0022 0.5525 --0.9284 0.5908 --0.8546 0.6224 --0.7808 0.6458 --0.7069 0.6600 --0.6331 0.6644 --0.5593 0.6588 --0.4855 0.6434 --0.4116 0.6190 --0.3378 0.5866 --0.2640 0.5475 --0.1901 0.5034 --0.1163 0.4558 --0.0425 0.4066 -0.0313 0.3573 -0.1052 0.3092 -0.1790 0.2636 -0.2528 0.2213 -0.3266 0.1830 -0.4005 0.1491 -0.4743 0.1197 -0.5481 0.0946 -0.6220 0.0736 -0.6958 0.0565 -0.7696 0.0426 -0.8434 0.0317 -0.9173 0.0233 -0.9911 0.0168 -1.0649 0.0119 -1.1387 0.0084 -1.2126 0.0058 -1.2864 0.0039 -1.3602 0.0026 -1.4341 0.0017 -1.5079 0.0011 -1.5817 0.0007 -1.6555 0.0005 -1.7294 0.0003 -1.8032 0.0002 -1.8770 0.0001 -1.9508 0.0001 -2.0247 0.0000 -2.0985 0.0000 -2.1723 0.0000 -2.2462 0.0000 -2.3200 0.0000 -2.3938 0.0000 -2.4676 0.0000 -2.5415 0.0000 -2.6153 0.0000 -2.6891 0.0000 -2.7629 0.0000 -2.8368 0.0000 -2.9106 0.0000 -2.9844 0.0000 -3.0583 0.0000 -3.1321 0.0000 -3.2059 0.0000 -3.2797 0.0000 -3.3536 0.0000 -3.4274 0.0000 -3.5012 0.0000 -3.5750 0.0000 -3.6489 0.0000 -3.7227 0.0000 -3.7965 0.0000 -Gene3 1 -250 150 -2 1 3 -1 5 --4.3571 0.0002 --4.2762 0.0002 --4.1954 0.0003 --4.1145 0.0004 --4.0336 0.0005 --3.9527 0.0007 --3.8719 0.0010 --3.7910 0.0013 --3.7101 0.0017 --3.6293 0.0022 --3.5484 0.0028 --3.4675 0.0036 --3.3866 0.0046 --3.3058 0.0059 --3.2249 0.0074 --3.1440 0.0093 --3.0632 0.0115 --2.9823 0.0143 --2.9014 0.0175 --2.8205 0.0214 --2.7397 0.0260 --2.6588 0.0313 --2.5779 0.0374 --2.4971 0.0445 --2.4162 0.0526 --2.3353 0.0617 --2.2544 0.0719 --2.1736 0.0833 --2.0927 0.0958 --2.0118 0.1095 --1.9310 0.1243 --1.8501 0.1403 --1.7692 0.1572 --1.6883 0.1750 --1.6075 0.1936 --1.5266 0.2127 --1.4457 0.2322 --1.3648 0.2518 --1.2840 0.2713 --1.2031 0.2904 --1.1222 0.3088 --1.0414 0.3263 --0.9605 0.3424 --0.8796 0.3570 --0.7987 0.3698 --0.7179 0.3806 --0.6370 0.3890 --0.5561 0.3951 --0.4753 0.3987 --0.3944 0.3996 --0.3135 0.3980 --0.2326 0.3937 --0.1518 0.3869 --0.0709 0.3778 -0.0100 0.3665 -0.0908 0.3532 -0.1717 0.3381 -0.2526 0.3216 -0.3335 0.3039 -0.4143 0.2852 -0.4952 0.2660 -0.5761 0.2464 -0.6569 0.2268 -0.7378 0.2074 -0.8187 0.1884 -0.8996 0.1700 -0.9804 0.1524 -1.0613 0.1358 -1.1422 0.1201 -1.2230 0.1056 -1.3039 0.0922 -1.3848 0.0800 -1.4657 0.0690 -1.5465 0.0591 -1.6274 0.0502 -1.7083 0.0425 -1.7891 0.0357 -1.8700 0.0297 -1.9509 0.0246 -2.0318 0.0203 -2.1126 0.0166 -2.1935 0.0135 -2.2744 0.0109 -2.3552 0.0087 -2.4361 0.0070 -2.5170 0.0055 -2.5979 0.0043 -2.6787 0.0034 -2.7596 0.0026 -2.8405 0.0020 -2.9213 0.0015 -3.0022 0.0012 -3.0831 0.0009 -3.1640 0.0007 -3.2448 0.0005 -3.3257 0.0004 -3.4066 0.0003 -3.4874 0.0002 -3.5683 0.0001 -3.6492 0.0001 -3.7301 0.0001 -Phenotype 1 -250 150 -2 3 4 -0 --3.5574 0.0004 --3.4806 0.0006 --3.4037 0.0008 --3.3268 0.0012 --3.2499 0.0016 --3.1731 0.0022 --3.0962 0.0030 --3.0193 0.0040 --2.9425 0.0054 --2.8656 0.0071 --2.7887 0.0093 --2.7118 0.0121 --2.6350 0.0155 --2.5581 0.0198 --2.4812 0.0250 --2.4044 0.0313 --2.3275 0.0389 --2.2506 0.0479 --2.1737 0.0584 --2.0969 0.0706 --2.0200 0.0846 --1.9431 0.1005 --1.8663 0.1184 --1.7894 0.1381 --1.7125 0.1597 --1.6356 0.1831 --1.5588 0.2081 --1.4819 0.2343 --1.4050 0.2615 --1.3282 0.2893 --1.2513 0.3173 --1.1744 0.3448 --1.0975 0.3714 --1.0207 0.3966 --0.9438 0.4197 --0.8669 0.4402 --0.7901 0.4576 --0.7132 0.4716 --0.6363 0.4816 --0.5594 0.4875 --0.4826 0.4891 --0.4057 0.4864 --0.3288 0.4794 --0.2520 0.4684 --0.1751 0.4535 --0.0982 0.4353 --0.0213 0.4140 -0.0555 0.3904 -0.1324 0.3648 -0.2093 0.3379 -0.2861 0.3102 -0.3630 0.2822 -0.4399 0.2545 -0.5168 0.2275 -0.5936 0.2016 -0.6705 0.1770 -0.7474 0.1541 -0.8242 0.1329 -0.9011 0.1136 -0.9780 0.0963 -1.0549 0.0809 -1.1317 0.0673 -1.2086 0.0556 -1.2855 0.0455 -1.3623 0.0368 -1.4392 0.0296 -1.5161 0.0236 -1.5930 0.0186 -1.6698 0.0146 -1.7467 0.0113 -1.8236 0.0087 -1.9004 0.0066 -1.9773 0.0050 -2.0542 0.0037 -2.1311 0.0028 -2.2079 0.0020 -2.2848 0.0015 -2.3617 0.0011 -2.4385 0.0008 -2.5154 0.0005 -2.5923 0.0004 -2.6692 0.0003 -2.7460 0.0002 -2.8229 0.0001 -2.8998 0.0001 -2.9766 0.0001 -3.0535 0.0000 -3.1304 0.0000 -3.2073 0.0000 -3.2841 0.0000 -3.3610 0.0000 -3.4379 0.0000 -3.5147 0.0000 -3.5916 0.0000 -3.6685 0.0000 -3.7454 0.0000 -3.8222 0.0000 -3.8991 0.0000 -3.9760 0.0000 -4.0528 0.0000 -4.1297 0.0000 diff --git a/sourcecodes/data/example_sci_bk/Llunlevels.txt b/sourcecodes/data/example_sci_bk/Llunlevels.txt deleted file mode 100644 index 714e56bd..00000000 --- a/sourcecodes/data/example_sci_bk/Llunlevels.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype 1 2 - diff --git a/sourcecodes/data/example_sci_bk/Llunnode.txt b/sourcecodes/data/example_sci_bk/Llunnode.txt deleted file mode 100644 index 7ed6ff82..00000000 --- a/sourcecodes/data/example_sci_bk/Llunnode.txt +++ /dev/null @@ -1 +0,0 @@ -5 diff --git a/sourcecodes/data/example_sci_bk/Llunrows.txt b/sourcecodes/data/example_sci_bk/Llunrows.txt deleted file mode 100644 index c15fb720..00000000 --- a/sourcecodes/data/example_sci_bk/Llunrows.txt +++ /dev/null @@ -1 +0,0 @@ -501 diff --git a/sourcecodes/data/example_sci_bk/Lluparent.txt b/sourcecodes/data/example_sci_bk/Lluparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/example_sci_bk/Lluparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/example_sci_bk/Llurun_evidencemodified.sh b/sourcecodes/data/example_sci_bk/Llurun_evidencemodified.sh deleted file mode 100644 index ee0dde13..00000000 --- a/sourcecodes/data/example_sci_bk/Llurun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified Llu -fi -exit diff --git a/sourcecodes/data/example_sci_bk/Llurun_initialstructure.sh b/sourcecodes/data/example_sci_bk/Llurun_initialstructure.sh deleted file mode 100644 index adde14dd..00000000 --- a/sourcecodes/data/example_sci_bk/Llurun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Llu -fi -exit diff --git a/sourcecodes/data/example_sci_bk/Llustructure_input.txt b/sourcecodes/data/example_sci_bk/Llustructure_input.txt deleted file mode 100644 index bcf72d97..00000000 --- a/sourcecodes/data/example_sci_bk/Llustructure_input.txt +++ /dev/null @@ -1,6 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -0 1 0 0 1 -0 0 0 1 0 -0 1 0 1 0 -0 0 0 0 0 -0 0 1 0 0 diff --git a/sourcecodes/data/example_sci_bk/Llustructure_input_temp.txt b/sourcecodes/data/example_sci_bk/Llustructure_input_temp.txt deleted file mode 100644 index 95aa7a5d..00000000 --- a/sourcecodes/data/example_sci_bk/Llustructure_input_temp.txt +++ /dev/null @@ -1,6 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -0.000000 0.999929 0.183248 0.000431 1.000000 -0.000000 0.000000 0.000000 1.000000 0.000000 -0.000000 0.935752 0.000000 1.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.053385 0.881001 0.156255 0.000000 diff --git a/sourcecodes/data/example_sci_bk/Llustructure_old.txt b/sourcecodes/data/example_sci_bk/Llustructure_old.txt deleted file mode 100644 index 5b464577..00000000 --- a/sourcecodes/data/example_sci_bk/Llustructure_old.txt +++ /dev/null @@ -1,5 +0,0 @@ -Genotype 0.4860 0.5140 -Gene3 0.0001 0.0001 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0006 0.0008 0.0010 0.0013 0.0018 0.0023 0.0029 0.0037 0.0047 0.0059 0.0074 0.0092 0.0113 0.0139 0.0170 0.0206 0.0248 0.0297 0.0354 0.0419 0.0493 0.0576 0.0669 0.0773 0.0887 0.1012 0.1147 0.1292 0.1447 0.1610 0.1781 0.1958 0.2139 0.2323 0.2507 0.2688 0.2866 0.3036 0.3197 0.3345 0.3479 0.3597 0.3695 0.3773 0.3828 0.3861 0.3870 0.3855 0.3817 0.3756 0.3673 0.3570 0.3449 0.3311 0.3160 0.2996 0.2824 0.2645 0.2463 0.2279 0.2095 0.1915 0.1740 0.1570 0.1409 0.1256 0.1114 0.0981 0.0859 0.0747 0.0646 0.0555 0.0474 0.0402 0.0340 0.0285 0.0237 0.0197 0.0162 0.0132 0.0108 0.0087 0.0070 0.0056 0.0044 0.0035 0.0027 0.0021 0.0016 0.0013 0.0010 0.0007 0.0006 -Gene1 0.0009 0.0012 0.0015 0.0019 0.0024 0.0030 0.0037 0.0046 0.0056 0.0069 0.0083 0.0101 0.0121 0.0145 0.0174 0.0206 0.0243 0.0286 0.0335 0.0389 0.0451 0.0520 0.0597 0.0682 0.0775 0.0876 0.0986 0.1105 0.1231 0.1366 0.1508 0.1657 0.1811 0.1971 0.2134 0.2300 0.2467 0.2633 0.2797 0.2956 0.3110 0.3256 0.3392 0.3517 0.3629 0.3726 0.3808 0.3873 0.3920 0.3948 0.3958 0.3948 0.3920 0.3872 0.3807 0.3726 0.3628 0.3516 0.3391 0.3254 0.3108 0.2955 0.2795 0.2631 0.2465 0.2299 0.2133 0.1969 0.1810 0.1655 0.1507 0.1365 0.1230 0.1103 0.0985 0.0875 0.0774 0.0681 0.0596 0.0520 0.0451 0.0389 0.0334 0.0286 0.0243 0.0206 0.0173 0.0145 0.0121 0.0101 0.0083 0.0068 0.0056 0.0046 0.0037 0.0030 0.0024 0.0019 0.0015 0.0012 0.0009 -Phenotype 0.0010 0.0013 0.0016 0.0021 0.0026 0.0033 0.0042 0.0052 0.0065 0.0080 0.0098 0.0120 0.0146 0.0176 0.0212 0.0253 0.0300 0.0354 0.0416 0.0486 0.0564 0.0651 0.0748 0.0854 0.0970 0.1096 0.1230 0.1374 0.1526 0.1685 0.1850 0.2021 0.2195 0.2370 0.2545 0.2718 0.2887 0.3049 0.3202 0.3344 0.3473 0.3587 0.3684 0.3763 0.3822 0.3860 0.3877 0.3872 0.3846 0.3798 0.3731 0.3644 0.3539 0.3418 0.3283 0.3136 0.2979 0.2813 0.2643 0.2468 0.2293 0.2118 0.1945 0.1777 0.1614 0.1458 0.1310 0.1170 0.1039 0.0918 0.0806 0.0704 0.0612 0.0529 0.0454 0.0388 0.0329 0.0278 0.0234 0.0195 0.0162 0.0134 0.0110 0.0090 0.0073 0.0059 0.0047 0.0038 0.0030 0.0024 0.0019 0.0015 0.0011 0.0009 0.0007 0.0005 0.0004 0.0003 0.0002 0.0002 0.0001 -Gene2 0.0008 0.0010 0.0013 0.0016 0.0020 0.0026 0.0032 0.0041 0.0050 0.0062 0.0077 0.0094 0.0114 0.0138 0.0166 0.0199 0.0237 0.0281 0.0331 0.0388 0.0453 0.0526 0.0607 0.0696 0.0795 0.0903 0.1021 0.1147 0.1282 0.1426 0.1578 0.1736 0.1900 0.2069 0.2241 0.2414 0.2587 0.2758 0.2924 0.3084 0.3236 0.3377 0.3506 0.3621 0.3719 0.3800 0.3863 0.3905 0.3927 0.3929 0.3910 0.3870 0.3811 0.3732 0.3636 0.3524 0.3397 0.3258 0.3108 0.2949 0.2783 0.2613 0.2440 0.2267 0.2095 0.1925 0.1760 0.1601 0.1449 0.1304 0.1167 0.1039 0.0920 0.0811 0.0711 0.0620 0.0537 0.0464 0.0398 0.0340 0.0288 0.0243 0.0205 0.0171 0.0142 0.0117 0.0097 0.0079 0.0064 0.0052 0.0042 0.0034 0.0027 0.0021 0.0017 0.0013 0.0010 0.0008 0.0006 0.0005 0.0004 diff --git a/sourcecodes/data/example_sci_bk/Lluthr.txt b/sourcecodes/data/example_sci_bk/Lluthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/example_sci_bk/Lluthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/example_sci_bk/Llutier.txt b/sourcecodes/data/example_sci_bk/Llutier.txt deleted file mode 100644 index da7084fb..00000000 --- a/sourcecodes/data/example_sci_bk/Llutier.txt +++ /dev/null @@ -1 +0,0 @@ -3,Tier1,1,Genotype,Tier2,3,Gene1,Gene2,Gene3,Tier3,1,Phenotype, \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Llutype.txt b/sourcecodes/data/example_sci_bk/Llutype.txt deleted file mode 100644 index 9ea66ce4..00000000 --- a/sourcecodes/data/example_sci_bk/Llutype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Genotype Gene3 Gene2 Phenotype Gene1 -2 1 1 1 1 diff --git a/sourcecodes/data/example_sci_bk/Lluvar.txt b/sourcecodes/data/example_sci_bk/Lluvar.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/example_sci_bk/Lluvar.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluvardata.txt b/sourcecodes/data/example_sci_bk/Lluvardata.txt deleted file mode 100644 index 56a6051c..00000000 --- a/sourcecodes/data/example_sci_bk/Lluvardata.txt +++ /dev/null @@ -1 +0,0 @@ -1 \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluvarname.txt b/sourcecodes/data/example_sci_bk/Lluvarname.txt deleted file mode 100644 index 3fe283bd..00000000 --- a/sourcecodes/data/example_sci_bk/Lluvarname.txt +++ /dev/null @@ -1 +0,0 @@ -Genotype \ No newline at end of file diff --git a/sourcecodes/data/example_sci_bk/Lluwhite.txt b/sourcecodes/data/example_sci_bk/Lluwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/example_sci_bk/Lluwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/example_sci_bk/old/Llurun_evidencemodified.sh b/sourcecodes/data/example_sci_bk/old/Llurun_evidencemodified.sh deleted file mode 100644 index ee0dde13..00000000 --- a/sourcecodes/data/example_sci_bk/old/Llurun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified Llu -fi -exit diff --git a/sourcecodes/data/example_sci_bk/old/Llurun_initialstructure.sh b/sourcecodes/data/example_sci_bk/old/Llurun_initialstructure.sh deleted file mode 100644 index adde14dd..00000000 --- a/sourcecodes/data/example_sci_bk/old/Llurun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure Llu -fi -exit diff --git a/sourcecodes/data/example_time_series/TEbrun_evidencemodified.sh b/sourcecodes/data/example_time_series/TEbrun_evidencemodified.sh deleted file mode 100644 index ff2eafcd..00000000 --- a/sourcecodes/data/example_time_series/TEbrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified TEb -fi -exit diff --git a/sourcecodes/data/example_time_series/TEbrun_initialstructure.sh b/sourcecodes/data/example_time_series/TEbrun_initialstructure.sh deleted file mode 100644 index 3417deda..00000000 --- a/sourcecodes/data/example_time_series/TEbrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure TEb -fi -exit diff --git a/sourcecodes/data/examplecar/OVIban.txt b/sourcecodes/data/examplecar/OVIban.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/examplecar/OVIban.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/examplecar/OVIcontinuous_input.txt b/sourcecodes/data/examplecar/OVIcontinuous_input.txt deleted file mode 100644 index 3a2846cf..00000000 --- a/sourcecodes/data/examplecar/OVIcontinuous_input.txt +++ /dev/null @@ -1,1004 +0,0 @@ -Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter -2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2 -2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2 -1 1 1 1 1 1 1 1.09219 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 8.35719 1 3 3 1 2 1 1 1 2 1 1 -2 1 1 1 1 2 1 4.87697 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.40886 2 3 3 1 2 1 1 1 2 1 1 -1 1 1 1 1 1 1 0.823531 1 1 1 1 1 1 1 1 2 1 1 -1 1 1 1 1 1 1 1.29151 1 1 1 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 3.2245 1 1 1 1 2 1 1 1 2 1 1 -2 2 2 1 1 2 1 3.32396 1 3 1 2 2 2 1 2 1 1 1 -2 1 2 1 1 2 1 4.81455 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 1.8855 2 2 2 2 1 1 2 2 1 1 1 -2 1 2 1 1 2 1 3.16074 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.32025 1 1 1 2 1 1 1 2 1 1 1 -2 1 1 1 1 1 1 0.725881 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 9.15429 2 3 3 1 2 1 1 2 2 1 2 -2 1 2 1 1 1 1 1.29503 2 3 2 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.55555 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.899695 2 1 1 1 1 1 2 2 1 1 1 -2 1 2 1 1 2 1 0.972723 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.62187 2 3 3 2 2 3 1 1 1 1 1 -1 1 2 1 1 1 1 7.11136 1 1 1 1 1 2 1 1 1 1 1 -1 1 1 1 1 1 1 1.10928 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.61643 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 6.2605 1 2 2 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 1 8.55173 1 1 1 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 1.86787 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.23631 1 3 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 0.728145 1 1 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 4.66434 2 3 3 1 2 3 2 2 1 1 1 -2 1 2 1 1 1 1 3.56254 2 3 3 1 1 2 1 1 2 2 1 -2 1 2 1 1 2 1 2.63999 2 3 3 1 2 3 1 2 2 2 1 -2 1 2 1 1 2 1 0.715897 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 1.85198 2 3 3 1 2 2 1 1 2 2 1 -2 1 1 1 1 1 1 3.63826 1 1 1 1 1 1 2 2 2 1 1 -2 1 2 1 1 1 1 7.73862 2 3 3 1 1 3 1 1 2 2 1 -2 1 2 1 1 2 1 10.1699 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 2 2 2.97722 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.50117 2 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 0.640869 2 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.72775 1 3 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 5.46047 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 2.21929 1 2 2 1 2 2 1 1 2 1 1 -1 1 1 1 1 1 1 0.438026 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.0684539 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.15012 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 0.161533 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.11862 2 3 3 1 2 2 1 1 2 1 2 -2 1 1 1 1 1 1 0.410719 1 1 1 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 0.0322208 2 3 3 1 2 1 1 1 2 2 1 -1 1 1 1 1 1 1 3.37212 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.78532 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.40432 1 1 1 1 1 1 2 1 1 1 1 -2 1 2 1 1 2 1 3.22403 2 3 3 1 1 3 1 1 2 1 1 -2 1 2 1 1 2 1 1.7234 2 3 3 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 1 0.674939 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 6.9812 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.82705 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.935587 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.992564 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 3.47892 1 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 6.52634 1 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.68841 1 1 1 1 1 3 1 1 2 2 1 -1 1 2 1 1 1 1 0.50506 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.33453 1 2 2 1 2 3 1 1 2 1 1 -2 1 2 1 1 1 1 3.39695 2 2 2 2 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.482289 1 2 1 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 0.385094 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 3.92753 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 9.63027 2 3 3 1 2 1 1 1 2 2 1 -1 1 1 1 1 1 1 1.77681 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 15.8749 2 2 2 1 1 1 2 2 1 1 1 -1 1 1 1 1 1 1 0.863939 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.5007 2 3 2 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.46447 1 1 1 2 1 1 2 2 1 1 1 -2 1 2 1 1 1 1 4.00622 2 2 2 1 1 3 1 1 2 1 1 -1 1 2 1 1 1 1 2.62894 1 1 1 1 1 2 1 1 1 1 1 -1 1 1 1 1 1 1 0.772251 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.254104 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 1 1 1.35669 1 1 1 1 1 3 1 1 2 2 1 -1 1 1 1 1 1 1 0.408515 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.73523 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 4.84404 2 3 3 1 2 1 1 1 1 1 1 -2 2 2 1 1 2 1 3.08909 2 3 3 2 2 1 1 1 2 2 1 -2 1 1 1 1 1 1 0.500373 1 1 1 2 1 1 1 2 1 1 1 -1 1 2 1 1 1 1 1.42352 1 1 1 1 1 3 2 1 1 1 1 -2 1 2 1 1 2 1 3.19283 2 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.65803 2 3 3 1 2 1 1 1 2 1 2 -1 1 1 1 1 1 1 4.35117 1 1 1 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 0.448913 1 1 1 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 4.59592 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.68035 1 1 1 1 1 3 2 2 2 2 1 -2 1 2 1 1 1 1 6.86362 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.88662 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 1 1 6.67913 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 1.72634 1 2 1 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.01307 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.1309 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.38128 2 2 2 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 2.01195 1 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 4.91973 2 3 3 1 1 2 1 1 2 1 1 -2 1 1 1 1 1 1 3.45795 1 1 1 2 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.66261 1 1 1 2 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 12.2823 1 3 3 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 4.98365 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 1 1 2.28812 1 1 1 1 1 2 1 1 2 2 1 -2 1 2 1 1 1 1 1.98491 2 2 2 2 1 3 1 1 2 1 1 -1 1 1 1 1 1 1 0.441825 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 6.80856 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.14798 1 3 1 2 1 1 2 1 1 1 1 -2 1 2 1 1 2 1 3.47334 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 4.29814 1 3 3 1 1 1 1 1 2 1 1 -1 1 2 1 1 1 1 2.14065 1 1 1 1 1 3 1 1 1 1 1 -2 1 1 1 1 1 1 1.96168 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.7237 2 3 3 1 2 3 1 2 1 1 1 -1 1 1 1 1 1 1 1.11832 1 1 1 2 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.56047 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.452531 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 4.76471 2 3 3 2 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 3.72712 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 1.60393 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 2.22538 1 1 1 1 1 3 1 1 2 2 1 -1 1 1 1 1 1 1 0.778349 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 1 1 0.136355 2 3 3 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.559837 2 2 2 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 2 1.5521 2 3 3 2 2 1 1 1 2 2 2 -1 1 1 1 1 1 1 1.1683 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 3.20792 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.0294523 2 2 2 1 1 3 1 1 2 2 1 -2 1 1 1 1 1 1 1.51016 1 1 1 1 2 1 1 1 2 1 1 -2 1 2 1 1 1 1 1.46157 2 2 2 1 1 1 1 1 2 2 1 -2 1 2 1 1 1 1 7.31961 2 3 3 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 2.25565 1 2 2 1 1 1 1 1 2 2 1 -2 1 2 1 1 1 1 0.332537 1 3 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.16328 2 3 3 1 2 1 2 2 2 2 1 -1 1 2 1 1 1 1 4.18322 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 8.04276 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 4.12436 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.66478 1 1 1 1 1 1 1 1 1 1 1 -1 1 2 1 1 1 1 6.44237 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 3.30168 2 3 3 1 1 2 2 2 1 1 1 -1 1 1 1 1 1 1 2.57221 1 1 1 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.5302 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.23714 2 3 3 1 1 1 1 2 2 2 1 -2 1 2 1 1 2 1 8.72277 2 3 3 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 5.18702 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 2 1 4.1361 1 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 4.03663 2 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 2.09322 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 1.87756 2 3 3 2 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 14.1937 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.41049 1 1 1 1 1 3 1 1 2 2 1 -1 1 1 1 1 1 1 2.93445 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 10.5414 1 2 2 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 4.09177 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.39508 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 3.50173 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 6.21675 1 3 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.703114 1 2 2 2 2 1 1 1 2 1 1 -2 1 2 1 1 1 1 0.894215 2 3 2 1 1 3 1 2 1 1 1 -2 1 2 1 1 1 1 1.0471 1 2 2 1 1 3 1 1 1 1 1 -1 1 1 1 1 1 1 1.31589 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.68824 1 2 1 1 2 1 1 1 2 2 2 -2 1 2 1 1 2 1 5.48787 2 3 3 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 3.34192 1 1 1 2 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 9.5016 2 3 3 1 2 1 1 1 2 1 2 -2 1 2 1 1 2 1 6.07059 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 19.5523 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.31889 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.87967 1 1 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 2.77823 2 3 3 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 3.5956 1 1 1 1 1 3 1 1 1 1 1 -2 1 1 1 1 1 1 1.31325 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.75989 2 2 2 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.621366 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 1 1 3.14788 2 2 2 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 2.41881 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 4.3647 2 3 3 1 2 3 1 1 2 1 1 -2 1 2 1 1 1 1 0.227306 2 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 0.0613263 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 13.2932 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.64929 1 1 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 7.26046 2 3 3 1 2 1 1 1 2 1 1 -1 1 2 1 1 1 1 0.198224 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 6.24718 2 3 3 1 2 2 1 1 2 1 1 -1 1 1 1 1 1 1 0.818786 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.367484 2 3 3 2 2 1 2 2 1 1 1 -2 1 2 1 1 1 1 3.24863 1 3 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 3.67769 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.659442 1 3 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 3.40058 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 2.95923 1 1 1 2 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.80303 1 1 1 1 2 2 1 1 2 1 1 -1 1 1 1 1 1 1 4.64104 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 6.81146 1 3 3 1 2 2 1 1 1 1 1 -1 1 1 1 1 1 1 1.74035 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.33846 2 2 2 1 2 1 1 2 1 1 1 -2 1 2 1 1 1 1 10.5625 1 2 2 1 1 3 1 2 1 1 1 -2 1 2 1 1 1 1 1.75197 2 2 2 2 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 2.57664 1 2 2 1 1 2 2 2 2 1 1 -1 1 2 1 1 1 1 1.31431 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 0.703583 1 2 1 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 4.1339 2 3 3 1 2 3 1 1 2 2 1 -2 1 2 1 1 2 1 0.689182 2 3 3 1 2 1 2 2 1 1 1 -2 1 1 1 1 1 1 1.70247 1 1 1 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 3.16831 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 2.60872 1 1 1 2 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 5.17883 1 1 1 1 1 1 1 1 1 1 1 -1 1 2 1 1 1 1 1.24226 2 2 2 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 16.3393 1 1 1 1 1 1 1 2 1 1 1 -2 1 1 1 1 1 1 0.355235 1 1 1 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 10.1607 2 3 3 1 2 2 1 1 2 1 1 -1 1 1 1 1 1 1 0.0379707 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.73676 2 3 3 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 1 0.411721 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 5.80853 2 3 3 1 2 1 1 2 1 1 1 -1 1 1 1 1 1 1 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1 1 1 1 -2 1 2 1 1 2 1 2.28195 2 3 3 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 2.51306 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.287996 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.41019 2 3 3 1 2 1 1 2 1 1 1 -2 1 1 1 1 1 1 4.85756 1 1 1 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.913549 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 1 1 3.19129 1 1 1 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 0.910357 2 2 2 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.43587 1 1 1 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 1 7.62571 2 3 3 2 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 2.0177 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.03181 2 3 3 1 2 3 2 2 1 1 1 -2 1 2 1 1 1 1 4.41653 1 2 2 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.98272 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 6.1215 2 3 3 2 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 0.504951 2 3 3 1 2 2 1 1 2 2 1 -2 1 2 1 1 2 1 3.43942 2 3 3 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 1 0.168117 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.7116 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.73236 2 3 3 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.40971 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 10.4031 1 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.09535 2 2 2 1 1 1 2 2 2 1 1 -2 1 2 1 1 1 1 0.710853 1 1 1 1 1 3 1 2 1 1 1 -2 1 2 1 1 1 1 2.21968 1 3 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.05657 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.0965595 2 3 3 1 2 1 2 1 1 1 1 -1 1 2 1 1 1 1 2.20098 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 1.65946 2 3 3 1 2 3 1 1 2 1 1 -2 1 2 1 1 2 1 1.35011 2 3 3 1 2 1 1 1 2 1 1 -1 1 1 1 1 1 1 0.864032 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.6766 2 2 2 1 2 2 1 1 2 2 1 -2 1 1 1 1 1 1 1.12958 1 1 1 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 1.17241 2 3 3 1 2 1 2 1 2 1 1 -1 1 2 1 1 1 1 18.4318 1 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.82519 2 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 1.5247 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.75458 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 10.7041 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 9.98006 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 1.76827 2 3 3 2 2 1 2 1 2 1 1 -2 1 1 1 1 1 1 4.03522 1 1 1 1 1 1 2 2 1 1 1 -2 1 1 1 1 1 1 2.74773 1 1 1 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 4.37994 1 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.89003 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.380096 1 3 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.86974 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 1 1 2.84481 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.337754 2 2 2 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 10.0524 1 1 1 1 1 1 1 1 2 1 1 -2 1 2 1 1 1 1 2.83316 2 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.287686 2 3 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.57857 2 3 3 1 2 1 1 2 2 2 1 -2 1 2 1 1 1 1 10.9705 1 2 2 1 2 3 1 1 2 1 1 -2 1 2 1 1 2 1 5.6787 2 3 3 1 2 3 2 2 2 2 1 -2 1 1 1 1 1 1 4.84172 1 1 1 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 0.447668 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 8.37605 2 3 3 1 2 1 1 2 1 1 1 -2 1 2 1 1 2 1 4.4099 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 1 1 5.29519 2 2 2 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 3.60551 1 1 1 1 1 3 1 2 1 1 1 -2 1 1 1 1 2 2 1.10078 1 1 1 2 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.142979 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.238895 2 2 2 1 2 1 2 1 2 1 2 -2 1 2 1 1 2 1 1.98115 2 3 3 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 1.10228 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 3.88951 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 7.72912 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 1.98225 2 3 3 1 2 2 1 1 2 1 1 -1 1 1 1 1 1 1 4.67034 1 1 1 2 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.37675 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 5.00484 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.96131 1 1 1 1 1 3 1 1 2 1 2 -2 1 2 1 1 1 1 2.94174 1 1 1 1 2 2 1 1 2 2 1 -2 1 2 1 1 2 1 3.40327 2 3 2 1 2 1 2 2 1 1 1 -1 1 2 1 1 1 1 2.81788 1 1 1 1 1 2 1 1 2 1 1 -1 1 1 1 1 1 1 3.95297 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 13.659 2 3 3 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 1.40142 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 4.21091 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.75431 2 3 3 2 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 5.70335 2 3 3 1 2 2 1 1 1 1 1 -2 1 1 1 1 1 1 2.54218 1 1 1 1 2 1 1 1 2 1 1 -1 1 1 1 1 1 1 0.807303 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.04839 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.140617 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.581715 2 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.22689 1 1 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 0.892442 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 4.29428 2 3 3 1 2 1 2 2 1 1 1 -1 1 1 1 1 1 1 4.83098 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 4.74817 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.49175 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 0.710378 2 3 3 1 2 2 2 2 1 1 1 -2 1 2 1 1 1 1 5.10286 2 2 2 1 1 1 1 1 2 2 1 -1 1 1 1 1 1 1 0.918882 1 1 1 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 0.0441354 1 1 1 1 1 1 1 1 2 1 1 -1 1 2 1 1 1 1 0.956322 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 0.501229 1 2 2 1 2 3 1 1 2 2 1 -2 1 2 1 1 2 1 2.03462 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.49454 1 2 2 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 3.47399 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 3.42912 1 1 1 1 1 2 2 1 2 2 1 -1 1 2 1 1 1 1 3.92437 1 1 1 1 1 3 1 1 1 1 1 -2 1 1 1 1 1 1 0.51396 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.12695 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 2.44146 2 3 3 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 9.60595 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.0039 2 2 2 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 4.10378 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 0.386532 1 1 1 1 1 1 2 2 1 1 1 -2 1 2 1 1 1 1 0.75722 1 1 1 1 1 3 1 1 1 1 1 -1 1 1 1 1 1 1 0.506289 1 1 1 1 1 1 1 2 1 1 1 -1 1 1 1 1 1 1 1.84871 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 6.89466 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.30596 2 2 2 1 1 3 1 1 2 2 1 -2 1 2 1 1 1 1 6.80188 1 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 4.86438 1 3 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.90783 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.971687 2 3 2 1 1 1 2 2 1 1 1 -2 1 2 1 1 2 1 1.88183 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.17229 1 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.927847 2 3 3 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.36548 2 2 2 1 1 3 1 1 1 1 1 -2 1 2 1 1 2 1 2.00101 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 2.28421 1 1 1 1 2 1 2 2 1 1 1 -1 1 1 1 1 1 1 1.86953 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 9.0133 1 2 2 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 0.439457 2 2 2 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 4.34038 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.32347 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 6.60777 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 0.806183 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 7.83139 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.49472 1 1 1 1 2 2 1 1 1 1 1 -2 1 2 1 1 1 1 0.942534 1 2 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.70449 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.0436 2 3 3 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.93414 1 3 3 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 2.13185 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.262005 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 12.7252 1 2 2 1 2 3 1 1 1 1 1 -1 1 1 1 1 1 1 0.465012 1 1 1 1 1 1 2 2 1 1 1 -1 1 2 1 1 1 1 0.455832 1 1 1 1 1 3 1 1 1 1 1 -2 1 1 1 1 1 1 5.52702 1 1 1 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 4.37922 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 8.52767 1 2 2 1 1 1 1 1 1 1 1 -1 1 2 1 1 1 1 2.53081 1 2 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.34317 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 2.24552 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.39164 2 3 3 1 2 1 1 2 1 1 1 -2 1 1 1 1 1 1 0.635824 1 1 1 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 0.810242 2 3 3 2 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 20.3734 1 2 2 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 0.314643 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.93743 2 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.55162 2 3 3 1 2 3 1 2 1 1 1 -1 1 2 1 1 1 1 0.729802 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.0873788 2 3 3 1 2 2 1 1 1 1 1 -1 1 1 1 1 1 1 2.09206 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 0.834649 2 3 3 1 2 3 1 1 1 1 1 -1 1 2 1 1 1 1 9.7003 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 4.45689 1 1 1 1 1 2 1 1 2 1 1 -2 1 1 1 1 1 1 0.802165 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 5.66099 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.61237 1 1 1 1 1 3 1 1 2 2 1 -1 1 1 1 1 1 1 2.97608 1 1 1 2 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.48756 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.87253 2 2 2 2 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 7.42702 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.209732 2 3 3 2 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.55715 2 2 2 1 1 2 2 2 1 1 1 -2 1 2 1 1 1 1 0.207224 2 2 2 1 2 1 1 1 1 1 1 -2 1 1 1 1 2 1 7.37554 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.11792 2 3 3 2 2 1 2 2 1 1 1 -2 1 1 1 1 1 1 1.53867 1 1 1 1 1 1 2 2 2 1 2 -2 1 2 1 1 2 1 0.0302816 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 1 1 2.28003 1 1 1 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 2.9777 2 3 3 1 2 1 2 1 2 2 1 -1 1 1 1 1 1 1 0.0199808 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.29523 1 3 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 2 1 1.64431 2 3 3 1 2 1 1 2 1 1 1 -1 1 1 1 1 1 1 1.65059 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.37525 1 1 1 1 1 1 1 2 1 1 1 -2 1 2 1 1 2 1 1.73187 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 1.01163 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 1.87413 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 4.35695 2 2 2 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 0.273621 2 3 3 1 1 3 1 1 1 1 1 -2 1 1 1 1 2 1 3.43754 1 1 1 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 0.69945 2 2 2 1 1 3 1 1 1 1 1 -1 1 1 1 1 1 1 6.24086 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.112064 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 3.88415 1 2 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 1.06286 2 2 2 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 2.17353 2 3 3 1 2 1 1 2 1 1 1 -1 1 1 1 1 1 1 1.49488 1 1 1 2 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 8.26156 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.29956 2 3 3 1 2 1 1 1 2 1 2 -2 1 2 1 1 2 1 5.02241 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.79705 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.41045 1 2 2 1 2 2 1 2 1 1 1 -2 1 2 1 1 1 1 3.62587 1 2 2 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.03338 2 3 3 1 2 3 1 1 2 2 1 -2 1 1 1 1 1 1 1.32098 1 1 1 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 2.90188 1 1 1 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 2.5172 2 2 2 1 1 1 1 1 1 1 1 -1 1 2 1 1 1 1 1.59161 1 1 1 1 1 2 1 1 1 1 1 -2 1 2 1 1 1 1 1.51327 1 2 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.61682 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.582747 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.78714 1 1 1 1 1 1 1 1 2 1 1 -2 1 2 1 1 2 1 3.90871 2 3 3 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 2.12194 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 2.85085 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 2.63259 1 1 1 1 1 3 1 1 1 1 1 -2 1 2 1 1 1 1 1.90261 1 1 1 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 1.12473 2 3 3 2 2 2 1 1 1 1 1 -1 1 2 1 1 1 1 0.744409 2 2 2 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 0.553062 2 3 3 1 2 3 2 2 1 1 1 -2 1 2 1 1 2 1 4.13517 2 3 3 2 2 1 1 1 1 1 1 -2 1 2 1 1 1 1 5.34859 1 3 1 1 1 3 1 1 1 1 1 -1 1 2 1 1 1 1 4.14217 2 2 2 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 4.68854 1 1 1 1 1 1 1 1 1 1 1 -2 1 1 1 1 1 1 2.47433 1 1 1 1 2 1 1 1 2 1 1 -2 1 2 1 1 1 1 4.04289 2 3 3 1 2 1 1 1 1 1 1 -1 1 2 1 1 1 1 4.64514 2 2 2 1 1 1 1 2 1 1 1 -2 1 1 1 1 1 1 3.52575 1 1 1 2 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 0.0085396 2 3 3 1 2 1 1 1 2 2 1 -2 1 2 1 1 2 1 3.75628 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.46408 2 3 3 1 2 1 2 2 1 1 1 -1 1 2 1 1 1 1 4.407 1 2 2 1 1 1 2 1 1 1 1 -2 1 2 1 1 2 1 12.9879 2 3 3 1 2 1 1 1 2 1 1 -2 1 2 1 1 2 1 5.42745 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 2.27077 2 3 3 1 2 1 1 1 2 1 1 -1 1 1 1 1 1 1 4.19191 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.43925 1 1 1 1 1 1 1 2 1 1 1 -1 1 1 1 1 1 1 4.98537 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 1.71189 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 4.91003 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 2 2 1 0.809663 2 3 3 1 2 1 1 1 1 1 1 -2 1 2 1 1 2 1 3.78373 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 1 1 1.64728 1 1 1 1 2 1 1 2 2 1 1 -2 1 2 1 1 2 1 0.977114 2 3 3 1 2 2 1 1 1 1 1 -2 1 2 1 1 2 1 4.78619 2 3 3 1 2 1 1 1 1 1 1 -2 1 1 1 1 2 1 4.88483 1 1 1 2 2 1 1 1 2 1 1 -1 1 1 1 1 1 1 0.0447191 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 2 1 6.22958 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 4.02524 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 5.10729 1 3 2 1 1 1 1 1 2 2 1 -2 1 2 1 1 2 1 8.97099 2 3 3 1 2 3 1 1 1 1 1 -2 1 2 1 1 2 1 5.59486 2 3 3 1 2 1 1 1 1 1 1 -1 1 1 1 1 1 1 1.13786 1 1 1 1 1 1 1 1 1 1 1 -2 1 2 1 1 1 1 11.3795 1 2 2 1 1 1 1 1 1 1 1 - diff --git a/sourcecodes/data/examplecar/OVIgraphviz.txt b/sourcecodes/data/examplecar/OVIgraphviz.txt deleted file mode 100644 index 2aaaecb2..00000000 --- a/sourcecodes/data/examplecar/OVIgraphviz.txt +++ /dev/null @@ -1,70 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -Dist -> BatAge; -Dist -> Timing; -Dist -> Plugs; -Dist -> AirFilter; -Dist -> GasTank; -Dist -> GasFilter; -SpkQual -> Starts; -MFuse -> Starts; -MFuse -> Dist; -MFuse -> SpkQual; -MFuse -> Starter; -MFuse -> BatAge; -MFuse -> Charging; -MFuse -> Timing; -MFuse -> Cranks; -MFuse -> Plugs; -MFuse -> AirFilter; -MFuse -> Air; -MFuse -> Fuel; -MFuse -> GasTank; -MFuse -> GasFilter; -Alter -> Dist; -Alter -> MFuse; -Alter -> BatAge; -Alter -> Charging; -Alter -> Timing; -Alter -> Plugs; -Alter -> AirFilter; -Alter -> Air; -Alter -> GasTank; -Alter -> GasFilter; -Starter -> Cranks; -StMotor -> MFuse; -StMotor -> Alter; -StMotor -> Starter; -StMotor -> BatAge; -StMotor -> Timing; -StMotor -> Plugs; -StMotor -> AirFilter; -StMotor -> Air; -StMotor -> Fuel; -StMotor -> GasTank; -StMotor -> GasFilter; -PlugVolt -> Starts; -PlugVolt -> Dist; -PlugVolt -> SpkQual; -PlugVolt -> MFuse; -PlugVolt -> Alter; -PlugVolt -> Starter; -PlugVolt -> StMotor; -PlugVolt -> Charging; -PlugVolt -> Cranks; -BatVolt -> Starts; -BatVolt -> Dist; -BatVolt -> SpkQual; -BatVolt -> MFuse; -BatVolt -> Alter; -BatVolt -> Starter; -BatVolt -> StMotor; -BatVolt -> Charging; -BatVolt -> PlugVolt; -BatVolt -> Cranks; -Plugs -> SpkQual; -AirFilter -> Air; -GasTank -> Fuel; -GasFilter -> Fuel; -} \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIk.txt b/sourcecodes/data/examplecar/OVIk.txt deleted file mode 100644 index d00491fd..00000000 --- a/sourcecodes/data/examplecar/OVIk.txt +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/sourcecodes/data/examplecar/OVImap.txt b/sourcecodes/data/examplecar/OVImap.txt deleted file mode 100644 index eda717d2..00000000 --- a/sourcecodes/data/examplecar/OVImap.txt +++ /dev/null @@ -1,19 +0,0 @@ -Starts 3 0.432505 1.751249 -Dist 3 0.094441 1.008991 -SpkQual 2 0.434234 1.748252 -MFuse 2 0.031607 1.000999 -Alter 2 0.054690 1.002997 -Starter 2 0.490666 1.402597 -StMotor 2 0.070534 1.004995 -BatAge 2 2.948418 3.295892 -Charging 2 0.500244 1.497502 -PlugVolt 2 0.908145 2.090909 -BatVolt 2 0.914876 1.999001 -Timing 2 0.293230 1.094905 -Cranks 2 0.500010 1.515485 -Plugs 2 0.819700 1.518482 -AirFilter 3 0.294607 1.095904 -Air 2 0.375671 1.169830 -Fuel 2 0.416982 1.223776 -GasTank 2 0.295974 1.096903 -GasFilter 1 0.164975 1.027972 diff --git a/sourcecodes/data/examplecar/OVImapdata.txt b/sourcecodes/data/examplecar/OVImapdata.txt deleted file mode 100644 index d1eac895..00000000 --- a/sourcecodes/data/examplecar/OVImapdata.txt +++ /dev/null @@ -1 +0,0 @@ -BatVolt PlugVolt StMotor Alter MFuse Charging Starter Cranks Dist GasFilter GasTank Fuel AirFilter Air Plugs SpkQual Starts Timing BatAge diff --git a/sourcecodes/data/examplecar/OVIname.txt b/sourcecodes/data/examplecar/OVIname.txt deleted file mode 100644 index e7901e87..00000000 --- a/sourcecodes/data/examplecar/OVIname.txt +++ /dev/null @@ -1 +0,0 @@ -Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter diff --git a/sourcecodes/data/examplecar/OVInet_figure.txt b/sourcecodes/data/examplecar/OVInet_figure.txt deleted file mode 100644 index ceed746e..00000000 --- a/sourcecodes/data/examplecar/OVInet_figure.txt +++ /dev/null @@ -1,237 +0,0 @@ -19 -2100 1800 -BatVolt 788 0 -PlugVolt 998 180 -StMotor 788 360 -Alter 998 540 -MFuse 788 720 -Charging 472 900 -Starter 998 900 -Cranks 0 1080 -Dist 1523 900 -GasFilter 263 1080 -GasTank 525 1080 -Fuel 472 1260 -AirFilter 788 1080 -Air 998 1260 -Plugs 1050 1080 -SpkQual 1523 1260 -Starts 788 1440 -Timing 1313 1080 -BatAge 1575 1080 -BatVolt 3 -250 150 -0 -10 2 3 4 5 6 7 8 9 16 17 -1 0.4184 -2 0.1639 -3 0.4177 -PlugVolt 3 -250 150 -1 1 -9 3 4 5 6 7 8 9 16 17 -1 0.3706 -2 0.1678 -3 0.4616 -StMotor 2 -250 150 -2 1 2 -11 4 5 7 10 11 12 13 14 15 18 19 -1 0.9955 -2 0.0045 -Alter 2 -250 150 -3 1 2 3 -10 5 6 9 10 11 13 14 15 18 19 -1 0.9970 -2 0.0030 -MFuse 2 -250 150 -4 1 2 3 4 -14 6 7 8 9 10 11 12 13 14 15 16 17 18 19 -1 0.9990 -2 0.0010 -Charging 2 -250 150 -4 1 2 4 5 -0 -1 0.5024 -2 0.4976 -Starter 2 -250 150 -4 1 2 3 5 -1 8 -1 0.5977 -2 0.4023 -Cranks 2 -250 150 -4 1 2 5 7 -0 -1 0.4848 -2 0.5152 -Dist 2 -250 150 -4 1 2 4 5 -6 10 11 13 15 18 19 -1 0.9910 -2 0.0090 -GasFilter 2 -250 150 -4 3 4 5 9 -1 12 -1 0.9725 -2 0.0275 -GasTank 2 -250 150 -4 3 4 5 9 -1 12 -1 0.9031 -2 0.0969 -Fuel 2 -250 150 -4 3 5 10 11 -0 -1 0.7756 -2 0.2244 -AirFilter 2 -250 150 -4 3 4 5 9 -1 14 -1 0.9040 -2 0.0960 -Air 2 -250 150 -4 3 4 5 13 -0 -1 0.8301 -2 0.1699 -Plugs 3 -250 150 -4 3 4 5 9 -1 16 -1 0.6922 -2 0.0970 -3 0.2109 -SpkQual 2 -250 150 -4 1 2 5 15 -1 17 -1 0.2568 -2 0.7432 -Starts 2 -250 150 -4 1 2 5 16 -0 -1 0.2497 -2 0.7503 -Timing 2 -250 150 -4 3 4 5 9 -0 -1 0.9053 -2 0.0947 -BatAge 1 -250 150 -4 3 4 5 9 -0 --2.1178 0.0437 --2.0287 0.0524 --1.9396 0.0623 --1.8505 0.0736 --1.7614 0.0862 --1.6723 0.1001 --1.5832 0.1155 --1.4941 0.1321 --1.4050 0.1499 --1.3159 0.1689 --1.2268 0.1888 --1.1377 0.2093 --1.0486 0.2303 --0.9595 0.2515 --0.8704 0.2725 --0.7813 0.2929 --0.6922 0.3124 --0.6031 0.3306 --0.5140 0.3471 --0.4249 0.3617 --0.3358 0.3740 --0.2467 0.3836 --0.1576 0.3905 --0.0685 0.3944 -0.0206 0.3952 -0.1097 0.3930 -0.1988 0.3877 -0.2879 0.3795 -0.3770 0.3687 -0.4661 0.3553 -0.5552 0.3398 -0.6443 0.3225 -0.7334 0.3036 -0.8225 0.2837 -0.9116 0.2629 -1.0007 0.2419 -1.0898 0.2207 -1.1789 0.1999 -1.2680 0.1796 -1.3571 0.1601 -1.4462 0.1417 -1.5353 0.1243 -1.6244 0.1083 -1.7135 0.0936 -1.8026 0.0803 -1.8917 0.0683 -1.9808 0.0576 -2.0699 0.0483 -2.1590 0.0401 -2.2481 0.0331 -2.3372 0.0271 -2.4263 0.0220 -2.5154 0.0177 -2.6045 0.0142 -2.6936 0.0112 -2.7827 0.0088 -2.8718 0.0069 -2.9609 0.0054 -3.0500 0.0041 -3.1391 0.0031 -3.2282 0.0024 -3.3173 0.0018 -3.4064 0.0013 -3.4954 0.0010 -3.5845 0.0007 -3.6736 0.0005 -3.7627 0.0004 -3.8518 0.0003 -3.9409 0.0002 -4.0300 0.0001 -4.1191 0.0001 -4.2082 0.0001 -4.2973 0.0000 -4.3864 0.0000 -4.4755 0.0000 -4.5646 0.0000 -4.6537 0.0000 -4.7428 0.0000 -4.8319 0.0000 -4.9210 0.0000 -5.0101 0.0000 -5.0992 0.0000 -5.1883 0.0000 -5.2774 0.0000 -5.3665 0.0000 -5.4556 0.0000 -5.5447 0.0000 -5.6338 0.0000 -5.7229 0.0000 -5.8120 0.0000 -5.9011 0.0000 -5.9902 0.0000 -6.0793 0.0000 -6.1684 0.0000 -6.2575 0.0000 -6.3466 0.0000 -6.4357 0.0000 -6.5248 0.0000 -6.6139 0.0000 -6.7030 0.0000 -6.7921 0.0000 diff --git a/sourcecodes/data/examplecar/OVInet_figure_new.txt b/sourcecodes/data/examplecar/OVInet_figure_new.txt deleted file mode 100644 index bd2ec975..00000000 --- a/sourcecodes/data/examplecar/OVInet_figure_new.txt +++ /dev/null @@ -1,138 +0,0 @@ -19 -19 -2100 1800 -BatVolt 788 0 -PlugVolt 998 180 -StMotor 788 360 -Alter 998 540 -MFuse 788 720 -Charging 472 900 -Starter 998 900 -Cranks 0 1080 -Dist 1523 900 -GasFilter 263 1080 -GasTank 525 1080 -Fuel 472 1260 -AirFilter 788 1080 -Air 998 1260 -Plugs 1050 1080 -SpkQual 1523 1260 -Starts 788 1440 -Timing 1313 1080 -BatAge 1575 1080 -BatVolt 3 -250 150 -0 -10 2 3 4 5 6 7 8 9 16 17 -1 0.4186 -2 0.1642 -3 0.4172 -PlugVolt 3 -250 150 -1 1 -9 3 4 5 6 7 8 9 16 17 -1 0.3716 -2 0.1684 -3 0.4600 -StMotor 2 -250 150 -2 1 2 -11 4 5 7 10 11 12 13 14 15 18 19 -1 0.9982 -2 0.0018 -Alter 2 -250 150 -3 1 2 3 -10 5 6 9 10 11 13 14 15 18 19 -1 0.9985 -2 0.0015 -MFuse 2 -250 150 -4 1 2 3 4 -14 6 7 8 9 10 11 12 13 14 15 16 17 18 19 -1 1.0000 -2 0.0000 -Charging 2 -250 150 -4 1 2 4 5 -0 -1 0.5027 -2 0.4973 -Starter 2 -250 150 -4 1 2 3 5 -1 8 -1 0.5996 -2 0.4004 -Cranks 2 -250 150 -4 1 2 5 7 -0 -1 0.4861 -2 0.5139 -Dist 2 -250 150 -4 1 2 4 5 -6 10 11 13 15 18 19 -1 0.9948 -2 0.0052 -GasFilter 2 -250 150 -4 3 4 5 9 -1 12 -1 0.9736 -2 0.0264 -GasTank 2 -250 150 -4 3 4 5 9 -1 12 -1 0.9048 -2 0.0952 -Fuel 2 -250 150 -4 3 5 10 11 -0 -1 0.7770 -2 0.2230 -AirFilter 2 -250 150 -4 3 4 5 9 -1 14 -1 0.9045 -2 0.0955 -Air 2 -250 150 -4 3 4 5 13 -0 -1 0.8304 -2 0.1696 -Plugs 3 -250 150 -4 3 4 5 9 -1 16 -1 0.6923 -2 0.0968 -3 0.2108 -SpkQual 2 -250 150 -4 1 2 5 15 -1 17 -1 0.2573 -2 0.7427 -Starts 2 -250 150 -4 1 2 5 16 -0 -1 0.2504 -2 0.7496 -Timing 2 -250 150 -4 3 4 5 9 -0 -1 0.9080 -2 0.0920 -BatAge 1 -250 150 -4 3 4 5 9 -0 --1.3159 1.0000 diff --git a/sourcecodes/data/examplecar/OVInnode.txt b/sourcecodes/data/examplecar/OVInnode.txt deleted file mode 100644 index d6b24041..00000000 --- a/sourcecodes/data/examplecar/OVInnode.txt +++ /dev/null @@ -1 +0,0 @@ -19 diff --git a/sourcecodes/data/examplecar/OVInrows.txt b/sourcecodes/data/examplecar/OVInrows.txt deleted file mode 100644 index 7d802a3e..00000000 --- a/sourcecodes/data/examplecar/OVInrows.txt +++ /dev/null @@ -1 +0,0 @@ -1002 diff --git a/sourcecodes/data/examplecar/OVIparent.txt b/sourcecodes/data/examplecar/OVIparent.txt deleted file mode 100644 index b8626c4c..00000000 --- a/sourcecodes/data/examplecar/OVIparent.txt +++ /dev/null @@ -1 +0,0 @@ -4 diff --git a/sourcecodes/data/examplecar/OVIrun_evidencemodified.sh b/sourcecodes/data/examplecar/OVIrun_evidencemodified.sh deleted file mode 100644 index dab5c39a..00000000 --- a/sourcecodes/data/examplecar/OVIrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified OVI -fi -exit diff --git a/sourcecodes/data/examplecar/OVIrun_initialstructure.sh b/sourcecodes/data/examplecar/OVIrun_initialstructure.sh deleted file mode 100644 index d47ae324..00000000 --- a/sourcecodes/data/examplecar/OVIrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure OVI -fi -exit diff --git a/sourcecodes/data/examplecar/OVIstructure_input.txt b/sourcecodes/data/examplecar/OVIstructure_input.txt deleted file mode 100644 index cad732f3..00000000 --- a/sourcecodes/data/examplecar/OVIstructure_input.txt +++ /dev/null @@ -1,20 +0,0 @@ -Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 1 0 0 0 1 0 1 1 0 0 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 1 1 0 0 1 0 1 1 0 0 1 1 1 1 1 1 1 1 -0 1 0 1 0 0 0 1 1 0 0 1 0 1 1 1 0 1 1 -0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 -0 0 0 1 1 1 0 1 0 0 0 1 0 1 1 1 1 1 1 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 1 1 1 1 1 1 0 1 0 0 0 1 0 0 0 0 0 0 -1 1 1 1 1 1 1 0 1 1 0 0 1 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 diff --git a/sourcecodes/data/examplecar/OVIstructure_input_temp.txt b/sourcecodes/data/examplecar/OVIstructure_input_temp.txt deleted file mode 100644 index 09d40aa3..00000000 --- a/sourcecodes/data/examplecar/OVIstructure_input_temp.txt +++ /dev/null @@ -1,20 +0,0 @@ -Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 -0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 diff --git a/sourcecodes/data/examplecar/OVIstructure_old.txt b/sourcecodes/data/examplecar/OVIstructure_old.txt deleted file mode 100644 index 22f14ba3..00000000 --- a/sourcecodes/data/examplecar/OVIstructure_old.txt +++ /dev/null @@ -1,19 +0,0 @@ -Dist 0.9910 0.0090 -BatAge 0.0437 0.0524 0.0623 0.0736 0.0862 0.1001 0.1155 0.1321 0.1499 0.1689 0.1888 0.2093 0.2303 0.2515 0.2725 0.2929 0.3124 0.3306 0.3471 0.3617 0.3740 0.3836 0.3905 0.3944 0.3952 0.3930 0.3877 0.3795 0.3687 0.3553 0.3398 0.3225 0.3036 0.2837 0.2629 0.2419 0.2207 0.1999 0.1796 0.1601 0.1417 0.1243 0.1083 0.0936 0.0803 0.0683 0.0576 0.0483 0.0401 0.0331 0.0271 0.0220 0.0177 0.0142 0.0112 0.0088 0.0069 0.0054 0.0041 0.0031 0.0024 0.0018 0.0013 0.0010 0.0007 0.0005 0.0004 0.0003 0.0002 0.0001 0.0001 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -Timing 0.9053 0.0947 -Plugs 0.6922 0.0970 0.2109 -AirFilter 0.9040 0.0960 -GasTank 0.9031 0.0969 -GasFilter 0.9725 0.0275 -SpkQual 0.2568 0.7432 -Starts 0.2497 0.7503 -MFuse 0.9990 0.0010 -Starter 0.5977 0.4023 -Charging 0.5024 0.4976 -Cranks 0.4848 0.5152 -Air 0.8301 0.1699 -Fuel 0.7756 0.2244 -Alter 0.9970 0.0030 -StMotor 0.9955 0.0045 -PlugVolt 0.3706 0.1678 0.4616 -BatVolt 0.4184 0.1639 0.4177 diff --git a/sourcecodes/data/examplecar/OVIthr.txt b/sourcecodes/data/examplecar/OVIthr.txt deleted file mode 100644 index 2eb3c4fe..00000000 --- a/sourcecodes/data/examplecar/OVIthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.5 diff --git a/sourcecodes/data/examplecar/OVItype.txt b/sourcecodes/data/examplecar/OVItype.txt deleted file mode 100644 index 0b76081c..00000000 --- a/sourcecodes/data/examplecar/OVItype.txt +++ /dev/null @@ -1,2 +0,0 @@ -Starts Dist SpkQual MFuse Alter Starter StMotor BatAge Charging PlugVolt BatVolt Timing Cranks Plugs AirFilter Air Fuel GasTank GasFilter -2 2 2 2 2 2 2 1 2 3 3 2 2 3 2 2 2 2 2 diff --git a/sourcecodes/data/examplecar/OVIvar.txt b/sourcecodes/data/examplecar/OVIvar.txt deleted file mode 100644 index dec2bf5d..00000000 --- a/sourcecodes/data/examplecar/OVIvar.txt +++ /dev/null @@ -1 +0,0 @@ -19 \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIvardata.txt b/sourcecodes/data/examplecar/OVIvardata.txt deleted file mode 100644 index e595bf94..00000000 --- a/sourcecodes/data/examplecar/OVIvardata.txt +++ /dev/null @@ -1 +0,0 @@ --1.3159 \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIvarname.txt b/sourcecodes/data/examplecar/OVIvarname.txt deleted file mode 100644 index 2453221d..00000000 --- a/sourcecodes/data/examplecar/OVIvarname.txt +++ /dev/null @@ -1 +0,0 @@ -BatAge \ No newline at end of file diff --git a/sourcecodes/data/examplecar/OVIwhite.txt b/sourcecodes/data/examplecar/OVIwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/examplecar/OVIwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/examplecar/old/OVIrun_evidencemodified.sh b/sourcecodes/data/examplecar/old/OVIrun_evidencemodified.sh deleted file mode 100644 index dab5c39a..00000000 --- a/sourcecodes/data/examplecar/old/OVIrun_evidencemodified.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/evidencemodified OVI -fi -exit diff --git a/sourcecodes/data/examplecar/old/OVIrun_initialstructure.sh b/sourcecodes/data/examplecar/old/OVIrun_initialstructure.sh deleted file mode 100644 index d47ae324..00000000 --- a/sourcecodes/data/examplecar/old/OVIrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure OVI -fi -exit diff --git a/sourcecodes/data/examplecar15node/MtXrun_initialstructure.sh b/sourcecodes/data/examplecar15node/MtXrun_initialstructure.sh deleted file mode 100644 index 8012f054..00000000 --- a/sourcecodes/data/examplecar15node/MtXrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure MtX -fi -exit diff --git a/sourcecodes/data/examplezoo/fSfban.txt b/sourcecodes/data/examplezoo/fSfban.txt deleted file mode 100644 index 9197eeec..00000000 --- a/sourcecodes/data/examplezoo/fSfban.txt +++ /dev/null @@ -1,261 +0,0 @@ -From To -aquatic airborne -aquatic venomous -aquatic predator -aquatic domestic -airborne aquatic -airborne venomous -airborne predator -airborne domestic -venomous aquatic -venomous airborne -venomous predator -venomous domestic -predator aquatic -predator airborne -predator venomous -predator domestic -domestic aquatic -domestic airborne -domestic venomous -domestic predator -eggs aquatic -eggs airborne -eggs venomous -eggs predator -eggs domestic -milk aquatic -milk airborne -milk venomous -milk predator -milk domestic -backbone aquatic -backbone airborne -backbone venomous -backbone predator -backbone domestic -breathes aquatic -breathes airborne -breathes venomous -breathes predator -breathes domestic -catsize aquatic -catsize airborne -catsize venomous -catsize predator -catsize domestic -tail aquatic -tail airborne -tail venomous -tail predator -tail domestic -toothed aquatic -toothed airborne -toothed venomous -toothed predator -toothed domestic -hair aquatic -hair airborne -hair venomous -hair predator -hair domestic -feathers aquatic -feathers airborne -feathers venomous -feathers predator -feathers domestic -fins aquatic -fins airborne -fins venomous -fins predator -fins domestic -legs aquatic -legs airborne -legs venomous -legs predator -legs domestic -type aquatic -type airborne -type venomous -type predator -type domestic -eggs aquatic -eggs airborne -eggs venomous -eggs predator -eggs domestic -milk aquatic -milk airborne -milk venomous -milk predator -milk domestic -backbone aquatic -backbone airborne -backbone venomous -backbone predator -backbone domestic -breathes aquatic -breathes airborne -breathes venomous -breathes predator -breathes domestic -catsize eggs -catsize milk -catsize backbone -catsize breathes -tail eggs -tail milk -tail backbone -tail breathes -toothed eggs -toothed milk -toothed backbone -toothed breathes -hair eggs -hair milk -hair backbone -hair breathes -feathers eggs -feathers milk -feathers backbone -feathers breathes -fins eggs -fins milk -fins backbone -fins breathes -legs eggs -legs milk -legs backbone -legs breathes -type eggs -type milk -type backbone -type breathes -catsize tail -catsize toothed -catsize hair -catsize feathers -catsize fins -catsize legs -tail catsize -tail toothed -tail hair -tail feathers -tail fins -tail legs -toothed catsize -toothed tail -toothed hair -toothed feathers -toothed fins -toothed legs -hair catsize -hair tail -hair toothed -hair feathers -hair fins -hair legs -feathers catsize -feathers tail -feathers toothed -feathers hair -feathers fins -feathers legs -fins catsize -fins tail -fins toothed -fins hair -fins feathers -fins legs -legs catsize -legs tail -legs toothed -legs hair -legs feathers -legs fins -catsize aquatic -catsize airborne -catsize venomous -catsize predator -catsize domestic -tail aquatic -tail airborne -tail venomous -tail predator -tail domestic -toothed aquatic -toothed airborne -toothed venomous -toothed predator -toothed domestic -hair aquatic -hair airborne -hair venomous -hair predator -hair domestic -feathers aquatic -feathers airborne -feathers venomous -feathers predator -feathers domestic -fins aquatic -fins airborne -fins venomous -fins predator -fins domestic -legs aquatic -legs airborne -legs venomous -legs predator -legs domestic -catsize eggs -catsize milk -catsize backbone -catsize breathes -tail eggs -tail milk -tail backbone -tail breathes -toothed eggs -toothed milk -toothed backbone -toothed breathes -hair eggs -hair milk -hair backbone -hair breathes -feathers eggs -feathers milk -feathers backbone -feathers breathes -fins eggs -fins milk -fins backbone -fins breathes -legs eggs -legs milk -legs backbone -legs breathes -type catsize -type tail -type toothed -type hair -type feathers -type fins -type legs -type aquatic -type airborne -type venomous -type predator -type domestic -type eggs -type milk -type backbone -type breathes -type catsize -type tail -type toothed -type hair -type feathers -type fins -type legs diff --git a/sourcecodes/data/examplezoo/fSfcontinuous_input.txt b/sourcecodes/data/examplezoo/fSfcontinuous_input.txt deleted file mode 100644 index 340ad4f6..00000000 --- a/sourcecodes/data/examplezoo/fSfcontinuous_input.txt +++ /dev/null @@ -1,104 +0,0 @@ -hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type -2 2 2 2 2 2 2 2 2 2 2 2 6 2 2 2 7 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 2 1 2 2 1 1 2 1 2 2 1 4 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 7 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4 -1 1 1 2 1 2 2 2 2 2 1 2 1 2 1 2 1 -1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 1 2 2 2 2 2 1 1 2 1 1 3 -1 1 1 2 1 2 2 2 2 2 1 2 1 2 1 2 1 -1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4 -2 1 1 2 1 2 2 2 2 2 1 2 1 1 1 2 1 -1 1 1 1 1 2 2 2 2 1 2 1 1 2 1 1 3 -1 1 2 1 1 2 2 1 1 1 2 1 1 1 1 1 7 -1 1 2 1 1 1 2 2 2 2 1 1 1 2 1 1 3 -1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 7 -1 1 2 1 1 2 1 2 2 1 1 2 1 2 1 1 4 -1 1 2 1 1 2 2 2 2 1 2 2 1 2 1 2 4 -1 1 2 1 1 2 2 2 2 1 1 2 1 2 1 2 4 -1 1 2 1 1 1 1 1 1 2 1 1 1 1 1 1 7 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2 -1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2 -1 2 2 1 2 2 1 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 2 2 -2 1 1 2 2 1 1 2 2 2 1 1 2 2 1 1 1 -2 1 1 2 1 1 2 2 2 2 1 1 2 1 2 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 2 1 1 2 1 -1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 1 1 2 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 1 1 1 1 2 2 1 1 2 2 1 2 2 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 2 1 2 -1 2 2 1 1 2 2 1 2 2 1 1 2 2 1 2 2 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 1 1 2 1 2 2 1 1 2 2 1 2 2 -2 1 1 2 1 2 2 2 2 2 1 2 2 2 1 2 1 -1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 2 2 2 1 2 2 1 1 2 2 1 1 2 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 -2 1 1 2 1 1 1 2 2 2 1 1 2 2 1 1 1 -1 2 2 1 2 2 1 1 2 2 1 1 2 2 1 2 2 -2 1 1 2 2 1 1 2 2 2 1 1 2 2 1 1 1 -1 2 2 1 2 1 2 1 2 2 1 1 2 2 1 2 2 -2 1 1 2 1 1 1 2 2 2 1 1 2 2 1 2 1 -1 2 2 1 2 1 1 1 2 2 1 1 2 2 1 1 2 -2 1 1 2 1 1 2 2 2 2 1 1 3 1 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 1 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 1 2 1 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -1 1 2 1 1 2 2 1 1 1 1 1 3 1 1 1 7 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 -1 1 2 1 1 2 2 2 2 2 1 1 3 1 1 1 5 -1 1 2 1 1 2 2 2 2 2 2 1 3 1 1 1 5 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 1 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 1 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 2 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 1 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -1 1 2 1 1 2 2 2 2 2 1 1 3 2 1 1 5 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 1 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 2 1 -2 1 2 2 1 2 2 1 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 2 2 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 2 2 1 -1 1 2 1 1 2 1 2 2 2 1 1 3 1 1 1 5 -1 1 2 1 1 1 1 1 2 2 1 1 3 2 1 2 3 -1 1 2 1 1 1 2 2 2 2 1 1 3 2 1 1 3 -2 1 1 2 1 1 1 2 2 2 1 1 3 2 1 1 1 -2 1 1 2 1 1 2 2 2 2 1 1 3 2 1 2 1 -1 1 2 1 1 2 2 1 1 1 1 1 4 1 1 1 7 -1 1 2 1 1 2 2 1 1 1 1 1 5 1 1 1 7 -1 1 2 1 1 1 1 1 1 2 1 1 5 1 1 1 6 -1 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6 -2 1 2 1 2 1 1 1 1 2 2 1 5 1 2 1 6 -2 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6 -1 1 2 1 2 1 2 1 1 2 1 1 5 1 1 1 6 -1 1 2 1 1 2 2 1 1 1 1 1 5 1 1 1 7 -2 1 2 1 2 1 1 1 1 2 1 1 5 1 1 1 6 -1 1 2 1 1 1 1 1 1 2 1 1 5 1 1 1 6 -2 1 2 1 2 1 1 1 1 2 2 1 5 1 1 1 6 -1 1 2 1 1 2 2 1 1 1 1 1 6 1 1 2 7 -1 1 1 1 1 1 2 1 1 2 2 1 6 2 1 1 7 - diff --git a/sourcecodes/data/examplezoo/fSfgraphviz.txt b/sourcecodes/data/examplezoo/fSfgraphviz.txt deleted file mode 100644 index 701801c6..00000000 --- a/sourcecodes/data/examplezoo/fSfgraphviz.txt +++ /dev/null @@ -1,61 +0,0 @@ -digraph G { -size="10,10"; ratio = fill; -node [shape=square,width=1.5]; -feathers -> type; -eggs -> hair; -eggs -> feathers; -eggs -> toothed; -eggs -> backbone; -eggs -> breathes; -eggs -> legs; -eggs -> tail; -eggs -> catsize; -milk -> hair; -milk -> feathers; -milk -> toothed; -milk -> backbone; -milk -> breathes; -milk -> legs; -milk -> tail; -milk -> catsize; -milk -> type; -airborne -> eggs; -airborne -> milk; -airborne -> backbone; -airborne -> breathes; -airborne -> catsize; -aquatic -> eggs; -aquatic -> milk; -aquatic -> breathes; -aquatic -> fins; -backbone -> hair; -backbone -> feathers; -backbone -> toothed; -backbone -> fins; -backbone -> legs; -backbone -> tail; -backbone -> type; -breathes -> hair; -breathes -> toothed; -breathes -> backbone; -breathes -> fins; -breathes -> legs; -breathes -> catsize; -breathes -> type; -venomous -> hair; -venomous -> feathers; -venomous -> eggs; -venomous -> milk; -venomous -> toothed; -venomous -> backbone; -venomous -> breathes; -venomous -> fins; -venomous -> legs; -venomous -> tail; -venomous -> catsize; -legs -> type; -domestic -> eggs; -domestic -> milk; -domestic -> fins; -domestic -> tail; -} \ No newline at end of file diff --git a/sourcecodes/data/examplezoo/fSfk.txt b/sourcecodes/data/examplezoo/fSfk.txt deleted file mode 100644 index f599e28b..00000000 --- a/sourcecodes/data/examplezoo/fSfk.txt +++ /dev/null @@ -1 +0,0 @@ -10 diff --git a/sourcecodes/data/examplezoo/fSfmap.txt b/sourcecodes/data/examplezoo/fSfmap.txt deleted file mode 100644 index 4a123441..00000000 --- a/sourcecodes/data/examplezoo/fSfmap.txt +++ /dev/null @@ -1,17 +0,0 @@ -hair 2 0.496921 1.425743 -feathers 2 0.400495 1.198020 -eggs 2 0.495325 1.584158 -milk 2 0.493522 1.405941 -airborne 2 0.427750 1.237624 -aquatic 2 0.481335 1.356436 -predator 2 0.499505 1.554455 -toothed 2 0.491512 1.603960 -backbone 2 0.384605 1.821782 -breathes 2 0.407844 1.792079 -venomous 2 0.271410 1.079208 -fins 6 0.376013 1.168317 -legs 2 1.253194 2.544554 -tail 2 0.439397 1.742574 -domestic 2 0.336552 1.128713 -catsize 7 0.498314 1.435644 -type 2 2.102709 2.831683 diff --git a/sourcecodes/data/examplezoo/fSfmapdata.txt b/sourcecodes/data/examplezoo/fSfmapdata.txt deleted file mode 100644 index 19d91997..00000000 --- a/sourcecodes/data/examplezoo/fSfmapdata.txt +++ /dev/null @@ -1 +0,0 @@ -domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair diff --git a/sourcecodes/data/examplezoo/fSfname.txt b/sourcecodes/data/examplezoo/fSfname.txt deleted file mode 100644 index c68267c4..00000000 --- a/sourcecodes/data/examplezoo/fSfname.txt +++ /dev/null @@ -1 +0,0 @@ -hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type diff --git a/sourcecodes/data/examplezoo/fSfnet_figure.txt b/sourcecodes/data/examplezoo/fSfnet_figure.txt deleted file mode 100644 index 0c8f9428..00000000 --- a/sourcecodes/data/examplezoo/fSfnet_figure.txt +++ /dev/null @@ -1,130 +0,0 @@ -17 -1800 1200 -domestic 43 0 -venomous 343 0 -predator 643 0 -aquatic 943 0 -airborne 1243 0 -milk 523 171 -eggs 1123 171 -breathes 643 343 -catsize 523 514 -backbone 1123 514 -tail 0 686 -legs 257 686 -fins 514 686 -toothed 771 686 -feathers 1029 686 -type 823 857 -hair 1286 686 -domestic 2 -250 150 -0 -4 6 7 11 13 -1 0.8672 -2 0.1328 -venomous 2 -250 150 -0 -11 6 7 8 9 10 11 12 13 14 15 17 -1 0.8860 -2 0.1140 -predator 2 -250 150 -0 -0 -1 0.4455 -2 0.5545 -aquatic 2 -250 150 -0 -4 6 7 8 13 -1 0.6726 -2 0.3274 -airborne 2 -250 150 -0 -5 6 7 8 9 10 -1 0.8149 -2 0.1851 -milk 2 -250 150 -4 1 2 4 5 -9 8 9 10 11 12 14 15 16 17 -1 0.4703 -2 0.5297 -eggs 2 -250 150 -4 1 2 4 5 -8 8 9 10 11 12 14 15 17 -1 0.4962 -2 0.5038 -breathes 2 -250 150 -5 2 4 5 6 7 -7 9 10 12 13 14 16 17 -1 0.1666 -2 0.8334 -catsize 2 -250 150 -5 2 5 6 7 8 -0 -1 0.4789 -2 0.5211 -backbone 2 -250 150 -5 2 5 6 7 8 -7 11 12 13 14 15 16 17 -1 0.1743 -2 0.8257 -tail 2 -250 150 -5 1 2 6 7 10 -0 -1 0.2426 -2 0.7574 -legs 6 -250 150 -5 2 6 7 8 10 -1 16 -1 0.1827 -2 0.2108 -3 0.4747 -4 0.0111 -5 0.0799 -6 0.0409 -fins 2 -250 150 -5 1 2 4 8 10 -0 -1 0.8751 -2 0.1249 -toothed 2 -250 150 -5 2 6 7 8 10 -0 -1 0.3799 -2 0.6201 -feathers 2 -250 150 -4 2 6 7 10 -1 16 -1 0.8693 -2 0.1307 -type 7 -250 150 -5 6 8 10 12 15 -0 -1 0.5297 -2 0.1307 -3 0.0476 -4 0.0854 -5 0.0323 -6 0.0578 -7 0.1165 -hair 2 -250 150 -5 2 6 7 8 10 -0 -1 0.4597 -2 0.5403 diff --git a/sourcecodes/data/examplezoo/fSfnnode.txt b/sourcecodes/data/examplezoo/fSfnnode.txt deleted file mode 100644 index 98d9bcb7..00000000 --- a/sourcecodes/data/examplezoo/fSfnnode.txt +++ /dev/null @@ -1 +0,0 @@ -17 diff --git a/sourcecodes/data/examplezoo/fSfnrows.txt b/sourcecodes/data/examplezoo/fSfnrows.txt deleted file mode 100644 index 257e5632..00000000 --- a/sourcecodes/data/examplezoo/fSfnrows.txt +++ /dev/null @@ -1 +0,0 @@ -102 diff --git a/sourcecodes/data/examplezoo/fSfparent.txt b/sourcecodes/data/examplezoo/fSfparent.txt deleted file mode 100644 index 7ed6ff82..00000000 --- a/sourcecodes/data/examplezoo/fSfparent.txt +++ /dev/null @@ -1 +0,0 @@ -5 diff --git a/sourcecodes/data/examplezoo/fSfrun_initialstructure.sh b/sourcecodes/data/examplezoo/fSfrun_initialstructure.sh deleted file mode 100644 index f20a9a29..00000000 --- a/sourcecodes/data/examplezoo/fSfrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure fSf -fi -exit diff --git a/sourcecodes/data/examplezoo/fSfstructure_input.txt b/sourcecodes/data/examplezoo/fSfstructure_input.txt deleted file mode 100644 index c49d600b..00000000 --- a/sourcecodes/data/examplezoo/fSfstructure_input.txt +++ /dev/null @@ -1,18 +0,0 @@ -hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 0 -1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 1 -0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 1 0 -0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 1 0 0 0 0 0 1 0 0 0 1 1 1 0 0 1 -1 0 0 0 0 0 0 1 1 0 0 1 1 0 0 1 1 -1 1 1 1 0 0 0 1 1 1 0 1 1 1 0 1 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 1 1 0 0 0 0 0 0 0 1 0 1 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/sourcecodes/data/examplezoo/fSfstructure_input_temp.txt b/sourcecodes/data/examplezoo/fSfstructure_input_temp.txt deleted file mode 100644 index 8910aaee..00000000 --- a/sourcecodes/data/examplezoo/fSfstructure_input_temp.txt +++ /dev/null @@ -1,18 +0,0 @@ -hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -1.000000 0.800011 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 0.000000 -1.000000 1.000000 0.500003 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 -0.000000 0.400004 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 -0.800018 0.799985 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 1.000000 1.000000 -1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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0.000000 diff --git a/sourcecodes/data/examplezoo/fSfstructure_old.txt b/sourcecodes/data/examplezoo/fSfstructure_old.txt deleted file mode 100644 index bf00f5d5..00000000 --- a/sourcecodes/data/examplezoo/fSfstructure_old.txt +++ /dev/null @@ -1,16 +0,0 @@ -feathers 0.8693 0.1307 -type 0.5297 0.1307 0.0476 0.0854 0.0323 0.0578 0.1165 -eggs 0.4962 0.5038 -hair 0.4597 0.5403 -toothed 0.3799 0.6201 -backbone 0.1743 0.8257 -breathes 0.1666 0.8334 -legs 0.1827 0.2108 0.4747 0.0111 0.0799 0.0409 -tail 0.2426 0.7574 -catsize 0.4789 0.5211 -milk 0.4703 0.5297 -airborne 0.8149 0.1851 -aquatic 0.6726 0.3274 -fins 0.8751 0.1249 -venomous 0.8860 0.1140 -domestic 0.8672 0.1328 diff --git a/sourcecodes/data/examplezoo/fSfthr.txt b/sourcecodes/data/examplezoo/fSfthr.txt deleted file mode 100644 index aec258df..00000000 --- a/sourcecodes/data/examplezoo/fSfthr.txt +++ /dev/null @@ -1 +0,0 @@ -0.8 diff --git a/sourcecodes/data/examplezoo/fSftier.txt b/sourcecodes/data/examplezoo/fSftier.txt deleted file mode 100644 index ca417b31..00000000 --- a/sourcecodes/data/examplezoo/fSftier.txt +++ /dev/null @@ -1 +0,0 @@ -4,Tier1,5,aquatic,airborne,venomous,predator,domestic,Tier2,4,eggs,milk,backbone,breathes,Tier3,7,catsize,tail,toothed,hair,feathers,fins,legs,Tier4,1,type, \ No newline at end of file diff --git a/sourcecodes/data/examplezoo/fSftype.txt b/sourcecodes/data/examplezoo/fSftype.txt deleted file mode 100644 index 41c0f73e..00000000 --- a/sourcecodes/data/examplezoo/fSftype.txt +++ /dev/null @@ -1,2 +0,0 @@ -hair feathers eggs milk airborne aquatic predator toothed backbone breathes venomous fins legs tail domestic catsize type -2 2 2 2 2 2 2 2 2 2 2 2 6 2 2 2 7 diff --git a/sourcecodes/data/examplezoo/fSfwhite.txt b/sourcecodes/data/examplezoo/fSfwhite.txt deleted file mode 100644 index 83e81b8b..00000000 --- a/sourcecodes/data/examplezoo/fSfwhite.txt +++ /dev/null @@ -1 +0,0 @@ -From To diff --git a/sourcecodes/data/examplezoo/old/fSfrun_initialstructure.sh b/sourcecodes/data/examplezoo/old/fSfrun_initialstructure.sh deleted file mode 100644 index f20a9a29..00000000 --- a/sourcecodes/data/examplezoo/old/fSfrun_initialstructure.sh +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# script for execution of deployed applications -# -# Sets up the MCR environment for the current $ARCH and executes -# the specified command. -# -exe_name=$0 -exe_dir=`dirname "$0"` -echo "------------------------------------------" -if [ "x$1" = "x" ]; then - echo Usage: - echo $0 \<deployedMCRroot\> args -else - echo Setting up environment variables - MCRROOT="$1" - echo --- - LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; - MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; - LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; - XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; - export LD_LIBRARY_PATH; - export XAPPLRESDIR; - echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; - shift 1 - args= - while [ $# -gt 0 ]; do - token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank - args="${args} ${token}" - shift - done - "${exe_dir}"/initialstructure fSf -fi -exit diff --git a/sourcecodes/data/examplezoo/standardized_data.txt b/sourcecodes/data/examplezoo/standardized_data.txt deleted file mode 100644 index 0975061e..00000000 --- a/sourcecodes/data/examplezoo/standardized_data.txt +++ /dev/null @@ -1,102 +0,0 @@ -domestic venomous predator aquatic airborne milk eggs breathes catsize backbone tail legs fins toothed feathers type hair -1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 -2 1 1 2 1 1 2 1 1 2 2 1 2 2 1 4 1 -1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 -1 1 2 2 1 1 2 1 1 2 2 1 2 2 1 4 1 -1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 7 1 -1 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1 6 1 -1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 1 -2 2 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 2 1 2 1 2 2 1 1 1 5 1 1 1 6 1 -1 1 2 2 1 1 2 1 1 1 1 5 1 1 1 7 1 -1 1 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 1 1 1 1 2 2 1 1 1 5 1 1 1 6 1 -1 2 1 1 2 1 2 2 1 1 1 5 1 1 1 6 2 -1 1 2 2 1 1 2 1 2 1 1 6 1 1 1 7 1 -1 2 2 1 1 1 1 2 1 1 2 6 1 1 1 7 1 diff --git a/sourcecodes/header_batchsearch.inc~ b/sourcecodes/header_batchsearch.inc~ deleted file mode 100644 index ff40409c..00000000 --- a/sourcecodes/header_batchsearch.inc~ +++ /dev/null @@ -1,253 +0,0 @@ -<html> -<head> -<LINK REL=StyleSheet HREF="./my_style.css" TYPE="text/css"> -<script language="JavaScript"> -<!-- hide - -function input_check(input) { - var valid_char = /^[a-zA-Z0-9/.]+$/; - if(valid_char.test(input)) - { - return true; - } - else - { - return false; - } -} -function demo_str() -{ - with(window.document.key_search) - { - searchkey.value="Genotype\tGene1\tGene2\tGene3\tPhenotype\n0\t1\t0\t1\t0\n0\t0\t1\t0\t0\n0\t0\t0\t0\t1\n0\t0\t0\t0\t1\n0\t0\t0\t0\t0\n"; - } -} - -function demo() -{ - with(window.document.key_search) - { - - // searchkey.value="Genotype\tGene1\tGene2\tGene3\tPhenotype\n9.287\t9.191\t9.206\t9.285\t9.284\n10.039\t9.976\t10.129\t9.985\t10.055\n9.785\t9.852\t9.955\t9.972\t10.067\n8.529\t8.663\t8.707\t8.691\t8.743\n9.122\t9.057\t9.139\t9.067\t9.065\n8.964\t8.888\t8.879\t8.887\t8.803\n10.264\t10.317\t10.406\t10.344\t10.26\n9.089\t9.017\t9.121\t9.072\t9.021\n9.329\t9.321\t9.408\t9.398\t9.363\n9.47\t9.112\t9.399\t9.423\t9.481\n8.575\t8.404\t8.39\t8.554\t8.523\n9.093\t8.89\t9.092\t9.028\t9.016\n8.421\t8.375\t8.467\t8.439\t8.436\n9.678\t9.522\t9.65\t9.517\t9.679\n8.114\t8.38\t8.387\t8.324\t8.344\n8.447\t8.341\t8.731\t8.262\t8.675\n9.522\t9.488\t9.612\t9.505\t9.569\n10.742\t10.597\t10.76\t10.566\t10.668\n9.266\t9.292\t9.37\t9.219\t9.454\n8.052\t8.358\t8.311\t8.225\t8.29\n9.82\t9.655\t9.788\t9.805\t9.75\n9.343\t9.473\t9.513\t9.601\t9.454\n10.249\t10.208\t10.24\t10.089\t10.29\n8.612\t8.472\t8.565\t8.586\t8.528\n8.749\t7.892\t8.736\t7.965\t8.711\n9.54\t9.584\t9.678\t9.807\t9.65\n9.327\t9.233\t9.316\t9.416\t9.341\n9.005\t8.718\t9.03\t8.952\t9.163\n9.356\t9.112\t9.28\t9.184\t9.255\n9.712\t9.362\t9.554\t9.566\t9.533\n9.369\t9.504\t9.519\t9.589\t9.529\n11.104\t10.966\t11.056\t11.224\t11.122\n9.689\t9.61\t9.715\t9.707\t9.739\n9.512\t9.241\t9.343\t9.362\t9.391\n9.21\t9.025\t9.231\t9.196\t9.109\n8.607\t8.753\t8.85\t8.822\t8.778\n9.762\t9.782\t9.783\t9.822\t9.812\n8.881\t8.764\t8.897\t8.816\t8.85\n9.368\t9.401\t9.435\t9.348\t9.487\n8.65\t8.489\t8.619\t8.606\t8.586\n8.58\t8.708\t8.468\t8.77\t8.452\n9.444\t9.279\t9.423\t9.445\t9.403\n8.656\t8.744\t8.755\t8.714\t8.704\n9.628\t9.372\t9.522\t9.379\t9.442\n9.586\t9.525\t9.67\t9.638\t9.562\n8.363\t8.363\t8.414\t8.455\t8.343\n11.008\t10.678\t10.886\t10.953\t10.696\n9.148\t9.058\t9.197\t9.185\t9.131\n8.936\t8.9\t8.909\t9.036\t8.808\n9.244\t9.13\t9.177\t9.321\t9.311\n7.707\t7.75\t7.752\t7.802\t7.704\n8.917\t8.785\t8.953\t8.871\t8.805\n9.121\t8.95\t9.031\t9.029\t9.018\n9.635\t9.615\t9.788\t9.662\t9.752\n9.214\t9.401\t9.565\t9.44\t9.504\n8.408\t8.47\t8.577\t8.496\t8.418\n9.252\t9.347\t9.432\t9.394\t9.443\n9.615\t9.43\t9.564\t9.399\t9.528\n9.202\t8.755\t9.124\t8.915\t8.954\n9.558\t9.736\t9.69\t9.813\t9.707\n9.066\t9.094\t9.027\t9.055\t9.067\n8.607\t8.516\t8.635\t8.661\t8.557\n9.266\t9.073\t9.141\t9.131\t9.078\n9.074\t8.944\t9.082\t9.075\t8.962\n10.191\t10.084\t10.192\t10.215\t10.222\n9.116\t8.656\t9.057\t9.007\t9.01\n10.25\t9.957\t10.151\t10.131\t10.095\n9.159\t9.196\t9.584\t9.291\t9.239\n8.397\t8.502\t8.453\t8.559\t8.598\n9.176\t9.095\t9.255\t9.256\t9.249\n9.648\t9.584\t9.788\t9.801\t9.652\n9.055\t9.151\t9.097\t9.169\t9.103\n8.799\t8.522\t8.756\t8.649\t8.712\n9.457\t9.062\t9.387\t9.363\t9.233\n9.389\t9.161\t9.316\t9.288\t9.353\n8.349\t8.54\t8.57\t8.555\t8.512\n9.708\t9.586\t9.688\t9.69\t9.731\n8.853\t9.128\t9.107\t9.152\t9.131\n9.349\t9.14\t9.28\t9.304\t9.318\n9.151\t9.131\t9.229\t9.305\t9.276\n8.471\t8.224\t8.394\t8.327\t8.393\n9.549\t9.661\t9.642\t9.717\t9.553\n9.74\t9.685\t9.838\t9.909\t9.876\n9.906\t9.706\t9.929\t9.822\t9.776\n9.261\t8.994\t9.154\t8.996\t9.208\n9.805\t9.613\t9.693\t9.644\t9.654\n8.806\t8.692\t8.857\t8.739\t8.899\n8.98\t8.627\t8.818\t8.669\t8.773\n8.396\t8.534\t8.574\t8.512\t8.579\n9.193\t9.079\t9.23\t9.038\t9.171\n9.255\t9.153\t9.321\t9.166\t9.102\n9.025\t8.98\t9.242\t9.116\t8.959\n9.142\t9.066\t9.254\t9.183\t9.067\n9.361\t9.204\t9.277\t9.251\t9.2\n"; -searchkey.value="Genotype\tGene1\tGene2\tGene3\tPhenotype\n2\t0.14036\t-1.9418\t-0.42948\t0.25915\n1\t-0.51633\t2.0851\t0.36011\t-1.4461\n2\t1.2073\t-0.66507\t-1.0782\t0.25577\n1\t-1.3816\t0.0015871\t1.6678\t-1.0284\n1\t0.02627\t-0.25511\t1.386\t-0.72776\n2\t1.4749\t-1.0507\t-1.1886\t0.5869\n1\t-0.81364\t0.15985\t1.3432\t-0.88628\n2\t0.66482\t0.37888\t-1.0411\t0.41452\n2\t0.74691\t-0.79568\t0.043531\t0.83479\n1\t-0.13122\t-0.2089\t1.0839\t0.26364\n1\t0.10727\t1.0991\t0.46907\t0.089453\n1\t-1.3152\t-0.96453\t0.1134\t0.76625\n2\t1.3244\t-1.2513\t-0.75496\t0.17869\n1\t-1.0526\t1.0432\t0.41152\t-1.2805\n1\t-0.97163\t0.048348\t1.2317\t-0.57484\n2\t1.6526\t-0.84306\t-0.58025\t1.0336\n2\t1.3678\t0.30984\t-0.8071\t0.2227\n2\t0.68011\t-0.40842\t-0.42178\t0.48112\n2\t1.7573\t-0.81682\t-1.1508\t1.2448\n1\t-0.38513\t0.87495\t0.62368\t-0.3029\n2\t1.6804\t-0.79057\t-0.54125\t0.86227\n1\t-0.8\t1.4548\t0.38404\t-0.61435\n1\t-0.4981\t0.77635\t-0.84664\t0.2084\n1\t-1.1284\t0.6439\t-1.346\t-0.69702\n1\t-1.1604\t-0.24286\t-1.1865\t0.84499\n1\t-0.46941\t0.90822\t0.42266\t-0.60657\n1\t-1.4694\t0.8425\t1.322\t-0.20931\n1\t-1.5602\t1.0644\t0.77609\t-1.0143\n1\t0.73219\t-2.3196\t-0.051471\t0.51013\n1\t-0.33907\t0.31261\t-0.23894\t0.34665\n2\t1.4875\t-1.2278\t-0.3665\t1.1055\n2\t1.7778\t-0.13868\t-0.79405\t-0.17391\n1\t-1.0143\t0.15579\t0.94312\t-0.81445\n1\t-0.79556\t0.34673\t0.80697\t-1.0352\n2\t1.0902\t0.40553\t-0.90835\t0.18326\n1\t-1.4082\t1.0887\t0.19177\t-0.37926\n1\t0.65948\t-0.29631\t1.4025\t-0.6577\n1\t-0.10541\t0.50632\t-0.62135\t-0.69439\n1\t-1.4274\t0.8999\t0.040714\t-0.64084\n1\t-0.049221\t0.37995\t0.34105\t0.14789\n1\t-0.27827\t0.44415\t0.75087\t-0.94544\n1\t-0.86182\t-0.20052\t-0.69887\t0.9523\n1\t-0.64715\t-0.57779\t0.14728\t-1.378\n1\t-1.4341\t0.047062\t0.22559\t-0.29402\n2\t0.63681\t-0.57975\t-1.4907\t0.78349\n1\t-0.51958\t0.99085\t0.80223\t-1.224\n1\t0.37793\t1.4098\t0.53726\t-1.4404\n2\t0.62224\t-0.74639\t-0.43616\t-0.10073\n1\t-0.27451\t0.48363\t0.51358\t-0.2455\n2\t1.7129\t-1.4765\t-0.46897\t1.0381\n1\t-1.2877\t1.2851\t0.094527\t-0.65207\n1\t-1.5119\t1.0398\t0.36671\t-0.099971\n2\t1.7707\t-1.6549\t-1.2189\t0.7862\n2\t2.9819\t-1.2002\t-1.1488\t1.5639\n1\t-1.4328\t1.428\t-0.30167\t-0.39427\n2\t1.3157\t-0.044003\t-1.5064\t1.0888\n2\t1.4134\t-2.0733\t-0.90404\t1.2135\n2\t1.3233\t-0.46672\t-0.97303\t0.41323\n1\t-0.0027834\t-1.4766\t0.23116\t0.74087\n1\t-0.23902\t0.085836\t-0.45144\t0.25977\n1\t-0.7959\t-0.092194\t0.48212\t-1.0995\n1\t-0.87981\t-0.2021\t1.0342\t-0.77157\n1\t0.073991\t-0.16933\t0.68415\t0.059864\n1\t-0.19906\t-0.88838\t1.4616\t-0.77209\n1\t0.33053\t-0.24742\t0.84394\t-0.47337\n1\t-2.4677\t1.9733\t0.15703\t-1.1391\n1\t-1.4296\t0.27178\t1.4961\t-0.57637\n1\t-1.9217\t0.69186\t0.62457\t-0.18303\n1\t-1.2431\t0.98661\t-0.66998\t-0.62435\n1\t-1.3104\t0.56634\t-0.41563\t-0.21244\n1\t-0.79584\t0.073539\t1.5764\t-0.5129\n1\t-1.4595\t-0.42548\t-1.4099\t2.1827\n2\t1.2151\t-1.5028\t-1.3091\t1.6489\n2\t-0.14578\t-0.27147\t-0.853\t-0.42563\n2\t0.74643\t1.0798\t-0.98467\t0.15834\n1\t-0.93086\t-0.3765\t0.79132\t0.43374\n1\t-0.26466\t-0.24432\t0.52009\t0.4509\n1\t-1.1895\t0.026542\t0.26611\t-0.23827\n1\t-0.42519\t1.2643\t0.1902\t-0.81237\n1\t-1.0248\t-0.49955\t0.064074\t0.47088\n2\t2.2907\t-1.4612\t-0.95431\t1.5863\n2\t1.5697\t-0.3165\t-1.4525\t1.136\n1\t-1.0159\t0.053298\t1.6214\t-1.2228\n1\t-0.40383\t1.8453\t0.4486\t-0.97178\n1\t0.5124\t-0.20628\t0.91974\t-0.82012\n2\t1.3073\t-1.7029\t-0.79974\t1.0053\n1\t-0.69588\t0.26406\t-0.53979\t-0.021947\n1\t-0.08423\t0.66182\t2.0539\t-1.9058\n2\t2.1006\t-1.12\t-0.94615\t0.67055\n2\t0.5511\t-0.69758\t-0.43734\t0.77074\n2\t1.3879\t-1.1487\t-1.0375\t1.4641\n1\t0.20633\t0.50759\t0.69341\t-0.58827\n1\t1.6753\t-1.0901\t-1.0288\t1.9808\n1\t-0.94533\t2.6526\t0.93921\t-1.6151\n1\t-1.2071\t-0.68996\t0.029818\t-0.19476\n2\t0.81414\t0.92509\t-0.1681\t-0.28887\n1\t0.18468\t-1.0249\t1.0538\t-0.34692\n1\t-0.96033\t1.0327\t-0.30184\t-0.8787\n2\t0.74032\t-0.15363\t-0.96792\t0.68449\n1\t-0.24615\t1.6257\t1.3952\t-1.0348\n"; - } -} - - -function demo1() -{ - with(window.document.key_search) - { - -searchkey.value="Gene1\tGene2\tGene3\tPhenotype\n2\t2\t1\t1\n2\t2\t1\t2\n1\t1\t2\t2\n1\t1\t2\t2\n2\t1\t1\t1\n1\t1\t2\t2\n1\t1\t2\t2\n2\t2\t1\t1\n2\t1\t2\t2\n1\t1\t2\t2\n1\t2\t2\t2\n2\t1\t2\t2\n2\t1\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n2\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n2\t2\t1\t1\n1\t1\t2\t2\n1\t2\t1\t1\n1\t1\t2\t2\n2\t2\t2\t1\n2\t1\t1\t1\n2\t1\t1\t1\n2\t2\t1\t1\n2\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n2\t2\t1\t1\n2\t2\t1\t2\n2\t2\t1\t1\n2\t1\t1\t2\n2\t2\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n2\t2\t2\t1\n1\t1\t2\t2\n2\t2\t1\t1\n2\t1\t2\t1\n1\t2\t1\t2\n1\t2\t2\t1\n2\t2\t1\t1\n2\t2\t2\t1\n2\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n1\t1\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n2\t1\t1\t1\n2\t2\t1\t1\n2\t1\t1\t1\n2\t2\t2\t1\n1\t1\t2\t2\n1\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n1\t1\t2\t2\n1\t1\t2\t2\n2\t1\t1\t2\n2\t2\t1\t2\n1\t1\t1\t2\n2\t1\t2\t2\n1\t1\t2\t2\n2\t2\t1\t1\n2\t1\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n2\t2\t1\t1\n1\t1\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n2\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n1\t1\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n1\t1\t2\t2\n2\t2\t1\t2\n2\t1\t2\t2\n1\t1\t2\t2\n2\t2\t1\t1\n2\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t2\n1\t1\t2\t2\n2\t2\t1\t2\n2\t2\t1\t1\n2\t2\t1\t1\n1\t1\t2\t2\n2\t2\t1\t1\n1\t2\t1\t1\n2\t2\t1\t2\n1\t1\t2\t2\n1\t1\t2\t2\n1\t1\t1\t2\n1\t2\t2\t2"; - } -} - -function demo2() -{ - with(window.document.key_search) - { - searchkey.value="GenotypeA\tGenotypeB\tGene1\tGene2\tGene3\tGene4\n1\t1\t0.0735451012188\t0.807744827105\t-0.141557122166\t0.871977046116\n2\t1\t0.0783291492541\t0.784023461068\t0.501395957396\t1.20598627055\n2\t1\t0.786243065384\t0.978600201012\t1.10615045137\t0.91427570527\n2\t1\t-0.133165253244\t1.09368397217\t0.943147613583\t1.28625182746\n2\t1\t0.849732696834\t0.701697179341\t1.1597647359\t1.10898527576\n2\t1\t0.117358779641\t1.27641582521\t1.07600246132\t0.837957699405\n1\t2\t0.260845541489\t0.126507267356\t0.134953769296\t1.05166904426\n2\t1\t0.277734881926\t1.07193390309\t0.282304188176\t1.11305323003\n1\t2\t0.23482774261\t1.22992089679\t0.0929753295409\t1.16341704702\n1\t2\t0.948183366714\t0.133267523413\t-0.218162396333\t0.906540379337\n2\t1\t-0.116613369121\t1.14203606435\t0.109901766308\t0.729527128692\n1\t1\t-0.179825551391\t0.10619275827\t0.937787825497\t1.03567603615\n2\t1\t0.293022973091\t1.08721255661\t-0.175473007708\t0.887010836361\n2\t1\t-0.0489346771642\t0.968137836317\t0.107834185199\t0.896061918536\n1\t2\t0.236140871956\t-0.0428030926592\t-0.318492104268\t0.570552965391\n2\t2\t-0.0800211950407\t0.69984329873\t0.188143588172\t1.31042305844\n1\t1\t-0.0036838396465\t0.115049518621\t1.23342471413\t-0.0310668924648\n1\t2\t0.821596343182\t-0.206883091797\t-0.176745465075\t1.00503814188\n2\t1\t0.968136985881\t0.17393492998\t1.10355204542\t1.50730341194\n1\t1\t-0.2529273487\t1.15825296446\t-0.296758267158\t0.334353609539\n2\t2\t0.996924729837\t0.79867304131\t-0.0654588195254\t1.14114632703\n1\t1\t1.11517699739\t1.04475472944\t1.01515337419\t-0.114835981744\n1\t1\t1.13306628335\t0.212806963119\t-0.331850695159\t1.3262481351\n2\t1\t-0.202717212277\t1.16180466017\t0.698481134231\t0.837229654056\n2\t1\t1.09703628172\t0.988374730515\t0.632905281073\t0.871944778559\n1\t1\t0.0877178138353\t0.92193353301\t0.0882061186606\t-0.109998053824\n2\t2\t-0.0465657805556\t1.0562741142\t0.203076906226\t0.947081854544\n1\t1\t0.253626344342\t0.774666759107\t0.160237735682\t0.137119974017\n2\t2\t0.958504778114\t0.696202219462\t0.837104986151\t1.22862239026\n2\t1\t0.0190762231091\t1.07363361357\t0.836517352782\t1.13138357074\n1\t2\t1.04546343625\t1.22248653304\t-0.177641501681\t0.938273372293\n1\t1\t-0.356538939133\t0.926691569307\t-0.0141334158342\t-0.333256032191\n2\t2\t-0.271616290794\t1.02237907773\t-0.0893323176884\t1.13812703435\n1\t1\t0.112310230451\t0.96903715979\t0.735229019751\t0.0718376819618\n2\t2\t-0.0541760888203\t0.910562906664\t0.237421737724\t1.12792106072\n2\t1\t0.140510085427\t1.14598129626\t0.684754216604\t1.37711161908\n1\t2\t0.673132921769\t1.16156481777\t0.828299174842\t1.23484148864\n1\t1\t-0.36576911038\t1.22402806897\t0.985794473424\t0.371258195776\n2\t1\t1.30745593323\t-0.305709792671\t1.18778090128\t0.773246386727\n2\t2\t-0.530650832006\t1.12852174836\t-0.242830565653\t0.83833485032\n1\t1\t-0.291997112416\t-0.0207658889693\t0.172776752193\t0.36694855027\n1\t2\t-0.161225357475\t1.16418585274\t0.00727443800449\t1.1352882361\n2\t2\t1.30343435031\t0.732902323978\t-0.172844997755\t0.874662524376\n2\t2\t0.85539635481\t1.29119106621\t0.016024964511\t1.13160810191\n1\t2\t0.839799562146\t-0.0698184772979\t0.064736024742\t0.888230930115\n1\t2\t0.95789577351\t-0.0042439536723\t0.0555580748795\t1.07993651996\n1\t1\t1.32802494815\t-0.214047314771\t0.329813058688\t0.728172901439\n1\t1\t-0.200890919169\t1.1000313421\t1.04401630691\t0.0521627161216\n2\t2\t0.937448394951\t1.08384634906\t-0.0899239635102\t1.07443211017\n2\t1\t-0.0666111295973\t0.607978461697\t0.178977027858\t0.996958995079\n2\t1\t0.98988279173\t0.936124382141\t1.16162098\t0.953396718798\n1\t1\t0.783923131778\t-0.185782423384\t0.234091790401\t1.05701020406\n1\t1\t0.761503655241\t1.10820714005\t0.784532435857\t-0.125970126396\n2\t1\t-0.0961115621732\t0.992263342859\t0.660910916217\t0.963055169574\n2\t2\t-0.154764213109\t0.730891518005\t-0.109545565909\t1.12272967655\n2\t2\t0.0479283751395\t0.928564948748\t0.0947967021058\t0.98105799191\n2\t2\t1.39168552274\t0.128331277089\t0.10146975109\t1.24231428304\n1\t1\t0.976982771784\t-0.146928630221\t-0.0608841220423\t0.972841874016\n2\t1\t1.15485099166\t0.935197552788\t0.965011443377\t1.34264634759\n1\t2\t-0.166427006522\t0.213464027262\t-0.031343375005\t0.8119490745\n2\t1\t0.602325327176\t1.47360525321\t1.40368030116\t0.887287145417\n1\t2\t1.12050355207\t1.18852964108\t0.0704081979976\t1.19584630693\n2\t1\t0.702485774332\t1.15988608636\t0.294782678413\t0.751491248655\n1\t2\t0.155516690813\t0.251086517248\t0.975388704705\t0.688269967741\n1\t2\t0.038035346805\t0.682904829816\t0.0951645619842\t0.665389726903\n1\t1\t0.339450864189\t0.116879724658\t-0.170951058396\t-0.370117675216\n2\t2\t-0.108372250446\t0.696218715139\t-0.00428297700477\t0.961335352653\n2\t2\t0.0146712646232\t1.12798531635\t0.778687243129\t1.27150673153\n1\t2\t0.704617012215\t1.08526662881\t0.799187464816\t1.13063944956\n1\t1\t1.10224639633\t1.09684843311\t1.13580106237\t0.186395861041\n1\t1\t1.13687210336\t0.592984795387\t0.20048850526\t-0.0553656796539\n1\t2\t0.0632700472019\t0.864610771614\t-0.242802029698\t0.848811159682\n2\t1\t0.0451786925492\t1.33573290418\t0.92973441898\t-0.344011193096\n1\t2\t1.26061879295\t1.09499325896\t0.0222202420765\t0.847629840625\n1\t2\t0.91681254794\t0.290800393334\t-0.0719474399104\t0.926496648214\n2\t1\t1.2172426262\t0.951648627857\t1.25202262128\t0.233889527648\n1\t2\t1.05048646769\t0.172566561404\t0.0550162349302\t0.750079764855\n1\t2\t0.675366500637\t-0.0673050997098\t0.1645804156\t0.781063579107\n2\t1\t0.204088201674\t0.886512802356\t1.05795947541\t0.185790058971\n2\t1\t-0.100901351663\t0.714436170991\t-0.505529978858\t0.647306701065\n1\t2\t0.907207625417\t1.16174653049\t-0.155199134127\t0.747382222584\n1\t2\t0.0672106257479\t0.603637849323\t-0.140625204522\t1.08080017243\n2\t1\t1.2385313097\t1.0695347389\t-0.176990709153\t0.848256839162\n1\t2\t0.186923583294\t0.119157644078\t0.0349289573077\t0.744803259527\n1\t2\t1.09352177593\t0.194715059877\t0.0236391004662\t0.499673191061\n2\t1\t-0.376369481804\t0.985546924317\t0.0945527339598\t0.948918281956\n1\t1\t1.18474855816\t-0.115831486698\t0.283152200427\t0.970403352935\n2\t2\t1.15179008534\t1.11293520284\t0.221811798026\t0.999871011204\n1\t2\t-0.270193067228\t1.1546656712\t-0.244378116913\t0.671654326382\n2\t2\t0.439331185377\t1.12197569445\t0.258362973013\t1.11146143747\n2\t2\t1.01095806207\t0.745930460781\t-0.0409015639874\t1.14791250376\n2\t1\t-0.26402775558\t1.0189980863\t0.0142629520115\t0.959203836932\n1\t1\t1.1622683144\t-0.0120889455187\t1.07714267283\t-0.177584275215\n1\t1\t0.942340790264\t0.254818931717\t0.0587741977709\t0.980453538135\n2\t2\t0.106324819492\t0.79161883369\t-0.16526611256\t0.916230483749\n2\t1\t1.19278065887\t0.913551161988\t-0.0956615348665\t1.05953140511\n1\t1\t0.99020996204\t-0.0516709802571\t0.785783698942\t1.47690006823\n2\t1\t1.1566705292\t1.05878794929\t0.0968404106402\t0.827720917511\n1\t2\t0.05207115921\t-0.252341077617\t-0.0848699551554\t1.19139462554\n2\t2\t0.991086851115\t-0.301180892331\t-0.00253197995383\t1.46608138294\n"; - //W\tL\tN\tM\n - } -} - -function demo3() -{ - with(window.document.key_search) - { - 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- } -} - - -function demo8nodes() -{ - with(window.document.key_search) - { - 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2\t1.2252\n1\t2\t0.44808\t-0.8165\t-0.080134\t-0.49618\t0.051011\t-0.71722\n2\t1\t2.0365\t1.5592\t1.3257\t1.2472\t-0.47899\t0.10943\n1\t1\t-0.16507\t-0.66011\t0.98739\t0.58519\t0.245\t-0.43277\n1\t2\t-0.028366\t-0.16961\t-1.3266\t0.14248\t-0.24634\t-1.1154\n2\t1\t0.92842\t1.8842\t1.3169\t1.0358\t-0.20988\t0.88021\n2\t2\t0.33158\t0.32463\t-0.50924\t0.40233\t0.54391\t-0.24309\n1\t2\t1.2555\t0.1928\t-0.487\t0.048779\t-0.23483\t-1.477\n2\t1\t0.75021\t0.85943\t-0.2323\t0.10748\t-0.68906\t0.84276\n2\t2\t0.6297\t1.7397\t-1.6136\t-0.43268\t-0.21442\t-0.77462\n2\t1\t0.53168\t1.0807\t1.0853\t0.62304\t0.44036\t0.48087\n1\t2\t-0.31256\t-0.69771\t-0.88556\t-1.333\t0.038614\t-1.5744\n1\t2\t-0.039695\t-0.52447\t0.91401\t-0.93272\t0.53434\t-0.080746\n2\t1\t-0.16596\t0.56821\t0.76008\t0.45442\t0.10286\t0.6539\n1\t2\t-0.4331\t-0.89669\t-1.3097\t-1.2157\t0.1065\t-0.8512\n1\t2\t-0.34708\t-0.51457\t-1.012\t-0.39437\t-0.55374\t-1.144\n2\t2\t0.024082\t0.7128\t-1.3702\t-1.4492\t-0.10228\t-0.59071\n1\t2\t-0.0037109\t-0.68845\t-0.649\t-0.91581\t0.066805\t-0.98583\n2\t1\t0.68706\t0.067424\t0.87139\t0.7938\t-0.099645\t1.529\n2\t2\t-0.31183\t0.57814\t-0.80815\t-0.66724\t-0.31919\t-0.61319\n1\t2\t-0.11153\t-0.6246\t-0.27979\t-0.18363\t0.83639\t0.014919\n2\t2\t0.20406\t1.5838\t-0.96334\t-1.1228\t-0.17808\t-1.2123\n2\t2\t-0.1134\t0.63358\t-0.53321\t-0.84276\t-0.27657\t-0.36992\n1\t2\t0.25517\t0.67006\t-0.1349\t0.18275\t0.40982\t-0.62487\n1\t1\t-1.2684\t0.31042\t0.91155\t0.66143\t0.2483\t-0.12434\n1\t1\t-0.97542\t-0.85419\t0.7663\t0.16362\t-0.18737\t0.67266\n1\t2\t-0.043882\t-0.62746\t-0.82816\t-0.40626\t-0.051048\t-0.61297\n1\t1\t0.59605\t-0.45852\t1.2962\t0.78156\t-0.48154\t0.17778\n2\t2\t-0.06266\t1.1144\t-0.80524\t-0.3189\t-0.16038\t-0.96372\n1\t2\t-1.1821\t1.0798\t-1.3407\t-0.52643\t0.12458\t-0.7871\n2\t2\t0.59446\t0.89186\t-0.97856\t-0.64658\t0.2712\t-1.5538\n1\t2\t0.15067\t0.41827\t-1.0487\t-1.0551\t0.19143\t-1.4537\n1\t2\t-1.073\t0.022587\t-1.7088\t-1.3777\t0.1964\t-0.84025\n2\t1\t0.20928\t1.8026\t1.2073\t2.78\t0.15131\t0.3448\n1\t2\t-1.1317\t-0.6359\t-0.70457\t-1.676\t-0.22886\t-0.58769\n1\t1\t-0.039428\t-0.58746\t0.56\t0.7896\t-0.052581\t0.99511\n1\t2\t0.55023\t-0.20403\t0.138\t-0.70518\t0.66927\t-0.28861\n2\t2\t0.57423\t1.1886\t0.092876\t0.025677\t-0.41099\t-1.2858\n2\t2\t-0.14179\t1.5827\t-0.94328\t0.7703\t-0.43967\t-0.50448\n2\t2\t0.14666\t1.0492\t-0.0030259\t-0.62418\t-0.087515\t-0.048386\n"; - } -} - -function demochl() -{ - with(window.document.key_search) - { - -searchkey.value="Ctrq3\tMAS\tNeutrophil\tLoad\tWeight\n2\t0.969230769\t3\t3.252367514\t1\n2\t0.925170068\t1.6\t2.46322088\t1.033472803\n1\t0.427272727\t33.8\t4.206610024\t0.831372549\n2\t0.877835951\t8.3\t3.764250875\t0.967153285\n2\t0.914862915\t4.4\t3.691700208\t1.046025105\n2\t0.560334528\t4.9\t2.604550033\t0.98046875\n1\t0.383073497\t13.1\t4.273556814\t0.812316716\n1\t0.101010101\t18.6\t5.089640217\t0.771929825\n1\t0.106719368\t18.9\t4.915125346\t0.80994152\n2\t0.894736842\t2.5\t2.691700208\t0.995515695\n1\t0.067226891\t19.8\t4.878194228\t0.846153846\n2\t0.921022067\t2.9\t4.127428778\t1.03875969\n2\t0.938701923\t0.7\t4.366310867\t0.984732824\n1\t0.658008658\t15.7\t4.531121115\t0.884210526\n2\t0.9\t4.8\t2.604550033\t0.913194444\n2\t0.790923825\t10.4\t2.390670213\t0.892857143\n1\t0.295539033\t8.6\t4.24137213\t0.85840708\n2\t0.317757009\t12.2\t4.449648073\t0.889830508\n1\t0.032418953\t20.2\t5.053428044\t0.811320755\n1\t0.603960396\t23.4\t4.283775979\t0.805460751\n2\t0.939351199\t3.6\t2.349277527\t0.952380952\n1\t0.978448276\t0.4\t3.495405563\t0.8875\n1\t0.1\t23.2\t4.675613388\t0.766101695\n1\t0.036363636\t32.6\t4.938109253\t0.828125\n1\t0.660247593\t9.2\t3.826398782\t0.921052632\n1\t0.078651685\t35.8\t4.513630383\t0.852112676\n1\t0.186915888\t20.7\t5.048247532\t0.779761905\n1\t0.071578947\t35.6\t4.574586809\t0.797356828\n1\t0.239520958\t15.4\t4.331548761\t0.941176471\n1\t0.205741627\t24.5\t5.058547488\t0.774193548\n1\t0.062300319\t13.4\t4.594790195\t0.832236842\n2\t0.599675851\t5\t4.18178644\t0.969348659\n1\t0.324246772\t13.5\t4.252367514\t0.858585859\n1\t0.87628866\t14.2\t2.929061124\t0.869863014\n1\t0.146103896\t15.6\t4.579726449\t0.9\n1\t0.257383966\t22.5\t5.210214148\t0.75\n1\t0.033333333\t31.1\t4.632578756\t0.718644068\n1\t0.29739777\t36.1\t3.880756445\t0.798353909\n2\t0.872979215\t4.2\t4.097465554\t0.856756757\n2\t0.909221902\t4.3\t3.650307523\t0.976\n1\t0.10041841\t28.3\t4.46322088\t0.757462687\n"; - } -} - -function demospnl() -{ - with(window.document.key_search) - { - -searchkey.value="rs3664317\tOas1a\tParp9\tDhx58\tCd1d1\tIrf7\tOas3\tPml\tMx1\tIfit1\tTrim25\tOas1g\tPglyrp3\tIfih1\n1\t8.34\t9.812\t8.774\t9.79\t9.663\t8.27\t11.036\t7.284\t8.286\t10.395\t8.521\t6.186\t8.83\n1\t8.368\t9.738\t8.566\t9.144\t9.484\t8.818\t11.03\t6.977\t8.294\t10.076\t8.529\t5.968\t8.828\n1\t8.178\t9.57\t8.726\t9.575\t10.106\t8.99\t10.878\t7.205\t8.676\t10.036\t8.61\t5.976\t9.024\n1\t8.116\t9.901\t8.904\t9.959\t9.793\t8.336\t11.105\t7.598\t8.316\t10.292\t8.401\t5.814\t8.836\n2\t8.099\t9.68\t8.876\t10.116\t9.771\t8.379\t11.028\t7.438\t8.541\t10.215\t8.32\t5.917\t9.073\n1\t8.262\t9.59\t8.24\t10.088\t8.938\t7.832\t10.486\t6.752\t7.825\t9.908\t8.196\t6.15\t8.446\n1\t7.915\t9.415\t8.308\t9.707\t9.12\t8.702\t11.102\t7.208\t8.243\t10.034\t7.897\t6.06\t8.892\n2\t8.565\t10.002\t8.96\t9.779\t10.322\t9.24\t11.278\t7.644\t8.893\t10.42\t8.773\t5.914\t9.407\n1\t8.189\t9.774\t8.541\t9.939\t9.134\t7.819\t10.766\t7.122\t8.352\t10.113\t8.492\t6.269\t9.055\n1\t8.476\t9.954\t8.908\t9.476\t9.92\t8.764\t11.134\t7.859\t8.788\t10.17\t8.862\t6.226\t9.17\n2\t8.119\t9.946\t8.876\t9.578\t10.02\t8.734\t11.244\t7.85\t8.838\t10.557\t8.56\t5.98\t9.353\n2\t8.305\t9.713\t8.972\t9.789\t9.839\t8.804\t10.948\t7.682\t8.896\t10.181\t8.854\t5.979\t9.567\n2\t8.654\t10\t9.306\t9.439\t10.457\t9.223\t10.922\t7.082\t8.942\t10.131\t9.162\t6.01\t9.74\n1\t8.105\t9.748\t8.725\t10.119\t9.782\t8.575\t11.113\t7.63\t8.674\t10.355\t8.59\t6.279\t8.908\n1\t8.247\t9.715\t8.829\t9.646\t9.953\t9.668\t11.112\t7.384\t9.221\t10.19\t8.64\t6\t9.552\n1\t8.511\t9.994\t9.014\t9.89\t10.266\t8.444\t10.599\t7.331\t9.153\t10.012\t8.837\t6.148\t9.023\n2\t8.947\t10.28\t9.483\t9.398\t11.23\t9.86\t11.324\t8.006\t9.772\t10.524\t9.587\t5.865\t10.067\n1\t8.526\t9.685\t8.921\t9.7\t10.126\t9.373\t11.121\t7.497\t9.003\t10.357\t8.156\t6.334\t9.678\n2\t8.06\t9.745\t9.092\t9.278\t10.231\t8.976\t10.998\t7.578\t9.145\t10.283\t8.611\t6.168\t9.413\n2\t7.93\t9.728\t8.694\t9.512\t9.826\t9.016\t11.276\t7.604\t8.767\t10.378\t8.577\t5.963\t9.264\n2\t8.511\t9.686\t9.014\t8.982\t10.508\t10.108\t11.304\t7.441\t9.133\t10.341\t9.04\t6.2\t9.974\n2\t8.645\t9.997\t8.97\t9.443\t10.393\t9.302\t11.409\t7.785\t8.894\t10.552\t9.051\t5.997\t9.412\n2\t8.293\t9.802\t9.001\t9.524\t10.156\t9.263\t11.212\t7.772\t8.581\t10.433\t8.514\t6.093\t9.177\n1\t7.781\t9.712\t8.97\t9.375\t10.12\t9.484\t11.317\t7.347\t8.972\t10.393\t8.352\t6.193\t9.587\n2\t8.465\t9.88\t8.913\t9.816\t9.965\t8.852\t11.138\t7.537\t8.625\t10.426\t8.617\t6.044\t9.556\n2\t8.657\t10.026\t9.189\t9.691\t10.302\t9.268\t11.194\t7.634\t9.143\t10.378\t9.05\t6.067\t9.679\n2\t7.634\t9.606\t8.36\t9.465\t8.41\t8.605\t11.183\t6.942\t8.174\t9.952\t7.478\t6.09\t9.535\n1\t7.669\t9.494\t8.779\t9.552\t9.362\t8.52\t11.024\t7.131\t8.378\t10.391\t8.114\t6.07\t8.851\n2\t8.618\t10.212\t9.433\t9.672\t10.442\t9.21\t11.328\t8.045\t9.322\t10.5\t9.128\t5.994\t9.656\n2\t8.731\t10.27\t9.342\t9.43\t10.697\t10.117\t11.286\t7.749\t9.734\t10.464\t9.322\t6.156\t9.876\n1\t7.554\t9.524\t8.759\t9.93\t9.52\t8.279\t10.82\t7.32\t8.316\t10.31\t8.186\t6.068\t9.046\n1\t8.262\t9.677\t8.75\t9.444\t10.052\t8.634\t10.888\t7.32\t8.562\t9.893\t8.644\t6.212\t8.918\n1\t7.823\t9.628\t8.66\t9.529\t9.578\t8.736\t11.206\t7.171\t8.408\t10.062\t8.111\t5.838\t9.033\n1\t8.28\t9.572\t8.784\t9.428\t9.862\t9.424\t11.27\t7.288\t8.505\t10.174\t8.642\t6.022\t9.313\n2\t9.09\t10.053\t9.599\t9.469\t11.004\t9.882\t11.436\t8.521\t9.814\t10.562\t9.704\t6.044\t10.061\n1\t8.446\t9.989\t9.297\t9.688\t10.577\t9.129\t11.102\t7.718\t9.484\t10.231\t9.072\t6.17\t9.21\n1\t8.668\t9.858\t9.195\t9.385\t10.695\t9.249\t11.028\t7.765\t9.367\t10.319\t9.179\t6.136\t9.563\n2\t8.574\t10.059\t9.281\t9.233\t10.508\t9.247\t11.145\t8.138\t9.505\t10.402\t9.192\t5.992\t9.848\n2\t8.523\t10.052\t9.131\t9.507\t10.418\t9.413\t11.187\t7.641\t9.304\t10.465\t9.063\t6.095\t9.733\n1\t7.987\t9.748\t8.766\t9.578\t9.781\t8.482\t11.279\t7.52\t8.364\t10.141\t8.207\t6.192\t9.133\n2\t8.466\t9.429\t8.946\t9.395\t9.715\t9.071\t11.388\t7.592\t8.078\t10.32\t8.326\t6.108\t9.021\n1\t7.668\t9.694\t8.493\t10.112\t9.561\t8.394\t10.922\t7.26\t8.19\t10.27\t7.916\t5.892\t8.974\n2\t8.379\t10.037\t9.155\t9.683\t10.281\t9.2\t10.913\t7.173\t9.404\t10.381\t9.097\t6.099\t9.714\n2\t7.805\t9.654\t8.454\t9.198\t10.065\t9.468\t11.217\t6.917\t8.43\t10.459\t8.11\t6.068\t9.068\n1\t7.981\t9.8\t8.553\t9.946\t9.862\t8.901\t11.085\t7.214\t8.393\t10.373\t8.19\t6.05\t9.015\n1\t7.746\t9.688\t8.578\t9.901\t9.358\t7.866\t10.928\t7.354\t7.929\t10.233\t8.066\t5.754\t8.883\n1\t7.997\t9.859\t8.795\t9.867\t9.817\t8.734\t11.109\t7.416\t8.67\t10.247\t8.176\t6.143\t9.081\n1\t8.674\t9.689\t9.06\t9.81\t10.544\t8.995\t11.189\t7.781\t9.219\t10.07\t8.98\t5.992\t9.143\n1\t8.088\t9.49\t8.676\t9.456\t10.184\t8.737\t10.998\t7.222\t8.538\t10.192\t8.441\t6.147\t8.55\n1\t8.001\t9.801\t8.669\t9.977\t9.383\t8.274\t11.055\t7.231\t7.913\t10.272\t8.277\t5.931\t9.009\n2\t8.218\t9.458\t8.781\t9.214\t9.66\t8.87\t10.738\t7.241\t8.289\t10.029\t8.612\t6.125\t9.38\n1\t7.684\t9.56\t8.75\t10.077\t9.686\t8.27\t11.102\t7.206\t8.13\t10.212\t8.07\t6.018\t8.984\n2\t8.326\t9.696\t8.88\t9.714\t10.014\t9.08\t11.055\t7.256\t8.494\t10.054\t8.63\t6.177\t9.162\n2\t8.906\t10.106\t9.412\t9.704\t11.06\t9.854\t11.335\t7.799\t10.103\t10.471\t9.25\t6.033\t9.97\n1\t8.073\t9.793\t8.626\t9.879\t9.262\t8.408\t10.844\t7.108\t8.368\t9.959\t8.261\t6.052\t8.916\n2\t8.527\t10.026\t9.143\t9.244\t10.597\t9.566\t11.108\t7.778\t9.748\t10.351\t9.153\t6.055\t9.698\n2\t8.614\t10.05\t9.202\t9.508\t10.66\t9.63\t11.156\t7.758\t9.789\t10.324\t9.068\t6.15\t9.948\n2\t8.522\t10.158\t8.992\t9.684\t9.992\t8.55\t11.125\t7.914\t8.976\t10.311\t8.574\t5.889\t9.566\n1\t8.086\t9.6\t8.522\t9.544\t9.641\t8.514\t10.99\t7.386\t8.506\t10.194\t8.234\t6.02\t8.736\n1\t7.873\t9.596\t8.452\t9.422\t9.278\t8.509\t10.958\t7.057\t8.081\t9.981\t7.969\t6.136\t8.958\n2\t8.371\t9.99\t8.949\t9.931\t10.195\t8.935\t10.83\t7.694\t9.183\t10.493\t9.124\t6.128\t9.396\n2\t8.476\t9.982\t9.115\t9.639\t10.465\t9.833\t11.105\t8.058\t9.9\t10.351\t9.182\t6.05\t9.884\n1\t8.512\t9.995\t8.846\t9.951\t9.561\t8.558\t10.769\t7.584\t8.901\t10.139\t8.769\t5.959\t9.203\n1\t8.358\t9.858\t8.99\t9.981\t10.123\t9.368\t10.989\t7.463\t9.327\t9.93\t8.54\t6.02\t9.543\n1\t8.23\t9.614\t8.806\t9.919\t9.939\t9.108\t11.184\t7.766\t8.793\t10.174\t8.605\t5.972\t9.068\n2\t8.238\t9.802\t8.926\t9.595\t10.062\t8.77\t11.202\t7.712\t9.131\t10.34\t8.57\t6.05\t9.464\n1\t8.533\t10.108\t9.083\t10.214\t10.514\t8.463\t11.008\t7.356\t9.344\t10.196\t8.736\t6.262\t9.257\n1\t7.866\t9.444\t8.223\t9.865\t8.95\t8.539\t10.935\t6.754\t7.748\t10.177\t7.826\t6.29\t8.716\n2\t8.888\t10.031\t9.158\t9.407\t10.8\t9.547\t11.238\t7.659\t9.602\t10.398\t9.337\t6.028\t9.529\n1\t8.026\t9.682\t8.398\t9.824\t9.202\t8.041\t10.703\t7.322\t8.352\t10.209\t8.196\t6.009\t9.001\n2\t8.974\t10.071\t9.451\t9.348\t11.061\t9.686\t11.255\t8.077\t10.101\t10.323\t9.557\t6.006\t10.072\n1\t8.181\t9.432\t9.045\t9.544\t10.651\t9.18\t10.832\t7.419\t8.742\t9.818\t8.546\t6.33\t9.201\n1\t8.137\t9.676\t9.024\t9.37\t10.206\t9.944\t10.985\t7.226\t8.9\t10.362\t8.918\t6.352\t9.367\n"; -} -} - -function demoksl() -{ - with(window.document.key_search) - { - 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-} -} - -function demorat() -{ - with(window.document.key_search) - { - -searchkey.value="Sex\tDrug\tW1\tW2\nM\tD1\t5.00\t6.00\nM\tD1\t7.00\t6.00\nM\tD1\t9.00\t9.00\nM\tD1\t5.00\t4.00\nM\tD2\t9.00\t12.00\nM\tD2\t7.00\t7.00\nM\tD2\t7.00\t6.00\nM\tD2\t6.00\t8.00\nM\tD3\t14.00\t11.00\nM\tD3\t21.00\t15.00\nM\tD3\t12.00\t10.00\nM\tD3\t17.00\t12.00\nF\tD1\t7.00\t10.00\nF\tD1\t8.00\t10.00\nF\tD1\t6.00\t6.00\nF\tD1\t9.00\t7.00\nF\tD2\t7.00\t6.00\nF\tD2\t10.00\t13.00\nF\tD2\t6.00\t9.00\nF\tD2\t8.00\t7.00\nF\tD3\t14.00\t9.00\nF\tD3\t14.00\t8.00\nF\tD3\t16.00\t12.00\nF\tD3\t10.00\t5.00\n"; -} -} - - -function Upload() -{ - - with(window.document.key_search) - { - MyUpload.value="YES"; - } -} - - -function SearchCheck() -{ - with(window.document.key_search) - { - if(trim(searchkey.value)=="") - { - alert("Sorry,the search field is empty"); - return false; - } - else - { - my_page.value=1; - Search.value="YES"; - return true; - } - } -} -function pheno() -{ - with(window.document.pheno) - { - my_page.value=1; - } -} -function clear_key() -{ - with(window.document.key_search) - { - my_snpid.value=""; - my_mirid.value=""; - my_run.value=0; - my_org.value="All"; - submit(); - } - -} - -function refresh() -{ - with(window.document.key_search) - { - if(my_org.value=="Human") - { - // search_method[3].disabled=true; - // my_phenodesc.disabled=true; - // pheno_sample.disabled=true; - } - else - { - search_method[3].disabled=false; - my_phenodesc.disabled=false; - pheno_sample.disabled=false; - } - } -} - - -function pheno_next() -{ - with(window.document.key_search) - { - Search.value="YES"; - my_run.value=2; - my_page.value++; - submit(); - } -} - -function pheno_previous() -{ - with(window.document.key_search) - { Search.value="YES"; - my_run.value=2; - my_page.value--; - submit(); - } -} - -function next_page() -{ - with(window.document.key_search) - { - Search.value="YES"; - my_page.value++; - submit(); - } - -} -function previous_page() -{ - with(window.document.key_search) - { - Search.value="YES"; - my_page.value--; - submit(); - } -} - -function wopen(url, name, param) -{ - window.open(url,name, param); - return ; -} - -function trim(inputString) -{ - if (typeof inputString != "string") - { - return inputString; - } - var retValue = inputString; - var ch = retValue.substring(0, 1); - while (ch == " ") - { // Check for spaces at the beginning of the string - retValue = retValue.substring(1, retValue.length); - ch = retValue.substring(0, 1); - } - ch = retValue.substring(retValue.length-1, retValue.length); - while (ch == " ") - { // Check for spaces at the end of the string - retValue = retValue.substring(0, retValue.length-1); - ch = retValue.substring(retValue.length-1, retValue.length); - } - while (retValue.indexOf(" ") != -1) - { // Note that there are two spaces in the string - look for multiple spaces within the string - retValue = retValue.substring(0, retValue.indexOf(" ")) + retValue.substring(retValue.indexOf(" ")+1, retValue.length); // Again, there are two -spac$ } - return retValue; // Return the trimmed string back to the user -} // Ends the "trim" function - - ---> -</script> diff --git a/sourcecodes/input_error_no_menu.php~ b/sourcecodes/input_error_no_menu.php~ deleted file mode 100644 index 7063cc3d..00000000 --- a/sourcecodes/input_error_no_menu.php~ +++ /dev/null @@ -1,3 +0,0 @@ -<br> - <h1>There was an error with your input. Input data can only contain <br>letters, numbers, underscores (_), periods (.), and whitespace.</h1> -</html> diff --git a/sourcecodes/layout.php~ b/sourcecodes/layout.php~ deleted file mode 100644 index c9b86997..00000000 --- a/sourcecodes/layout.php~ +++ /dev/null @@ -1,123 +0,0 @@ -<?php - -include("header_new.inc"); -include("input_validate.php"); -$keyval=valid_keyval($_GET["My_key"]); - -$dir="./data/"; - -$vf1=$dir.$keyval."var.txt"; -$vf2=$dir.$keyval."varname.txt"; -$vf3=$dir.$keyval."vardata.txt"; -unlink($vf1); -unlink($vf2); -unlink($vf3); - - -$radiovalue="Evidence"; -$valcompare="Evidence"; - - - if(isset($_POST["Datatype"])) - { - - $radiovalue=$_POST["Datatype"]; - if($radiovalue=="Evidence") $S1="checked=\"checked\""; - if($radiovalue=="Intervention") $S2="checked=\"checked\""; - } - else - { - $radiovalue="Evidence"; - $S1="checked=\"checked\""; - } - - - -?> -<script language="JavaScript"> -<!-- -function calcHeight() -{ - //find the height of the internal page - var the_height= - document.getElementById('the_iframe').contentWindow. - document.body.scrollHeight; - - //change the height of the iframe - document.getElementById('the_iframe').height= - the_height; -} -//--> -</script> -<form method="post" name="form"> -<table width="100%" align="center" style="background-color:" bordercolor=white border=0.5 cellspacing="0" cellpadding="0"> - <tr valign=top> - <td colspan=4><hr size=3></td> - </tr> -<tr > -<th align=right> <h3>Prediction Mode: </h3></th> - <td align=left> - <input name="Datatype" type="radio" value=<?php $radioval="Evidence"; echo $radioval; ?> checked <?php echo $S1; ?>" onClick="javascript:this.form.submit();">Evidence - <input name="Datatype" type="radio" value=<?php $radioval="Intervention"; echo $radioval; ?> <?php echo $S2; ?>" onClick="javascript:this.form.submit();"> Intervention - - </td> -</tr> - <tr valign=top> - <td colspan=4><hr size=3></td> - </tr> - -</table> -</form> - -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><p>Selected mode:<br><?php print($radiovalue);?></p></li> - <li><p>Network ID:<br><?php print($keyval);?></p></li> -</ul> - -<ul class="navbar"> - <li><a href="clear.php?My_key=<?php print($keyval);?>" target='_blank'>Clear evidence</a> -<li><a href="cv_predictions.php?My_key=<?php print($keyval);?>";>Cross validation and predictions</a> -<li><a href="modify_edges.php?My_key=<?php print($keyval);?>" target='_blank'>Modify network structure</a> - <li><a href="javascript:void(0);" -NAME="Model Averaging Matrix" title="Model Averaging Matrix" -onClick=window.open("matrix.php?My_key=<?php print($keyval);?>","Ratting","width=950,height=270,0,status=0,");>Display structure matrix</a> - <li><a href="javascript:void(0);" -NAME="Parameters" title="Parameters" -onClick=window.open("parameter_display.php?My_key=<?php print($keyval);?>","Ratting","width=950,height=270,0,status=0,");>View parameters</a> -<li><a href="modify_structure_learning.php?My_key=<?php print($keyval);?>";>Modify structure learning settings</a> - <li><a href="help.php" target='_blank'>Help</a> - <li><a href="../home.php">Home</a> -</ul> - -<?php - //echo "Selected mode:"; - //echo $radiovalue; - - - -if($radiovalue==$valcompare) -{ -?> -<div id="outernew"> - -<object type="text/html" data="network_layout_evd.php?My_key=<?php print($keyval);?>" style="width:3000; height:3000"> -<p>Error: Try again</p> -</object> - -</div> -<?php -} -else -{ -?> -<div id="outernew"> -<object type="text/html" data="network_layout_inv.php?My_key=<?php print($keyval);?>" style="width:3000; height:3000"> -<p>Error: Try again</p> -</object> - -</div> -<?php -} -?> - diff --git a/sourcecodes/parameter_learning/Predictmultipleintrvention.m b/sourcecodes/parameter_learning/Predictmultipleintrvention.m deleted file mode 100644 index 1b9fa2f4..00000000 --- a/sourcecodes/parameter_learning/Predictmultipleintrvention.m +++ /dev/null @@ -1,95 +0,0 @@ -function Predictmultipleintrvention(pre) -dfile=strcat(pre,'structure_input.txt'); -sfile=dfile; -dfile=strcat(pre,'continuous_input.txt'); -nnodefile=strcat(pre,'nnode.txt'); - -fnnode = fopen(nnodefile,'r'); -nnodes = fscanf(fnnode,'%d'); - -fvarnamefile=strcat(pre,'varname.txt'); - -varfile = fopen(fvarnamefile,'r'); - -Std_flag=true; -[labels,cases,bnet]=readInput(dfile,sfile,nnodes,Std_flag); - -[bnet]=parameterLearning(bnet,cases); - -fvarfile=strcat(pre,'var.txt'); -fvar = fopen(fvarfile,'r'); -select_var_new = fscanf(fvar,'%d'); - -nm = numel(select_var_new); - -varlabels = cell(1,nm); -varbuffer = fgetl(varfile); %get header line as a string -for j=1:nm - [varnext,varbuffer] = strtok(varbuffer); - varlabels{j} = varnext; - for i=1:nnodes - if strcmp(varlabels{j},labels{i}) - select_var_new(j)=i; - end - end - -end - - - - -fvardfile=strcat(pre,'vardata.txt'); - -fvard = fopen(fvardfile,'r'); - -select_var_data_new = fscanf(fvard,'%f'); - -means_orig = cell(1,nnodes); -stdevs_orig = cell(1,nnodes); -labels_orig = cell(1,nnodes); -%Read in original means and standard deviations -mapfile = strcat(pre,'map.txt'); -fmap = fopen(mapfile,'r'); -for i=1:nnodes - buffer = fgetl(mapfile); - temp = cell(1,4); - for j=1:4 - [next,buffer] = strtok(buffer); - temp{j} = next; - end - labels_orig{i} = temp{1}; - means_orig{i} = str2num(temp{4}); - stdevs_orig{i} = str2num(temp{3}); -end -fclose(fmap); - -%Need to map the means and stdevs to the correct labels -means = cell(1,nnodes); -stdevs = cell(1,nnodes); -%Read in labels in new order. -labelsnew = cell(1,nnodes); -mapdatafile = strcat(pre,'mapdata.txt'); -fmapdata = fopen(mapdatafile,'r'); -buffer = fgetl(fmapdata); -for i = 1:nnodes - [next,buffer ] = strtok(buffer); - labelsnew{i} = next; -end -fclose(fmapdata); -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labelsnew{i},labels_orig{j}) - means{i} = means_orig{j}; - stdevs{i} = stdevs_orig{j}; - break - end - end -end - -filename=strcat(pre,'net_figure_new.txt'); - -drawFigureM(nnodes,bnet,labels,filename,cases,stdevs,means,select_var_new,select_var_data_new); - -writeParameters_int(pre,bnet,nnodes,labels,cases,stdevs,means,select_var_new,select_var_data_new); - -end diff --git a/sourcecodes/parameter_learning/code_backup/Predictmultiple.m b/sourcecodes/parameter_learning/code_backup/Predictmultiple.m deleted file mode 100644 index 9d107628..00000000 --- a/sourcecodes/parameter_learning/code_backup/Predictmultiple.m +++ /dev/null @@ -1,72 +0,0 @@ -function Predictmultiple(pre) -dfile=strcat(pre,'structure_input.txt'); -sfile=dfile; -dfile=strcat(pre,'continuous_input.txt'); -nnodefile=strcat(pre,'nnode.txt'); - -fnnode = fopen(nnodefile,'r'); -nnodes = fscanf(fnnode,'%d'); - -Std_flag=true; -[labels,cases,bnet]=readInput(dfile,sfile,nnodes,Std_flag); - -[bnet]=parameterLearning(bnet,cases); - -fvarfile=strcat(pre,'var.txt'); -fvar = fopen(fvarfile,'r'); -select_var_new = fscanf(fvar,'%d'); - -fvardfile=strcat(pre,'vardata.txt'); -fvard = fopen(fvardfile,'r'); -select_var_data_new = fscanf(fvard,'%f'); - -means_orig = cell(1,nnodes); -stdevs_orig = cell(1,nnodes); -labels_orig = cell(1,nnodes); -%Read in original means and standard deviations -mapfile = strcat(pre,'map.txt'); -fmap = fopen(mapfile,'r'); -for i=1:nnodes - buffer = fgetl(mapfile); - temp = cell(1,3); - for j=1:3 - [next,buffer] = strtok(buffer); - temp{j} = next; - end - labels_orig{i} = temp{1}; - means_orig{i} = str2num(temp{3}); - stdevs_orig{i} = str2num(temp{2}); -end -fclose(fmap); - -%Need to map the means and stdevs to the correct labels -means = cell(1,nnodes); -stdevs = cell(1,nnodes); -%Read in labels in new order. -labelsnew = cell(1,nnodes); -mapdatafile = strcat(pre,'mapdata.txt'); -fmapdata = fopen(mapdatafile,'r'); -buffer = fgetl(fmapdata); -for i = 1:nnodes - [next,buffer ] = strtok(buffer); - labelsnew{i} = next; -end -fclose(fmapdata); -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labelsnew{i},labels_orig{j}) - means{i} = means_orig{j}; - stdevs{i} = stdevs_orig{j}; - break - end - end -end - - -filename=strcat(pre,'net_figure_new.txt'); - -drawFigureM(nnodes,bnet,labels,filename,cases,stdevs,means,select_var_new,select_var_data_new); - -writeParameters_ev(pre,bnet,nnodes,labels,cases,stdevs,means,select_var_new,select_var_data_new); - -end diff --git a/sourcecodes/parameter_learning/code_backup/Predictmultipleintrvention.m b/sourcecodes/parameter_learning/code_backup/Predictmultipleintrvention.m deleted file mode 100644 index e9f741f2..00000000 --- a/sourcecodes/parameter_learning/code_backup/Predictmultipleintrvention.m +++ /dev/null @@ -1,95 +0,0 @@ -function Predictmultipleintrvention(pre) -dfile=strcat(pre,'structure_input.txt'); -sfile=dfile; -dfile=strcat(pre,'continuous_input.txt'); -nnodefile=strcat(pre,'nnode.txt'); - -fnnode = fopen(nnodefile,'r'); -nnodes = fscanf(fnnode,'%d'); - -fvarnamefile=strcat(pre,'varname.txt'); - -varfile = fopen(fvarnamefile,'r'); - -Std_flag=true; -[labels,cases,bnet]=readInput(dfile,sfile,nnodes,Std_flag); - -[bnet]=parameterLearning(bnet,cases); - -fvarfile=strcat(pre,'var.txt'); -fvar = fopen(fvarfile,'r'); -select_var_new = fscanf(fvar,'%d'); - -nm = numel(select_var_new); - -varlabels = cell(1,nm); -varbuffer = fgetl(varfile); %get header line as a string -for j=1:nm - [varnext,varbuffer] = strtok(varbuffer); - varlabels{j} = varnext; - for i=1:nnodes - if strcmp(varlabels{j},labels{i}) - select_var_new(j)=i; - end - end - -end - - - - -fvardfile=strcat(pre,'vardata.txt'); - -fvard = fopen(fvardfile,'r'); - -select_var_data_new = fscanf(fvard,'%f'); - -means_orig = cell(1,nnodes); -stdevs_orig = cell(1,nnodes); -labels_orig = cell(1,nnodes); -%Read in original means and standard deviations -mapfile = strcat(pre,'map.txt'); -fmap = fopen(mapfile,'r'); -for i=1:nnodes - buffer = fgetl(mapfile); - temp = cell(1,3); - for j=1:3 - [next,buffer] = strtok(buffer); - temp{j} = next; - end - labels_orig{i} = temp{1}; - means_orig{i} = str2num(temp{3}); - stdevs_orig{i} = str2num(temp{2}); -end -fclose(fmap); - -%Need to map the means and stdevs to the correct labels -means = cell(1,nnodes); -stdevs = cell(1,nnodes); -%Read in labels in new order. -labelsnew = cell(1,nnodes); -mapdatafile = strcat(pre,'mapdata.txt'); -fmapdata = fopen(mapdatafile,'r'); -buffer = fgetl(fmapdata); -for i = 1:nnodes - [next,buffer ] = strtok(buffer); - labelsnew{i} = next; -end -fclose(fmapdata); -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labelsnew{i},labels_orig{j}) - means{i} = means_orig{j}; - stdevs{i} = stdevs_orig{j}; - break - end - end -end - -filename=strcat(pre,'net_figure_new.txt'); - -drawFigureM(nnodes,bnet,labels,filename,cases,stdevs,means,select_var_new,select_var_data_new); - -writeParameters_int(pre,bnet,nnodes,labels,cases,stdevs,means,select_var_new,select_var_data_new); - -end diff --git a/sourcecodes/parameter_learning/code_backup/checkDiscreteNodes.m b/sourcecodes/parameter_learning/code_backup/checkDiscreteNodes.m deleted file mode 100644 index c9d0692c..00000000 --- a/sourcecodes/parameter_learning/code_backup/checkDiscreteNodes.m +++ /dev/null @@ -1,37 +0,0 @@ -function [ ] = checkDiscreteNodes( bnet, cases) - %checkDiscreteNodes Checks if states of discrete nodes are be integers from 1 to M - % where M is the number of states of the node. (M should be the same as - % node_sizes in the bnet). - % - %Input: - % bnet: BNT bnet - % cases: cell array of data - % -% -node_sizes = bnet.node_sizes; -dnodes = bnet.dnodes; -ndisc = size(dnodes,2); -ncases = size(cases,2); - -%check to see that all data for discrete nodes are integers -for i = 1:ndisc - inode = dnodes(i); - data = cases(inode,:); - isize = node_sizes(inode); - states = zeros(1,isize); - for j = 1:isize - states(j) = j; - end - for j = 1:ncases - k = int64(data{j}); - if ~any(k==states) - error(['Discrete nodes must be integers from 1 to the number of states']); - end - end -end - - -end - - - diff --git a/sourcecodes/parameter_learning/code_backup/checkStructure.m b/sourcecodes/parameter_learning/code_backup/checkStructure.m deleted file mode 100644 index b4de9403..00000000 --- a/sourcecodes/parameter_learning/code_backup/checkStructure.m +++ /dev/null @@ -1,78 +0,0 @@ -function [ labels, cases, dag, node_sizes, ord_flag ] = checkStructure(labels, cases, dag, node_sizes) - %checkStructure Check to see if nodes are sorted correctly. Nodes must be - % in topological order (i.e., parents before children) before parameter - % learning can take place. This function performs this sorting. - % - %Input and output have the same meaning. The output has just been - %topologically ordered. - % labels = cell array with the names of the nodes. - % cases = cell array with the data. - % dag = matrix with the strucutre of the network. - % node_sizes = vector with the size of each node. - -%make connections array -%count how big you need the connections array to be -nnodes = size(dag,1); -narcs = 0; -for i = 1:nnodes - for j = 1:nnodes - if dag(i,j) == 1 - narcs = narcs + 1; - end - end -end -%fill connections array with label names -connections = cell(narcs,2); -ncount = 0; -for i = 1:nnodes - for j = 1:nnodes - if dag(i,j) == 1 - ncount = ncount + 1; - connections{ncount,1} = labels{i}; - connections{ncount,2} = labels{j}; - end - end -end - -%get topologically sorted dag and labels -[new_dag, new_labels] = mk_adj_mat(connections, labels, 1); - -%check to see if order changed -ord_flag = 0; -for i = 1:nnodes - if ~strcmp(new_labels{i},labels{i}) - ord_flag = 1; - end -end - -if ord_flag - %get new ordering of nodes - order = cell(1,nnodes); - for i = 1:nnodes - for j = 1:nnodes - if strcmp(new_labels{j},labels{i}) - order{i} = j; - end - end - end - - %reorder cases and node_sizes - new_cases = cell(size(cases)); - for i = 1:nnodes - new_cases(order{i},:) = cases(i,:); - end - new_node_sizes = zeros(1,nnodes); - for i = 1:nnodes - new_node_sizes(order{i}) = node_sizes(i); - end - - - dag = new_dag; - cases = new_cases; - node_sizes = new_node_sizes; - labels = new_labels; -end - -end -%end checkStructure.m - diff --git a/sourcecodes/parameter_learning/code_backup/drawFigure.m b/sourcecodes/parameter_learning/code_backup/drawFigure.m deleted file mode 100644 index f84bffa3..00000000 --- a/sourcecodes/parameter_learning/code_backup/drawFigure.m +++ /dev/null @@ -1,390 +0,0 @@ -function [] = drawFigure(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata) -%drawFigure writes the parameters and data that are needed to draw the -%structure of a Bayesian network for BNW. -% This is the first function that - - - -if nargin < 8, - drawFigureNoEv(nnodes,bnet,labels,filename,cases,stdevs,means); -else - drawFigureEv(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata); -end; - -end - - - -function [] = drawFigureEv(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata) -%Function to use if there is no entered evidence. -% -% -%Before each printed line, I will have a line that starts with %%% -% that describes what will be on that line - -%Create an empty evidence cell array. - -%val=cases; -%for i = 1:nnodes -% val(i,1)=val(i,2); - -%end - -A=cell2mat(cases'); -Amax=max(A); -Amin=min(A); - - -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); - -evidence{selectvar}=selectdata; - -[engine,loglik]=enter_evidence(engine,evidence); - -%Open the file, and write the nodes to a file. -fileID = fopen(filename,'w'); - -%%%%Evidence node -fprintf(fileID,'%i\n',selectvar); -%%% The number of nodes -fprintf(fileID,'%i\n',nnodes); -%Get canvas size -labels_temp = cellstr(labels); -[x,y] = make_layout(bnet.dag); - -x = x - min(x); -y = 1 - y; -y = y - min(y); - -[x_dim,y_dim] = canvasSize(nnodes,x,y); - -%%% The dimensions of the canvas for the javascript code -fprintf(fileID,'%i\t%i\t\n',x_dim,y_dim) - -x = x*x_dim; -y = y*y_dim; -for i = 1:nnodes, -%%% The name and X- and Y-positions of each node - fprintf(fileID,'%s\t%i\t%i\n',labels{i},round(x(i)),round(y(i))); -end - -%Get the number of parents and children for each node. -num_par = zeros(1,nnodes); -%For parents, sum down columns -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - num_par(i) = num_par(i) + 1; - end - end -end -num_child = zeros(1,nnodes); -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - num_child(i) = num_child(i) + 1; - end - end -end - - -for i = 1:nnodes, - %%% The name and type of each node (1=continuous, the number of states - %%% if it is discrete - fprintf(fileID,'%s\t%i\n',labels{i},bnet.node_sizes(i)); - %%% The size of the node, I am going to keep them - %%% 250(width) by 150(height) for now - %Could modify this to change the width based on the length of the node - %name - fprintf(fileID,'%i\t%i\n',250,150); - %%% The number of parents of the node, and the parents - if num_par(i) == 0; - %%% If no parents: - fprintf(fileID,'%i\n',num_par(i)); - else - parents = zeros(1,num_par(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - parents(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_par(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_par(i),parents(1,:)); - end - - - %%% The number of children of the node, and the children - if num_child(i) == 0; - %%% If no children: - fprintf(fileID,'%i\n',num_child(i)); - else - children = zeros(1,num_child(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - children(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_child(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_child(i),children(1,:)); - end - - predict = marginal_nodes(engine,i); - if isempty(evidence{i}) - if bnet.node_sizes(i) ~= 1, - for j = 1:bnet.node_sizes(i), - %%%For discrete nodes, the state and the percent of that state - fprintf(fileID,'%i\t%6.4f\n',j,predict.T(j)); - end; - else - - [x_vals,y_vals] = calcGaussian(predict.mu,predict.Sigma,Amax(i),Amin(i)); - %%%For continuous nodes, print x and the pdf of a normal curve. - for j = 1:101, - %%Undo standardization - xvals(j,1) = xvals(j,1)*stdevs{i}+means{i} - fprintf(fileID,'%6.4f\t%6.4f\n',x_vals(j,1),y_vals(j,1)); - end; - end; - else - fprintf(fileID,'%6.4f\t%6.4f\n',selectdata,1); - end - -end -%fprintf(fileID,'%s\t %\n',labels_temp{:}); - - -fclose(fileID); - -end - - - - - - -function [] = drawFigureNoEv(nnodes,bnet,labels,filename,cases,stdevs,means) -%Function to use if there is no entered evidence. -% -% -%Before each printed line, I will have a line that starts with %%% -% that describes what will be on that line -A=cell2mat(cases'); -Amax=max(A); -Amin=min(A); - -%Create an empty evidence cell array. -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); -[engine,loglik] = enter_evidence(engine,evidence); - -%Open the file, and write the nodes to a file. -fileID = fopen(filename,'w'); -%%% The number of nodes -fprintf(fileID,'%i\n',nnodes); - -%Get canvas size - -labels_temp = cellstr(labels); -[x,y] = make_layout(bnet.dag); -%[x,y] = layout_dag(bnet.dag); - - -x = x - min(x); -y = 1 - y; -y = y - min(y); - -[x_dim,y_dim] = canvasSize(nnodes,x,y); - -%%% The dimensions of the canvas for the javascript code -fprintf(fileID,'%i\t%i\t\n',x_dim,y_dim) - -x = x*x_dim; -y = y*y_dim; -for i = 1:nnodes, -%%% The name and X- and Y-positions of each node - fprintf(fileID,'%s\t%i\t%i\n',labels{i},round(x(i)),round(y(i))); -end - -%Get the number of parents and children for each node. -num_par = zeros(1,nnodes); -%For parents, sum down columns -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - num_par(i) = num_par(i) + 1; - end - end -end -num_child = zeros(1,nnodes); -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - num_child(i) = num_child(i) + 1; - end - end -end - - -for i = 1:nnodes, - %%% The name and type of each node (1=continuous, the number of states - %%% if it is discrete - fprintf(fileID,'%s\t%i\n',labels{i},bnet.node_sizes(i)); - %%% The size of the node, I am going to keep them - %%% 250(width) by 150(height) for now - %Could modify this to change the width based on the length of the node - %name - fprintf(fileID,'%i\t%i\n',250,150); - %%% The number of parents of the node, and the parents - if num_par(i) == 0; - %%% If no parents: - fprintf(fileID,'%i\n',num_par(i)); - else - parents = zeros(1,num_par(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - parents(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_par(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_par(i),parents(1,:)); - end - - - %%% The number of children of the node, and the children - if num_child(i) == 0; - %%% If no children: - fprintf(fileID,'%i\n',num_child(i)); - else - children = zeros(1,num_child(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - children(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_child(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_child(i),children(1,:)); - end - - predict = marginal_nodes(engine,i); - if bnet.node_sizes(i) ~= 1, - for j = 1:bnet.node_sizes(i), - %%%For discrete nodes, the state and the percent of that state - fprintf(fileID,'%i\t%6.4f\n',j,predict.T(j)); - end; - else - %cases(i) - % MAX(cases(i)) - % MIN(cases(i)) - [x_vals,y_vals] = calcGaussian(predict.mu,predict.Sigma,Amax(i),Amin(i)); - %%%For continuous nodes, print x and the pdf of a normal curve. - for j = 1:101, - %%Undo standardization - x_vals(j,1) = x_vals(j,1)*stdevs{i}+means{i}; - fprintf(fileID,'%6.4f\t%6.4f\n',x_vals(j,1),y_vals(j,1)); - end; - end; -end -%fprintf(fileID,'%s\t %\n',labels_temp{:}); - - -fclose(fileID); - -end - - -function [x_dim, y_dim] = canvasSize(nnodes,x,y) -%canvasSize Function to calculate the size of the canvas to -% build the network structure - - -%I am going to assume that the node size will be -% height = 150, width = 250 -% so there will be a node spacing of -% 200 (in y-dim) and 300 (in x-dim). -y_space = 200; -x_space = 300; - -%Set default minimum x and y dimensions -x_dim = 1200; -y_dim = 1200; - -%get unique y values -y_unique = unique(y); -size_y = size(y_unique,2); -y_dim_temp = size_y*y_space; - -%get the maximum nodes in any layer -size_x = zeros(1,size_y); -for i = 1:size_y, - for j = 1:nnodes, - if y_unique(i) == y(j), - size_x(1,i) = size_x(1,i) + 1; - end; - end; -end; -size_x = max(size_x); -x_dim_temp = size_x*x_space; - -if x_dim_temp > x_dim, - x_dim = x_dim_temp; -end; - -if y_dim_temp > y_dim, - y_dim = y_dim_temp; -end; -end - -function [x_vals,y_vals] = calcGaussian(mu,Sigma,maxval,minval) -%Function to calculate 101 points of Gaussian function to use in plotting -% Gets the probability density of the mean value and 50 evenly spaced -% points up to 3Sigma below the mean and 50 evenly space points up to -% 3Sigma above the mean. -%maxval -%minval -x_vals = zeros(101,1); -y_vals = zeros(101,1); - -%x_vals(1,1) = mu - 3*Sigma; -x_vals(1,1) = minval - 1; -gap=((maxval+1)-(minval - 1))/100; -%x_vals(1,1) = 0;%mu - 3*Sigma; -for i = 1:100, - % x_vals(i+1,1) = x_vals(1,1) + i*6*Sigma/100; - x_vals(i+1,1) = x_vals(i,1) + gap; - %x_vals(i+1,1) = x_vals(i,1) + 1/100; -end - -for i = 1:101, - y_vals(i,1) = normpdf(x_vals(i,1),mu,Sigma); -end - -end diff --git a/sourcecodes/parameter_learning/code_backup/drawFigure.m~ b/sourcecodes/parameter_learning/code_backup/drawFigure.m~ deleted file mode 100644 index 404a65f7..00000000 --- a/sourcecodes/parameter_learning/code_backup/drawFigure.m~ +++ /dev/null @@ -1,388 +0,0 @@ -function [] = drawFigure(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata) -%drawFigure writes the parameters and data that are needed to draw the -%structure of a Bayesian network. - - -if nargin < 8, - drawFigureNoEv(nnodes,bnet,labels,filename,cases,stdevs,means); -else - drawFigureEv(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata); -end; - -end - - - -function [] = drawFigureEv(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata) -%Function to use if there is no entered evidence. -% -% -%Before each printed line, I will have a line that starts with %%% -% that describes what will be on that line - -%Create an empty evidence cell array. - -%val=cases; -%for i = 1:nnodes -% val(i,1)=val(i,2); - -%end - -A=cell2mat(cases'); -Amax=max(A); -Amin=min(A); - - -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); - -evidence{selectvar}=selectdata; - -[engine,loglik]=enter_evidence(engine,evidence); - -%Open the file, and write the nodes to a file. -fileID = fopen(filename,'w'); - -%%%%Evidence node -fprintf(fileID,'%i\n',selectvar); -%%% The number of nodes -fprintf(fileID,'%i\n',nnodes); -%Get canvas size -labels_temp = cellstr(labels); -[x,y] = make_layout(bnet.dag); - -x = x - min(x); -y = 1 - y; -y = y - min(y); - -[x_dim,y_dim] = canvasSize(nnodes,x,y); - -%%% The dimensions of the canvas for the javascript code -fprintf(fileID,'%i\t%i\t\n',x_dim,y_dim) - -x = x*x_dim; -y = y*y_dim; -for i = 1:nnodes, -%%% The name and X- and Y-positions of each node - fprintf(fileID,'%s\t%i\t%i\n',labels{i},round(x(i)),round(y(i))); -end - -%Get the number of parents and children for each node. -num_par = zeros(1,nnodes); -%For parents, sum down columns -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - num_par(i) = num_par(i) + 1; - end - end -end -num_child = zeros(1,nnodes); -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - num_child(i) = num_child(i) + 1; - end - end -end - - -for i = 1:nnodes, - %%% The name and type of each node (1=continuous, the number of states - %%% if it is discrete - fprintf(fileID,'%s\t%i\n',labels{i},bnet.node_sizes(i)); - %%% The size of the node, I am going to keep them - %%% 250(width) by 150(height) for now - %Could modify this to change the width based on the length of the node - %name - fprintf(fileID,'%i\t%i\n',250,150); - %%% The number of parents of the node, and the parents - if num_par(i) == 0; - %%% If no parents: - fprintf(fileID,'%i\n',num_par(i)); - else - parents = zeros(1,num_par(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - parents(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_par(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_par(i),parents(1,:)); - end - - - %%% The number of children of the node, and the children - if num_child(i) == 0; - %%% If no children: - fprintf(fileID,'%i\n',num_child(i)); - else - children = zeros(1,num_child(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - children(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_child(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_child(i),children(1,:)); - end - - predict = marginal_nodes(engine,i); - if isempty(evidence{i}) - if bnet.node_sizes(i) ~= 1, - for j = 1:bnet.node_sizes(i), - %%%For discrete nodes, the state and the percent of that state - fprintf(fileID,'%i\t%6.4f\n',j,predict.T(j)); - end; - else - - [x_vals,y_vals] = calcGaussian(predict.mu,predict.Sigma,Amax(i),Amin(i)); - %%%For continuous nodes, print x and the pdf of a normal curve. - for j = 1:101, - %%Undo standardization - xvals(j,1) = xvals(j,1)*stdevs{i}+means{i} - fprintf(fileID,'%6.4f\t%6.4f\n',x_vals(j,1),y_vals(j,1)); - end; - end; - else - fprintf(fileID,'%6.4f\t%6.4f\n',selectdata,1); - end - -end -%fprintf(fileID,'%s\t %\n',labels_temp{:}); - - -fclose(fileID); - -end - - - - - - -function [] = drawFigureNoEv(nnodes,bnet,labels,filename,cases,stdevs,means) -%Function to use if there is no entered evidence. -% -% -%Before each printed line, I will have a line that starts with %%% -% that describes what will be on that line -A=cell2mat(cases'); -Amax=max(A); -Amin=min(A); - -%Create an empty evidence cell array. -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); -[engine,loglik] = enter_evidence(engine,evidence); - -%Open the file, and write the nodes to a file. -fileID = fopen(filename,'w'); -%%% The number of nodes -fprintf(fileID,'%i\n',nnodes); - -%Get canvas size - -labels_temp = cellstr(labels); -[x,y] = make_layout(bnet.dag); -%[x,y] = layout_dag(bnet.dag); - - -x = x - min(x); -y = 1 - y; -y = y - min(y); - -[x_dim,y_dim] = canvasSize(nnodes,x,y); - -%%% The dimensions of the canvas for the javascript code -fprintf(fileID,'%i\t%i\t\n',x_dim,y_dim) - -x = x*x_dim; -y = y*y_dim; -for i = 1:nnodes, -%%% The name and X- and Y-positions of each node - fprintf(fileID,'%s\t%i\t%i\n',labels{i},round(x(i)),round(y(i))); -end - -%Get the number of parents and children for each node. -num_par = zeros(1,nnodes); -%For parents, sum down columns -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - num_par(i) = num_par(i) + 1; - end - end -end -num_child = zeros(1,nnodes); -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - num_child(i) = num_child(i) + 1; - end - end -end - - -for i = 1:nnodes, - %%% The name and type of each node (1=continuous, the number of states - %%% if it is discrete - fprintf(fileID,'%s\t%i\n',labels{i},bnet.node_sizes(i)); - %%% The size of the node, I am going to keep them - %%% 250(width) by 150(height) for now - %Could modify this to change the width based on the length of the node - %name - fprintf(fileID,'%i\t%i\n',250,150); - %%% The number of parents of the node, and the parents - if num_par(i) == 0; - %%% If no parents: - fprintf(fileID,'%i\n',num_par(i)); - else - parents = zeros(1,num_par(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - parents(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_par(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_par(i),parents(1,:)); - end - - - %%% The number of children of the node, and the children - if num_child(i) == 0; - %%% If no children: - fprintf(fileID,'%i\n',num_child(i)); - else - children = zeros(1,num_child(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - children(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_child(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_child(i),children(1,:)); - end - - predict = marginal_nodes(engine,i); - if bnet.node_sizes(i) ~= 1, - for j = 1:bnet.node_sizes(i), - %%%For discrete nodes, the state and the percent of that state - fprintf(fileID,'%i\t%6.4f\n',j,predict.T(j)); - end; - else - %cases(i) - % MAX(cases(i)) - % MIN(cases(i)) - [x_vals,y_vals] = calcGaussian(predict.mu,predict.Sigma,Amax(i),Amin(i)); - %%%For continuous nodes, print x and the pdf of a normal curve. - for j = 1:101, - %%Undo standardization - x_vals(j,1) = x_vals(j,1)*stdevs{i}+means{i}; - fprintf(fileID,'%6.4f\t%6.4f\n',x_vals(j,1),y_vals(j,1)); - end; - end; -end -%fprintf(fileID,'%s\t %\n',labels_temp{:}); - - -fclose(fileID); - -end - - -function [x_dim, y_dim] = canvasSize(nnodes,x,y) -%canvasSize Function to calculate the size of the canvas to -% build the network structure - - -%I am going to assume that the node size will be -% height = 150, width = 250 -% so there will be a node spacing of -% 200 (in y-dim) and 300 (in x-dim). -y_space = 200; -x_space = 300; - -%Set default minimum x and y dimensions -x_dim = 1200; -y_dim = 1200; - -%get unique y values -y_unique = unique(y); -size_y = size(y_unique,2); -y_dim_temp = size_y*y_space; - -%get the maximum nodes in any layer -size_x = zeros(1,size_y); -for i = 1:size_y, - for j = 1:nnodes, - if y_unique(i) == y(j), - size_x(1,i) = size_x(1,i) + 1; - end; - end; -end; -size_x = max(size_x); -x_dim_temp = size_x*x_space; - -if x_dim_temp > x_dim, - x_dim = x_dim_temp; -end; - -if y_dim_temp > y_dim, - y_dim = y_dim_temp; -end; -end - -function [x_vals,y_vals] = calcGaussian(mu,Sigma,maxval,minval) -%Function to calculate 101 points of Gaussian function to use in plotting -% Gets the probability density of the mean value and 50 evenly spaced -% points up to 3Sigma below the mean and 50 evenly space points up to -% 3Sigma above the mean. -%maxval -%minval -x_vals = zeros(101,1); -y_vals = zeros(101,1); - -%x_vals(1,1) = mu - 3*Sigma; -x_vals(1,1) = minval - 1; -gap=((maxval+1)-(minval - 1))/100; -%x_vals(1,1) = 0;%mu - 3*Sigma; -for i = 1:100, - % x_vals(i+1,1) = x_vals(1,1) + i*6*Sigma/100; - x_vals(i+1,1) = x_vals(i,1) + gap; - %x_vals(i+1,1) = x_vals(i,1) + 1/100; -end - -for i = 1:101, - y_vals(i,1) = normpdf(x_vals(i,1),mu,Sigma); -end - -end diff --git a/sourcecodes/parameter_learning/code_backup/drawFigureM.m b/sourcecodes/parameter_learning/code_backup/drawFigureM.m deleted file mode 100644 index 91b8698f..00000000 --- a/sourcecodes/parameter_learning/code_backup/drawFigureM.m +++ /dev/null @@ -1,230 +0,0 @@ -function [] = drawFigureM(nnodes,bnet,labels,filename,cases,stdevs,means,selectvar,selectdata) -%drawFigureM writes the parameters and data that are needed to draw the -%structure of a Bayesian network after added evidence or intervention - -fileID = fopen(filename,'w'); - - -A=cell2mat(cases'); -Amax=max(A); -Amin=min(A); - - -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); - -m = size(selectvar,1); - -ev_dat = zeros(1,nnodes); -for i = 1:m, - di=selectvar(i,1); - ev_dat(di)=selectdata(i,1); -%Need to standardized evidence for continuous nodes. - if bnet.node_sizes(di) == 1 - ev_dat(di) = (ev_dat(di) - means{di}) / stdevs{di}; - end - evidence{di}=ev_dat(di); - fprintf(fileID,'%i\t',di); -end - -fprintf(fileID,'\n'); - -[engine,loglik]=enter_evidence(engine,evidence); - -%Open the file, and write the nodes to a file. -%%% The number of nodes -fprintf(fileID,'%i\n',nnodes); -%Get canvas size -labels_temp = cellstr(labels); -[x,y] = make_layout(bnet.dag); -x = x - min(x); -y = 1 - y; -y = y - min(y); -[x_dim,y_dim] = canvasSize(nnodes,x,y); - -%%% The dimensions of the canvas for the javascript code -fprintf(fileID,'%i\t%i\t\n',x_dim,y_dim); -x = x*x_dim; -y = y*y_dim; -for i = 1:nnodes, -%%% The name and X- and Y-positions of each node - fprintf(fileID,'%s\t%i\t%i\n',labels{i},round(x(i)),round(y(i))); -end - -%Get the number of parents and children for each node. -num_par = zeros(1,nnodes); -%For parents, sum down columns -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - num_par(i) = num_par(i) + 1; - end - end -end -num_child = zeros(1,nnodes); -for i = 1:nnodes, - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - num_child(i) = num_child(i) + 1; - end - end -end - -for i = 1:nnodes, - %%% The name and type of each node (1=continuous, the number of states - %%% if it is discrete - fprintf(fileID,'%s\t%i\n',labels{i},bnet.node_sizes(i)); - %%% The size of the node, I am going to keep them - %%% 250(width) by 150(height) for now - %Could modify this to change the width based on the length of the node - %name - fprintf(fileID,'%i\t%i\n',250,150); - %%% The number of parents of the node, and the parents - if num_par(i) == 0; - %%% If no parents: - fprintf(fileID,'%i\n',num_par(i)); - else - parents = zeros(1,num_par(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(j,i) == 1, - parents(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_par(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_par(i),parents(1,:)); - end - - - %%% The number of children of the node, and the children - if num_child(i) == 0; - %%% If no children: - fprintf(fileID,'%i\n',num_child(i)); - else - children = zeros(1,num_child(i)); - k = 1; - for j = 1:nnodes, - if bnet.dag(i,j) == 1, - children(1,k) = j; - k = k + 1; - end - end - format = '%i\t'; - for j = 1:num_child(i)-1, - format = strcat(format,'%i\t'); - end - format = strcat(format,'%i\n'); - %%%If there are parents: - fprintf(fileID,format,num_child(i),children(1,:)); - end - - predict = marginal_nodes(engine,i); - if isempty(evidence{i}) - if bnet.node_sizes(i) ~= 1, - for j = 1:bnet.node_sizes(i), - %%%For discrete nodes, the state and the percent of that state - fprintf(fileID,'%i\t%6.4f\n',j,predict.T(j)); - end; - else - [x_vals,y_vals] = calcGaussian(predict.mu,predict.Sigma,Amax(i),Amin(i)); - %%%For continuous nodes, print x and the pdf of a normal curve. - for j = 1:101, - %%Undo standardization - x_vals(j,1) = x_vals(j,1)*stdevs{i}+means{i}; - fprintf(fileID,'%6.4f\t%6.4f\n',x_vals(j,1),y_vals(j,1)); - end; - end; - else - if bnet.node_sizes(i) == 1, - fprintf(fileID,'%6.4f\t%6.4f\n',ev_dat(i)*stdevs{i}+means{i},1); - else - fprintf(fileID,'%6.4f\t%6.4f\n',ev_dat(i),1); - endif - end - -end - -fclose(fileID); -end - - - - - - - - - -function [x_dim, y_dim] = canvasSize(nnodes,x,y) -%canvasSize Function to calculate the size of the canvas to -% build the network structure - - -%I am going to assume that the node size will be -% height = 150, width = 250 -% so there will be a node spacing of -% 200 (in y-dim) and 300 (in x-dim). -y_space = 200; -x_space = 300; - -%Set default minimum x and y dimensions -x_dim = 1200; -y_dim = 1200; - -%get unique y values -y_unique = unique(y); -size_y = size(y_unique,2); -y_dim_temp = size_y*y_space; - -%get the maximum nodes in any layer -size_x = zeros(1,size_y); -for i = 1:size_y, - for j = 1:nnodes, - if y_unique(i) == y(j), - size_x(1,i) = size_x(1,i) + 1; - end; - end; -end; -size_x = max(size_x); -x_dim_temp = size_x*x_space; - -if x_dim_temp > x_dim, - x_dim = x_dim_temp; -end; - -if y_dim_temp > y_dim, - y_dim = y_dim_temp; -end; -end - -function [x_vals,y_vals] = calcGaussian(mu,Sigma,maxval,minval) -%Function to calculate 101 points of Gaussian function to use in plotting -% Gets the probability density of the mean value and 50 evenly spaced -% points up to 3Sigma below the mean and 50 evenly space points up to -% 3Sigma above the mean. -%maxval -%minval -x_vals = zeros(101,1); -y_vals = zeros(101,1); - -%x_vals(1,1) = mu - 3*Sigma; -x_vals(1,1) = minval - 1; -gap=((maxval+1)-(minval - 1))/100; -%x_vals(1,1) = 0;%mu - 3*Sigma; -for i = 1:100, - % x_vals(i+1,1) = x_vals(1,1) + i*6*Sigma/100; - x_vals(i+1,1) = x_vals(i,1) + gap; - %x_vals(i+1,1) = x_vals(i,1) + 1/100; -end - -for i = 1:101, - y_vals(i,1) = normpdf(x_vals(i,1),mu,Sigma); -end - -end diff --git a/sourcecodes/parameter_learning/code_backup/getParams.m b/sourcecodes/parameter_learning/code_backup/getParams.m deleted file mode 100644 index 31f84ffb..00000000 --- a/sourcecodes/parameter_learning/code_backup/getParams.m +++ /dev/null @@ -1,22 +0,0 @@ -function [ bnet ] = getParams( bnet, cases ) -%getParams Code to initialize CPT and do parameter learning. -%This will be very basic for now. I can add more options later. - -dnodes = bnet.dnodes; -cnodes = bnet.cnodes; -nnodes = size(dnodes,2)+size(cnodes,2); - -%make dnodes tabular_CPT -for i = 1:size(dnodes,2) - bnet.CPD{dnodes(i)} = tabular_CPD(bnet,dnodes(i)); -end - -for i = 1:size(cnodes,2) - bnet.CPD{cnodes(i)} = gaussian_CPD(bnet,cnodes(i)); -end - -bnet = learn_params(bnet,cases); - - -end - diff --git a/sourcecodes/parameter_learning/code_backup/parameterLearning.m b/sourcecodes/parameter_learning/code_backup/parameterLearning.m deleted file mode 100644 index 872e94b1..00000000 --- a/sourcecodes/parameter_learning/code_backup/parameterLearning.m +++ /dev/null @@ -1,17 +0,0 @@ -function [ bnet ] = parameterLearning( bnet,cases,engine_name ) -%parameterLearning Do parameter learning and inference - -%engine is an optional argument -if nargin < 3 - engine_name = 'jtree_inf_engine'; -end - - -%First do parameter learning with all the data -[bnet] = getParams(bnet,cases); - - - - -end - diff --git a/sourcecodes/parameter_learning/code_backup/prepareInput.m b/sourcecodes/parameter_learning/code_backup/prepareInput.m deleted file mode 100644 index 838dcd2c..00000000 --- a/sourcecodes/parameter_learning/code_backup/prepareInput.m +++ /dev/null @@ -1,294 +0,0 @@ -function [ ] = prepareInput( pre ) - % - % This function takes files that are uploaded to BNW and creates output - % files that can be used for structure and parameter learning. - % It replaces php code that was previously in bn_file_load_gom.php. - % There are several improvements in performance and ease of use: - % 1) Loading files is significantly (~5x) faster for large input files. - % 2) The allowed values for discrete variables are more flexible. - % (e.g., A genotype variable be 'B' and 'D' instead of having - % to replace to make them '1' and '2'.) - % 3) Continuous variables may be identified as continuous in some cases - % even if there is not a period. - % 4) The states of discrete variables should be correctly ordered in - % almost all cases. - % 5) An additional output file is written that will let users check if - % the input file has been uploaded and parsed correctly. - % 6) Future updates to this code should be easier than updating the php. - % - % - % Input: ???continuous_input_orig.txt - % This is the input file that is uploaded to BNW. - % It is directly written out by the BNW php code with no modification. - % The file format is a header line containing the variable names - % followed by the data, with each case in a row. - % - % Output: There are many output files. - % 1) The main output file is ???continuous_input.txt that can be - % used by the structure learning code and parameter learning codes. - % The first line is variable names, the second line is the node type - % (continuous nodes should have 1, discrete nodes have the number - % of states), and the rest is the data. - % 2) A new output file is ???input_desc.txt, a file that describes the - % data so users can check that it has been parsed correctly. - % 3) ???nlevels.txt: The states of discrete variables. - % 4) ???name.txt: The names of the variables as uploaded. - % 5) ???type.txt: The number of states for each variables - % (1 indicates a continuous variable.) - % 6/7) ???nnode.txt and ???nrows.txt: number of nodes and cases - % 8-12) ???ban.txt, ???white.txt, ???k.txt, ???thr.txt, and - % ???parent.txt: Files with default values for structure learning. - % - -% open file for input, include error handling -dfile=strcat(pre,'continuous_input_orig.txt'); - -fin = fopen(dfile,'r'); -if fin < 0 - error(['Could not open ',dfile,' for input']); -end - -% Get the number of cases (the number of rows in the file excluding the header) -ncases = fskipl(fin,Inf) - 1; - -frewind(fin); - -% Read in first line to get the number of nodes and the node labels. -buffer = fgetl(fin); %get header line as a string -nnodes = numel(strfind(buffer,"\t")) + 1; -labels = cell(1,nnodes); -for j=1:nnodes - [next,buffer] = strtok(buffer); - labels{j} = next; -end - -% Read in the data -data = cell(ncases,nnodes); -for i = 1:ncases - buffer = fgetl(fin); - for j = 1:nnodes - [next,buffer] = strtok(buffer); - data{i,j} = next; - end -end - -% Determine whether or not the nodes are continuous or discrete. -% First, treat them as all discrete and get the states and number of stats(levels). -levels = cell(1,nnodes); -states = []; -for j = 1:nnodes - states{end+1} = unique(data(:,j)); - levels{j} = size(states{j},1); -end - -reason = cell(1,nnodes); -%Now do some checks to see if nodes are discrete or continuous -for j = 1:nnodes - % If there are 3 or less unique values, I will assume that the node is discrete. - if levels{j} < 4; - reason{j} = "It was determined to be discrete because there are a small number (<4) of possible values."; - continue - % If there are as many unique values as a third of the number of cases, - % I will assume that the node is continuous. - elseif levels{j} > ncases/3; - levels{j} = 1; - reason{j} = "It was determined to be continuous because there are a large number of possible values compared to the number of cases."; - continue - % If there are more than twenty unique values, - % I will assume that the node is continuous. - elseif levels{j} > 20; - levels{j} = 1; - reason{j} = "It was determined to be continuous because there are many (>20) possible values."; - continue - % Otherwise, I will scan through the individual values. - % If any of the values contain a '.', I will assume it is continuous. - else - reason{j} = "It was determined to be discrete by default."; - period_test = 0; - column = data(:,j); - k = 1; - while period_test == 0 - period_test = sum(cell2mat(strfind(column(k),"."))); - if period_test != 0; - reason{j} = "This variable was determined to be continuous because there were several possible values and at least one value contained a period(.)."; - levels{j} = 1; - end - k++; - if k > ncases - break - end - end - end -end - -%I need to check if any discrete nodes are listed after continuous nodes. -%If so, I need to rearrange the columns. -max_disc = 0; -min_cont = nnodes + 1; -for i = 1:nnodes - if levels{i} > 1 - max_disc = i; - elseif min_cont == nnodes+1 - min_cont = i; - end -end -%If max_disc > min_cont, you need to rearrange the nodes -% to put the discrete nodes first. -if max_disc > min_cont - levels_old = levels; - labels_old = labels; - data_old = data; - states_old = states; - reason_old = reason; - new_order = {}; - for i=1:nnodes - if levels_old{i} > 1 - new_order{end+1} = i; - end - end - for i=1:nnodes - if levels_old{i} == 1 - new_order{end+1} = i; - end - end - labels = {}; - levels = {}; - states = {}; - reason = {}; - for i =1:nnodes - labels{i} = labels_old{new_order{i}}; - levels{i} = levels_old{new_order{i}}; - states{i} = states_old{new_order{i}}; - reason{i} = reason_old{new_order{i}}; - for j=1:ncases - data{j,i} = data_old{j,new_order{i}}; - end - end - -endif - - -%Write other files that are used by BNW for this key. -%The first group of files establish default settings for structure learning. -outfile = strcat(pre,'white.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'From\tTo\n'); -fclose(fout); - -outfile = strcat(pre,'ban.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'From\tTo\n'); -fclose(fout); - -outfile = strcat(pre,'k.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'1\n'); -fclose(fout); - -outfile = strcat(pre,'parent.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'4\n'); -fclose(fout); - -outfile = strcat(pre,'thr.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'0.5\n'); -fclose(fout); - - -%The next group of files have information about the uploaded file. -outfile = strcat(pre,'name.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\n',labels{end}); -fclose(fout); - -outfile = strcat(pre,'nnode.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%i\n',nnodes); -fclose(fout); - -outfile = strcat(pre,'nrows.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%i\n',ncases); -fclose(fout); - -outfile = strcat(pre,'type.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\n',labels{end}); -fprintf(fout,'%i\t',levels{1:end-1}); -fprintf(fout,'%i\n',levels{end}); -fclose(fout); - -%This output file contains the states for discrete nodes. -% The unique matlab function already sorts the states. -outfile = strcat(pre,'nlevels.txt'); -fout = fopen(outfile,'w'); -for i = 1:nnodes - if levels{i} > 1 - fprintf(fout,'%s\t',labels{i},states{i}{1:end-1}); - fprintf(fout,'%s\n',states{i}{end}); - end -end -fclose(fout); - - -%Print a file with a short description of the input. -descfile = strcat(pre,'input_desc.txt'); -dout = fopen(descfile,'w'); -fprintf(dout,['As loaded, the input file had the following properties:\n\n']); -dout = fopen(descfile,'a'); -fprintf(dout,'There are %i variables and %i cases(rows).\n',size(labels,2),ncases); -fprintf(dout,'The variable names are:\n'); -fprintf(dout,'%s\t',labels{1:end-1}); -fprintf(dout,'%s\n\n',labels{end}); -for i=1:nnodes - if levels{i} == 1 - fprintf(dout,'%s is a continuous variable.\n',labels{i}); - fprintf(dout,'%s\n',reason{i}); - column = str2double(data(:,i)); - colmean = mean(column); - colstd = std(column); - fprintf(dout,'It has a mean of %6.3f and a standard deviation of %6.3f\n\n',mean(column),std(column)) - else - fprintf(dout,'%s is a discrete variable with %i states.\n',labels{i},levels{i}); - fprintf(dout,'%s\n',reason{i}); - fprintf(dout,'The states are: '); - fprintf(dout,'%s ',states{i}{1:end-1}); - fprintf(dout,'%s\n\n',states{i}{end}); - end -end -fclose(fout); - -outfile = strcat(pre,'continuous_input.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\n',labels{end}); -fprintf(fout,'%i\t',levels{1:end-1}); -fprintf(fout,'%i\n',levels{end}); -%Need to replace states in discrete variables with integers for BNT -for i = 1:nnodes - if levels{i} > 1 - for j = 1:ncases - for k=1:size(states{i},1) - if data{j,i} == states{i}{k} - data{j,i} = sprintf('%i',num2cell(k){1});; - break - end - end - end - end -end -for i = 1:ncases - fprintf(fout,'%s\t',data{i,1:end-1}); - fprintf(fout,'%s\n',data{i,end}); -end -fclose(fout); - - - - - -end -% end of prepareInput.m \ No newline at end of file diff --git a/sourcecodes/parameter_learning/code_backup/prepareInput.m~ b/sourcecodes/parameter_learning/code_backup/prepareInput.m~ deleted file mode 100644 index 9fc0f97f..00000000 --- a/sourcecodes/parameter_learning/code_backup/prepareInput.m~ +++ /dev/null @@ -1,294 +0,0 @@ -function [ ] = prepareInput( pre ) - % - % This function takes files that are uploaded to BNW and creates output - % files that can be used for structure and parameter learning. - % It replaces php code that was previously in bn_file_load_gom.php. - % There are several improvements in performance and ease of use: - % 1) Loading files is significantly (~5x) faster for large input files. - % 2) The allowed values for discrete variables are more flexible. - % (e.g., A genotype variable be 'B' and 'D' instead of having - % to replace to make them '1' and '2'.) - % 3) Continuous variables may be identified as continuous in some cases - % even if there is not a period. - % 4) The states of discrete variables should be correctly ordered in - % almost all cases. - % 5) An additional output file is written that will let users check if - % the input file has been uploaded and parsed correctly. - % 6) Future updates to this code should be easier than updating the php. - % - % - % Input: ???continuous_input_orig.txt - % This is the input file that is uploaded to BNW. - % It is directly written out by the BNW php code with no modification. - % The file format is a header line containing the variable names - % followed by the data, with each case in a row. - % - % Output: There are many output files. - % 1) The main output file is ???continuous_input.txt that can be - % used by the structure learning code and parameter learning codes. - % The first line is variable names, the second line is the node type - % (continuous nodes should have 1, discrete nodes have the number - % of states), and the rest is the data. - % 2) A new output file is ???input_desc.txt, a file that describes the - % data so users can check that it has been parsed correctly. - % 3) ???nlevels.txt: The states of discrete variables. - % 4) ???name.txt: The names of the variables as uploaded. - % 5) ???type.txt: The number of states for each variables - % (1 indicates a continuous variable.) - % 6/7) ???nnode.txt and ???nrows.txt: number of nodes and cases - % 8-12) ???ban.txt, ???white.txt, ???k.txt, ???thr.txt, and - % ???parent.txt: Files with default values for structure learning. - % - -% open file for input, include error handling -dfile=strcat(pre,'continuous_input_orig.txt'); - -fin = fopen(dfile,'r'); -if fin < 0 - error(['Could not open ',dfile,' for input']); -end - -% Get the number of cases (the number of rows in the file excluding the header) -ncases = fskipl(fin,Inf) - 1; - -frewind(fin); - -% Read in first line to get the number of nodes and the node labels. -buffer = fgetl(fin); %get header line as a string -nnodes = numel(strfind(buffer,"\t")) + 1; -labels = cell(1,nnodes); -for j=1:nnodes - [next,buffer] = strtok(buffer); - labels{j} = next; -end - -% Read in the data -data = cell(ncases,nnodes); -for i = 1:ncases - buffer = fgetl(fin); - for j = 1:nnodes - [next,buffer] = strtok(buffer); - data{i,j} = next; - end -end - -% Determine whether or not the nodes are continuous or discrete. -% First, treat them as all discrete and get the states and number of stats(levels). -levels = cell(1,nnodes); -states = []; -for j = 1:nnodes - states{end+1} = unique(data(:,j)); - levels{j} = size(states{j},1); -end - -reason = cell(1,nnodes); -%Now do some checks to see if nodes are discrete or continuous -for j = 1:nnodes - % If there are 3 or less unique values, I will assume that the node is discrete. - if levels{j} < 4; - reason{j} = "This was determined to be discrete because there are few (<4) different values."; - continue - % If there are as many unique values as a third of the number of cases, - % I will assume that the node is continuous. - elseif levels{j} > ncases/3; - levels{j} = 1; - reason{j} = "This was determined to be continuous because there are a large number of different values compared to the number of cases."; - continue - % If there are more than twenty unique values, - % I will assume that the node is continuous. - elseif levels{j} > 20; - levels{j} = 1; - reason{j} = "This was determined to be continuous because there are many (>20) possible values."; - continue - % Otherwise, I will scan through the individual values. - % If any of the values contain a '.', I will assume it is continuous. - else - reason{j} = "This variable was determined to be discrete."; - period_test = 0; - column = data(:,j); - k = 1; - while period_test == 0 - period_test = sum(cell2mat(strfind(column(k),"."))); - if period_test != 0; - reason{j} = "This variable was determined to be continuous because there were several possible values and at least one value contained a period (".")."; - levels{j} = 1; - end - k++; - if k > ncases - break - end - end - end -end - -%I need to check if any discrete nodes are listed after continuous nodes. -%If so, I need to rearrange the columns. -max_disc = 0; -min_cont = nnodes + 1; -for i = 1:nnodes - if levels{i} > 1 - max_disc = i; - elseif min_cont == nnodes+1 - min_cont = i; - end -end -%If max_disc > min_cont, you need to rearrange the nodes -% to put the discrete nodes first. -if max_disc > min_cont - levels_old = levels; - labels_old = labels; - data_old = data; - states_old = states; - reason_old = reason; - new_order = {}; - for i=1:nnodes - if levels_old{i} > 1 - new_order{end+1} = i; - end - end - for i=1:nnodes - if levels_old{i} == 1 - new_order{end+1} = i; - end - end - labels = {}; - levels = {}; - states = {}; - reason = {}; - for i =1:nnodes - labels{i} = labels_old{new_order{i}}; - levels{i} = levels_old{new_order{i}}; - states{i} = states_old{new_order{i}}; - reason{i} = reason_old{new_order{i}}; - for j=1:ncases - data{j,i} = data_old{j,new_order{i}}; - end - end - -endif - - -%Write other files that are used by BNW for this key. -%The first group of files establish default settings for structure learning. -outfile = strcat(pre,'white.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'From\tTo\n'); -fclose(fout); - -outfile = strcat(pre,'ban.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'From\tTo\n'); -fclose(fout); - -outfile = strcat(pre,'k.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'1\n'); -fclose(fout); - -outfile = strcat(pre,'parent.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'4\n'); -fclose(fout); - -outfile = strcat(pre,'thr.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'0.5\n'); -fclose(fout); - - -%The next group of files have information about the uploaded file. -outfile = strcat(pre,'name.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\n',labels{end}); -fclose(fout); - -outfile = strcat(pre,'nnode.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%i\n',nnodes); -fclose(fout); - -outfile = strcat(pre,'nrows.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%i\n',ncases); -fclose(fout); - -outfile = strcat(pre,'type.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\n',labels{end}); -fprintf(fout,'%i\t',levels{1:end-1}); -fprintf(fout,'%i\n',levels{end}); -fclose(fout); - -%This output file contains the states for discrete nodes. -% The unique matlab function already sorts the states. -outfile = strcat(pre,'nlevels.txt'); -fout = fopen(outfile,'w'); -for i = 1:nnodes - if levels{i} > 1 - fprintf(fout,'%s\t',labels{i},states{i}{1:end-1}); - fprintf(fout,'%s\n',states{i}{end}); - end -end -fclose(fout); - - -%Print a file with a short description of the input. -descfile = strcat(pre,'input_desc.txt'); -dout = fopen(descfile,'w'); -fprintf(dout,['As loaded, the input file had the following properties:\n\n']); -dout = fopen(descfile,'a'); -fprintf(dout,'There are %i variables and %i cases(rows)\n',size(labels,2),ncases); -fprintf(dout,'The variable names are:\n'); -fprintf(dout,'%s\t',labels{1:end-1}); -fprintf(dout,'%s\n\n',labels{end}); -for i=1:nnodes - if levels{i} == 1 - fprintf(dout,'%s is a continuous variable\n',labels{i}); - fprintf(dout,'%s\n',reason{i}); - column = str2double(data(:,i)); - colmean = mean(column); - colstd = std(column); - fprintf(dout,'It has a mean of %6.3f and a standard deviation of %6.3f\n\n',mean(column),std(column)) - else - fprintf(dout,'%s is a discrete variable with %i states\n',labels{i},levels{i}); - fprintf(dout,'%s\n',reason{i}); - fprintf(dout,'The states are: '); - fprintf(dout,'%s ',states{i}{1:end-1}); - fprintf(dout,'%s\n\n',states{i}{end}); - end -end -fclose(fout); - -outfile = strcat(pre,'continuous_input.txt'); -fout = fopen(outfile,'w'); -fprintf(fout,'%s\t',labels{1:end-1}); -fprintf(fout,'%s\n',labels{end}); -fprintf(fout,'%i\t',levels{1:end-1}); -fprintf(fout,'%i\n',levels{end}); -%Need to replace states in discrete variables with integers for BNT -for i = 1:nnodes - if levels{i} > 1 - for j = 1:ncases - for k=1:size(states{i},1) - if data{j,i} == states{i}{k} - data{j,i} = sprintf('%i',num2cell(k){1});; - break - end - end - end - end -end -for i = 1:ncases - fprintf(fout,'%s\t',data{i,1:end-1}); - fprintf(fout,'%s\n',data{i,end}); -end -fclose(fout); - - - - - -end -% end of prepareInput.m \ No newline at end of file diff --git a/sourcecodes/parameter_learning/code_backup/readInput.m b/sourcecodes/parameter_learning/code_backup/readInput.m deleted file mode 100644 index 891d7f36..00000000 --- a/sourcecodes/parameter_learning/code_backup/readInput.m +++ /dev/null @@ -1,63 +0,0 @@ -function [ labels, cases, bnet, node_sizes, data,labelsold] = readInput( dfile, sfile, nnodes, std_flag ) - %readInput is to be used when reading in a network with a known structure - % - %Input: - % dfile = name of the file containing the data (required) - % sfile = name of the file containing the structure (required) - % nnodes = number of nodes in the network (required) - % std_flag = flag for whether or not to standardize the data. - % (optional-- Default is FALSE) - % - % See readInputData.m and readInputStructure.m for description of the - % format of the dfile and sfile, respectively. - % - %Output: - % labels = cell array with the names of the nodes. - % cases = cell array with the data. - % bnet = BNT bayesian network with the input structure. - -if nargin < 4 - std_flag = false(1); -end - - -% read in the file with the data -[labelsold,node_sizes,cases, data] = readInputData(dfile,nnodes); - - -% read in the file with the structure -[dag] = readInputStructure(sfile,labelsold); - - -% check the ordering of the nodes and reorder if necessary -[labels,cases,dag,node_sizes,ord_flag] = checkStructure(labelsold,cases,dag,node_sizes); - -dcount = 0; -for i = 1:nnodes - if node_sizes(i) ~= 1 - dcount = dcount + 1; - end -end -discrete = zeros(1,dcount); -dcount = 0; -for i = 1:nnodes - if node_sizes(i) ~= 1 - dcount = dcount + 1; - discrete(dcount) = i; - end -end - -bnet = mk_bnet(dag,node_sizes,'discrete',discrete,'names',labels); - -%bnet.dag - -checkDiscreteNodes(bnet,cases); - -% standardize continuous data to have a mean = 0 and std = 1 -if (std_flag) - [cases] = standardizeData(labels,node_sizes,cases); -end - - -end -% end of readInput.m diff --git a/sourcecodes/parameter_learning/code_backup/readInputData.m b/sourcecodes/parameter_learning/code_backup/readInputData.m deleted file mode 100644 index 706e2751..00000000 --- a/sourcecodes/parameter_learning/code_backup/readInputData.m +++ /dev/null @@ -1,75 +0,0 @@ -function [ labels , node_sizes, cases, data] = readInputData( dfile , nnodes ) - % readColData reads data from a file containing data in columns - % that have text titles, and possibly other header text - % - % Input: - % dfile = name of the file containing the data.(required) - % nnodes = number of columns in the data file. (required) - % - % Function assumes the following format for the input file: - % 1) First line has labels for each of the nodes. There cannot - % be spaces in any node label. - % 2) The next line is the "node_sizes" of the nodes. If the - % nodes are discrete, this number will be equal to the number - % of states. If the nodes are continuous, they should be - % equal to 1. The function assumes that any nodes with - % node_size = 1 is continuous. - % 3) The rest of the file is numeric data. The data in the input - % data has the number of columns equal to the number of - % nodes in the network and the number of rows equal to - % the number of samples. - % - % - % Output: - % labels = cell array with node (column) labels. - % node_sizes = vector with the size of each node - % cases = cell array with the data. The cases array is transposed - % in comparison with the input data to agree with the format of - % cell data used in BNT. - -% open file for input, include error handling -fin = fopen(dfile,'r'); -if fin < 0 - error(['Could not open ',dfile,' for input']); -end - -% Read in first line to get the node labels. -labels = cell(1,nnodes); -buffer = fgetl(fin); %get header line as a string -for j=1:nnodes - [next,buffer] = strtok(buffer); - labels{j} = next; -end - -% Read in the data. Use the vetorized fscanf function to load all -% numerical values into one vector. Then reshape this vector into a -% matrix. - -data = fscanf(fin,'%f'); % Load the numerical values into one long vector - - - - -nd = length(data); % total number of data points -nr = nd/nnodes; % number of rows; check (next statement) to make sure -if nr ~= round(nd/nnodes) - fprintf(1,'\ndata: nrow = %f\tncol = %d\n',nr,nnodes); - fprintf(1,'number of data points = %d does not equal nrow*ncol\n',nd); - error('data is not rectangular') -end - -data = reshape(data,nnodes,nr)'; % have to transpose the reshaped array - - -node_sizes = zeros(1,nnodes); -for j = 1:nnodes - node_sizes(j) = data(1,j); -end - -nr = nr - 1; -data(1,:) = []; -cases = cell(nnodes,nr); -cases(:,:) = num2cell(data'); - -end -% end of readInputData.m \ No newline at end of file diff --git a/sourcecodes/parameter_learning/code_backup/readInputStructure.m b/sourcecodes/parameter_learning/code_backup/readInputStructure.m deleted file mode 100644 index 6b3cbece..00000000 --- a/sourcecodes/parameter_learning/code_backup/readInputStructure.m +++ /dev/null @@ -1,72 +0,0 @@ -function [ dag ] = readInputStructure( sfile, labels ) -%readInputStructure Read in file with structure information - % - %Input: - % sfile = name of the file containing the data (required) - % labels = cell array with node labels. (required) - % nnodes = number of columns in the data file. (required) - % - % Function assumes the following format for the structure input file: - % 1) The first line has node labels. These must be the same as - % in the input data file. They cannot contain spaces. - % 2) The remainder of the file contains the structure of the dag. - % The structure of a graph is a N-by-N matrix, where N is the - % number of nodes. There are 1's in the matrix representing - % parent-child relationships. For each 1, the row indicates - % the parent and the column indicates the child. For - % example, a 1 in the (2,3) position of the matrix indicates - % that there is an arc pointing from node 2 to node 3. - % - % - % Output: - % dag = matrix with the structure. -% -% Read in first line of the structure file -% open file for input, include error handling -fin = fopen(sfile,'r'); -if fin < 0 - error(['Could not open ',sfile,' for input']); -end - -nnodes = size(labels,2); -% Read in first line to get the node labels. -labels_test = cell(1,nnodes); -buffer = fgetl(fin); %get header line as a string -for j=1:nnodes - [next,buffer] = strtok(buffer); - labels_test{j} = next; -end - -for j=1:nnodes - if labels_test{j} ~= labels{j} - fprintf(['Label of node ',j,' is not consistent in input and structure files']) - end -end - -data = fscanf(fin,'%f'); - -nd = length(data); % total number of data points -nr = nd/nnodes; % number of rows; check (next statement) to make sure -if nr ~= round(nd/nnodes) - fprintf(1,'\ndata: nrow = %f\tncol = %d\n',nr,nnodes); - fprintf(1,'number of data points = %d does not equal nrow*ncol\n',nd); - error('Structure file does not have the correct dimensions (1)') -end -% check to make sure that structure is square -if nr ~= nnodes - error('Structure file does not have the correct dimensions (2)') -end - -data = reshape(data,nnodes,nr)'; % have to transpose the reshaped array - - -dag = zeros(nnodes,nnodes); -for i = 1:size(data,1) - for j = 1:size(data,2) - dag(i,j) = data(i,j); - end -end - - -end -% end of readInputStructure.m diff --git a/sourcecodes/parameter_learning/code_backup/runBN_initial.m b/sourcecodes/parameter_learning/code_backup/runBN_initial.m deleted file mode 100644 index 0deff1b5..00000000 --- a/sourcecodes/parameter_learning/code_backup/runBN_initial.m +++ /dev/null @@ -1,57 +0,0 @@ -function runBN_initial(pre) -sfile=strcat(pre,'structure_input.txt'); -dfile=strcat(pre,'continuous_input.txt'); - -nnodefile=strcat(pre,'nnode.txt'); -fnnode = fopen(nnodefile,'r'); -nnodes = fscanf(fnnode,'%d'); - - -mapfilename=strcat(pre,'mapdata.txt'); -mapvalfilename=strcat(pre,'map.txt'); - -mapfile = fopen(mapfilename,'w'); - -mapval = fopen(mapvalfilename,'w'); - - -Std_flag=true; -[labels,cases,bnet,node_sizes,data,labelsold]=readInput(dfile,sfile,nnodes,Std_flag); -s=std(data,0,1); -m=mean(data); - -for i=1:nnodes - fprintf(mapval,'%s\t%f\t%f\n',labelsold{i},s(i),m(i)); -end - -fprintf(mapfile,'%s',labels{1}); -for i=2:nnodes - fprintf(mapfile,'\t%s',labels{i}); -end -fprintf(mapfile,'\n'); -fclose(mapval); -fclose(mapfile); - -%Need to rearrange the means and stdevs to match the new labeling. -means = cell(1,nnodes); -stdevs = cell(1,nnodes); -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labels{i},labelsold{j}) - means{i} = m(j); - stdevs{i} = s(j); - break - end - end -end - - -[bnet]=parameterLearning(bnet,cases); - -filename=strcat(pre,'net_figure.txt'); - -drawFigure(nnodes,bnet,labels,filename,cases,stdevs,means); - -writeParameters(pre,nnodes,bnet,labels,cases,labelsold,s,m); - -end diff --git a/sourcecodes/parameter_learning/code_backup/standardizeData.m b/sourcecodes/parameter_learning/code_backup/standardizeData.m deleted file mode 100644 index db5e04c7..00000000 --- a/sourcecodes/parameter_learning/code_backup/standardizeData.m +++ /dev/null @@ -1,25 +0,0 @@ -function [ cases ] = standardizeData( labels, node_sizes, cases ) -%standardizeData standardizes continuous nodes so they have a mean = 0 -% and standard deviation = 1 - - -nnodes = size(labels,2); - -%fprintf(['Standardizing data for continuous nodes\n']) -for i = 1:nnodes - if node_sizes(i) == 1 - temp = cell2num(cases(i,:)); - [temp] = standardize(temp); - cases(i,:) = num2cell(temp); - end -end - -%write standardized data to file -%fprintf(['Standardized data is written to file standardized_data.txt\n']) -%fout = 'standardized_data.txt'; -%txt = sprintf([repmat('%s\t',1,size(labels,2))],labels{:}); -%dlmwrite(fout,txt,''); -%dlmwrite(fout,cell2num(cases'),'-append','delimiter','\t'); - -end - diff --git a/sourcecodes/parameter_learning/code_backup/writeParameters.m b/sourcecodes/parameter_learning/code_backup/writeParameters.m deleted file mode 100644 index 0790a8e2..00000000 --- a/sourcecodes/parameter_learning/code_backup/writeParameters.m +++ /dev/null @@ -1,106 +0,0 @@ -function [] = writeParameters(pre,nnodes,bnet,labels,cases,labelsold,s,m) -%Writes a file that contains the parameters of the network with no evidence. - - -%%Get the types of the nodes. -typefile = strcat(pre,'type.txt'); -ftype = fopen(typefile,'r'); -types = cell(1,nnodes); -buffer = fgetl(ftype); -buffer = fgetl(ftype); -for j = 1:nnodes - [next,buffer] = strtok(buffer); - types{j} = uint16(str2num(next)); -end - -max_states = 0; -disc_nodes = 0; -for j = 1:nnodes - if types{j} > max_states - max_states = types{j}; - end - if types{j} > 1 - disc_nodes = disc_nodes + 1; - end -end - -%Add 1 to max_states to account for node name -max_states = max_states + 1; - -%%Get mapping of discrete levels. -levelfile = strcat(pre,'nlevels.txt'); -flevels = fopen(levelfile,'r'); -levels = cell(disc_nodes,max_states); -ndisc_nodes = 0; -for i=1:disc_nodes - ndisc_nodes = ndisc_nodes + 1; - buffer = fgetl(flevels); - for j = 1:max_states - [next,buffer] = strtok(buffer); - if j == 1 - levels{i,j} = next; - else -% levels{i,j} = uint16(str2num(next)); - levels{i,j} = next; - end - if length(buffer) < 1 - break - end - end -end - - -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); -[engine,loglik] = enter_evidence(engine,evidence); - -%Open output file. -filename = strcat(pre,'parameters.txt'); -fileID = fopen(filename,'w'); - -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labelsold{i},labels{j}); - nodeid = j; - break - end - end - predict = marginal_nodes(engine,nodeid); - %%%Print the name of the node - fprintf(fileID,'%s\n',labels{nodeid}); - %%%Print the type of node - if bnet.node_sizes(nodeid) == 1; - line = 'Continuous node\n'; - fprintf(fileID,line); - %%% 'i' in the line below is correct: m and s are had original node labeling - adj_mu = predict.mu*s(i)+m(i); - adj_sigma = s(i)*predict.Sigma; - fprintf(fileID,'%6.4f\t%6.4f\n\n',adj_mu,adj_sigma); - else - line = 'Discrete node with %i states\n'; - fprintf(fileID,line,bnet.node_sizes(nodeid)); - %line = 'Probability of each state\n'; - %fprintf(fileID,line); - nodeid2 = 0; - for k = 1:ndisc_nodes, - if strcmp(levels{k,1},labels{nodeid}), - nodeid2 = k; - break - end - end - for j = 1:bnet.node_sizes(nodeid), - %%%For discrete nodes, the state and the percent of that state -% fprintf(fileID,'%i\t%6.4f\n',levels{nodeid2,j+1},predict.T(j)); - fprintf(fileID,'%s\t%6.4f\n',levels{nodeid2,j+1},predict.T(j)); - end; - fprintf(fileID,'\n') - - end -end - - - -fclose(fileID); - -end - diff --git a/sourcecodes/parameter_learning/code_backup/writeParameters_ev.m b/sourcecodes/parameter_learning/code_backup/writeParameters_ev.m deleted file mode 100644 index fc24e2e5..00000000 --- a/sourcecodes/parameter_learning/code_backup/writeParameters_ev.m +++ /dev/null @@ -1,151 +0,0 @@ -function [] = writeParameters_ev(pre,bnet,nnodes,labels,cases,stdevs,means,selectvar,selectdata) -%Writes a file that contains the parameters of the network after entering evidence. - -%Read in original node labels to get node IDs. -infile = strcat(pre,'continuous_input.txt'); -fin = fopen(infile,'r'); -labelsold = cell(1,nnodes); -buffer = fgetl(fin); -for j = 1:nnodes - [next,buffer] = strtok(buffer); - labelsold{j} = next; -end -fclose(fin); - - -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); - -m = size(selectvar,1); - -%%Get the types of the nodes. -typefile = strcat(pre,'type.txt'); -ftype = fopen(typefile,'r'); -types = cell(1,nnodes); -buffer = fgetl(ftype); -buffer = fgetl(ftype); -for j = 1:nnodes - [next,buffer] = strtok(buffer); - types{j} = uint16(str2num(next)); -end - -max_states = 0; -disc_nodes = 0; -for j = 1:nnodes - if types{j} > max_states - max_states = types{j}; - end - if types{j} > 1 - disc_nodes = disc_nodes + 1; - end -end - -%Add 1 to max_states to account for node name -max_states = max_states + 1; - -%%Get mapping of discrete levels. -levelfile = strcat(pre,'nlevels.txt'); -flevels = fopen(levelfile,'r'); -levels = cell(disc_nodes,max_states); -ndisc_nodes = 0; -for i=1:disc_nodes - ndisc_nodes = ndisc_nodes + 1; -buffer = fgetl(flevels); -for j = 1:max_states - [next,buffer] = strtok(buffer); - if j == 1 - levels{i,j} = next; - else -% levels{i,j} = uint16(str2num(next)); - levels{i,j} = next; - end - if length(buffer) < 1 - break - end - end -end - - -ev_dat = zeros(1,nnodes); -for i = 1:m, - di=selectvar(i,1); - ev_dat(di)=selectdata(i,1); -%Need to standardize evidence for continuous nodes. - if bnet.node_sizes(di) == 1, - ev_dat(di) = (ev_dat(di) - means{di})/stdevs{di}; - end - evidence{di} = ev_dat(di); -end - -[engine,loglik]=enter_evidence(engine,evidence); - -%Open output file. -filename = strcat(pre,'parameters_ev.txt'); -fileID = fopen(filename,'w'); - -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labelsold{i},labels{j}); - nodeid = j; - break - end - end - %%%Print the name of the node - fprintf(fileID,'%s\n',labels{nodeid}); - predict = marginal_nodes(engine,nodeid); - if isempty(evidence{nodeid}) - %%%Print the type of node - if bnet.node_sizes(nodeid) == 1; - line = 'Continuous parameters considering evidence:\n'; - fprintf(fileID,line); - %line = 'Mean and standard deviation of Gaussian distribution\n'; - %fprintf(fileID,line); - adj_mu = predict.mu*stdevs{nodeid}+means{nodeid}; - adj_sigma = stdevs{nodeid}*predict.Sigma; - fprintf(fileID,'%6.4f\t%6.4f\n\n',adj_mu,adj_sigma); - else - line = 'Probability of states considering evidence:\n'; - fprintf(fileID,line); - nodeid2 = 0; - for k = 1:ndisc_nodes, - if strcmp(levels{k,1},labels{nodeid}), - nodeid2 = k; - break - end - end - for j = 1:bnet.node_sizes(nodeid), - %%%For discrete nodes, the state and the percent of that state -% fprintf(fileID,'%i\t%6.4f\n',levels{nodeid2,j+1},predict.T(j)); - fprintf(fileID,'%s\t%6.4f\n',levels{nodeid2,j+1},predict.T(j)); - end; - fprintf(fileID,'\n') - end - else - if bnet.node_sizes(nodeid) == 1; - line = 'Evidence was observed for this node. The observed value was:\n'; - fprintf(fileID,line); - adj_mu = ev_dat(nodeid)*stdevs{nodeid}+means{nodeid}; - fprintf(fileID,'%6.4f\n\n',adj_mu); - else - nodeid2 = 0; - for k = 1:ndisc_nodes, - if strcmp(levels{k,1},labels{nodeid}), - nodeid2 = k; - break - end - end - line = 'Evidence was observed for this node. The observed state was:\n'; - fprintf(fileID,line); - state_ev = uint16(ev_dat(nodeid)); -% fprintf(fileID,'%i\n\n',levels{nodeid2,state_ev+1}); - fprintf(fileID,'%s\n\n',levels{nodeid2,state_ev+1}); - end - end -end - - - -fclose(fileID); - -end - diff --git a/sourcecodes/parameter_learning/code_backup/writeParameters_int.m b/sourcecodes/parameter_learning/code_backup/writeParameters_int.m deleted file mode 100644 index ed92d593..00000000 --- a/sourcecodes/parameter_learning/code_backup/writeParameters_int.m +++ /dev/null @@ -1,186 +0,0 @@ -function [] = writeParameters_int(pre,bnet,nnodes,labels,cases,stdevs,means,selectvar,selectdata) -%Writes a file that contains the parameters of the network after intervention. - - -%First read input file to get node labels to get node IDs. -infile = strcat(pre,'continuous_input.txt'); -fin = fopen(infile,'r'); -labelsold = cell(1,nnodes); -buffer = fgetl(fin); -for j = 1:nnodes - [next,buffer] = strtok(buffer); - labelsold{j} = next; -end - -evidence = cell(1,nnodes); -engine = jtree_inf_engine(bnet); - -m = size(selectvar,1); - -%%Get the types of the nodes. -typefile = strcat(pre,'type.txt'); -ftype = fopen(typefile,'r'); -types = cell(1,nnodes); -buffer = fgetl(ftype); -buffer = fgetl(ftype); -for j = 1:nnodes - [next,buffer] = strtok(buffer); - types{j} = uint16(str2num(next)); -end - -max_states = 0; -disc_nodes = 0; -for j = 1:nnodes - if types{j} > max_states - max_states = types{j}; - end - if types{j} > 1 - disc_nodes = disc_nodes + 1; - end -end - -%Add 1 to max_states to account for node name -max_states = max_states + 1; - -%%Get mapping of discrete levels. -levelfile = strcat(pre,'nlevels.txt'); -flevels = fopen(levelfile,'r'); -levels = cell(disc_nodes,max_states); -ndisc_nodes = 0; -for i=1:disc_nodes - ndisc_nodes = ndisc_nodes + 1; -buffer = fgetl(flevels); -for j = 1:max_states - [next,buffer] = strtok(buffer); - if j == 1 - levels{i,j} = next; - else -% levels{i,j} = uint16(str2num(next)); - levels{i,j} = next; - end - if length(buffer) < 1 - break - end - end -end - - -ev_dat = zeros(1,nnodes); -for i = 1:m, - di=selectvar(i,1); - ev_dat(di)=selectdata(i,1); -%Need to standardize evidence for continuous nodes. - if bnet.node_sizes(di) == 1, - ev_dat(di) = (ev_dat(di) - means{di})/stdevs{di}; - end - evidence{di} = ev_dat(di); -end - -[engine,loglik]=enter_evidence(engine,evidence); - -%Get list of nodes that are children, grandchildren, etc. of intervened nodes -%int_nodes contains the list of these children nodes -int_nodes = zeros(1,nnodes); -%new_nodes is just a temporary array to know when to keep looking -new_nodes = zeros(1,nnodes); -for i = 1:nnodes - if !isempty(evidence{i}); - new_nodes(i) = 1; - int_nodes(i) = 1; - end -end -while sum(new_nodes) != 0 - new_nodes_old = new_nodes; - new_nodes = zeros(1,nnodes); - for i = 1:nnodes - if new_nodes_old(i) == 1 - for j = 1:nnodes - if int_nodes(j) == 0 - if bnet.dag(i,j) == 1, - new_nodes(j) = 1; - end - end - end - end - end - for i = 1:nnodes - if new_nodes(i) == 1; - int_nodes(i) = 1; - end - end -end - - -%Open output file. -filename = strcat(pre,'parameters_ev.txt'); -fileID = fopen(filename,'w'); - -for i = 1:nnodes - for j = 1:nnodes - if strcmp(labelsold{i},labels{j}); - nodeid = j; - break - end - end - %check to see if this is a node impacted by intervention - if int_nodes(nodeid) == 1 - %%%Print the name of the node - fprintf(fileID,'%s\n',labels{nodeid}); - predict = marginal_nodes(engine,nodeid); - if isempty(evidence{nodeid}) - %%%Print the type of node - if bnet.node_sizes(nodeid) == 1; - line = 'Continuous parameters considering intervention:\n'; - fprintf(fileID,line); - %line = 'Mean and standard deviation of Gaussian distribution\n'; - %fprintf(fileID,line); - adj_mu = predict.mu*stdevs{nodeid}+means{nodeid}; - adj_sigma = stdevs{nodeid}*predict.Sigma; - fprintf(fileID,'%6.4f\t%6.4f\n\n',adj_mu,adj_sigma); - else - line = 'Probability of states considering intervention:\n'; - fprintf(fileID,line); - nodeid2 = 0; - for k = 1:ndisc_nodes, - if strcmp(levels{k,1},labels{nodeid}), - nodeid2 = k; - break - end - end - for j = 1:bnet.node_sizes(nodeid), - %%%For discrete nodes, the state and the percent of that state -% fprintf(fileID,'%i\t%6.4f\n',levels{nodeid2,j+1},predict.T(j)); - fprintf(fileID,'%s\t%6.4f\n',levels{nodeid2,j+1},predict.T(j)); - end; - fprintf(fileID,'\n') - end - else - if bnet.node_sizes(nodeid) == 1; - line = 'Intervention on this node assigned the following value:\n'; - fprintf(fileID,line); - adj_mu = ev_dat(nodeid)*stdevs{nodeid}+means{nodeid}; - fprintf(fileID,'%6.4f\n\n',adj_mu); - else - nodeid2 = 0; - for k = 1:ndisc_nodes, - if strcmp(levels{k,1},labels{nodeid}), - nodeid2 = k; - break - end - end - line = 'Intervention on this node assigned the following state:\n'; - fprintf(fileID,line); - state_ev = uint16(ev_dat(nodeid)); -% fprintf(fileID,'%i\n\n',levels{nodeid2,state_ev+1}); - fprintf(fileID,'%s\n\n',levels{nodeid2,state_ev+1}); - end - end - end -end - - - -fclose(fileID); - -end - diff --git a/sourcecodes/parameter_learning/getParams.m b/sourcecodes/parameter_learning/getParams.m deleted file mode 100644 index 31f84ffb..00000000 --- a/sourcecodes/parameter_learning/getParams.m +++ /dev/null @@ -1,22 +0,0 @@ -function [ bnet ] = getParams( bnet, cases ) -%getParams Code to initialize CPT and do parameter learning. -%This will be very basic for now. I can add more options later. - -dnodes = bnet.dnodes; -cnodes = bnet.cnodes; -nnodes = size(dnodes,2)+size(cnodes,2); - -%make dnodes tabular_CPT -for i = 1:size(dnodes,2) - bnet.CPD{dnodes(i)} = tabular_CPD(bnet,dnodes(i)); -end - -for i = 1:size(cnodes,2) - bnet.CPD{cnodes(i)} = gaussian_CPD(bnet,cnodes(i)); -end - -bnet = learn_params(bnet,cases); - - -end - diff --git a/sourcecodes/parameter_learning/kfoldCrossValid.m b/sourcecodes/parameter_learning/kfoldCrossValid.m index 6306c511..02f34866 100644 --- a/sourcecodes/parameter_learning/kfoldCrossValid.m +++ b/sourcecodes/parameter_learning/kfoldCrossValid.m @@ -149,6 +149,9 @@ for i = 1:ncases fprintf(fileID,'%6.4f\t%6.4f\n',kfoldPredictions(i,:)); end +fflush(fileID); +fclose(fileID); + end @@ -283,6 +286,9 @@ for i = 1:ncases fprintf(fileID,'%6.4f\n',kfoldPredictions(i,end)); end +fflush(fileID); +fclose(fileID); + end diff --git a/sourcecodes/parameter_learning/looCrossValid.m b/sourcecodes/parameter_learning/looCrossValid.m index 67b04409..840e486e 100644 --- a/sourcecodes/parameter_learning/looCrossValid.m +++ b/sourcecodes/parameter_learning/looCrossValid.m @@ -126,6 +126,10 @@ for i = 1:ncases fprintf(fileID,'%6.4f\t%6.4f\n',loopredictions(i,:)); end +fflush(fileID); +fclose(fileID); + + end @@ -247,4 +251,7 @@ for i = 1:ncases fprintf(fileID,'%6.4f\n',loopredictions(i,end)); end +fflush(fileID); +fclose(fileID); + end diff --git a/sourcecodes/parameter_learning/modifyEdges.m b/sourcecodes/parameter_learning/modifyEdges.m new file mode 100644 index 00000000..2b336710 --- /dev/null +++ b/sourcecodes/parameter_learning/modifyEdges.m @@ -0,0 +1,133 @@ +function [ ] = modifyEdges( pre_old, pre_new ) + % This function will allow users to add or delete edges from the network. + % + % Input: + % 1) pre_oldstructure_input.txt + % Original structure file. + % 2) pre_olddel_edge.txt + % A list of the edges that should be deleted. + % 3) pre_oldadd_edge.txt + % A list of the edges that should be added. + % + % Output: + % pre_newstructure_input.txt-- structure file with edges added/deleted. + % + + +% open file for input, include error handling +dfile=strcat(pre_old,'structure_input.txt'); + +fin = fopen(dfile,'r'); +if fin < 0 + error(['Could not open ',dfile,' for input']); +end + +% Read in first line to get the number of nodes and the node labels. +buffer = fgetl(fin); %get header line as a string +nnodes = numel(strfind(buffer,"\t")); +labels = cell(1,nnodes); +for j=1:nnodes + [next,buffer] = strtok(buffer); + labels{j} = next; +end + +% Read in the edges +edges = cell(nnodes,nnodes); +for i = 1:nnodes + buffer = fgetl(fin); + for j = 1:nnodes + [next,buffer] = strtok(buffer); + edges{i,j} = next; + end +end + + +% open file with edges to be deleted +dedgefile=strcat(pre_old,'del_edge.txt'); +fin2 = fopen(dedgefile,'r'); +ndel=fskipl(fin2,Inf) - 1; +frewind(fin2); + +delfrom = cell(1,ndel); +delto = cell(1,ndel); + +buffer = fgetl(fin2); %get header line +for j=1:ndel + buffer = fgetl(fin2); %get line with actual variables + [next,buffer] = strtok(buffer); + delfrom{j} = next; + [next,buffer] = strtok(buffer); + delto{j} = next; +end + +%get index of edges to delete +idel_from = []; +idel_to = []; +for j = 1:ndel + for k = 1:nnodes + if strcmp(labels{k},delfrom{j}) + idel_from = [idel_from;k]; + endif + if strcmp(labels{k},delto{j}) + idel_to = [idel_to;k]; + endif + end +end + +for i = 1:ndel + edges(idel_from(i),idel_to(i)) = "0"; +end + +fclose(fin2); + +% open file with edges to be added +aedgefile=strcat(pre_old,'add_edge.txt'); +fin3 = fopen(aedgefile,'r'); +nadd=fskipl(fin3,Inf) - 1; +frewind(fin3); + +addfrom = cell(1,nadd); +addto = cell(1,nadd); + +buffer = fgetl(fin3); %get header line +for j=1:nadd + buffer = fgetl(fin3); %get line with actual variables + [next,buffer] = strtok(buffer); + addfrom{j} = next; + [next,buffer] = strtok(buffer); + addto{j} = next; +end + +%get index of edges to added +iadd_from = []; +iadd_to = []; +for j = 1:nadd + for k = 1:nnodes + if strcmp(labels{k},addfrom{j}) + iadd_from = [iadd_from;k]; + endif + if strcmp(labels{k},addto{j}) + iadd_to = [iadd_to;k]; + endif + end +end + +for i = 1:nadd + edges(iadd_from(i),iadd_to(i)) = "1"; +end + + + + + +outfile = strcat(pre_new,'structure_input.txt'); +fout = fopen(outfile,'w'); +fprintf(fout,'%s\t',labels{1:end-1}); +fprintf(fout,'%s\n',labels{end}); +for i = 1:nnodes + fprintf(fout,'%s\t',edges{i,1:end-1}); + fprintf(fout,'%s\n',edges{i,end}); +end +fclose(fout); + +end diff --git a/sourcecodes/parameter_learning/prepareInput.m b/sourcecodes/parameter_learning/prepareInput.m index 5268f872..3147d54e 100644 --- a/sourcecodes/parameter_learning/prepareInput.m +++ b/sourcecodes/parameter_learning/prepareInput.m @@ -1,4 +1,5 @@ function [ ] = prepareInput( pre ) + % Jan. 2019: Modifying to allow for missing data. % % This function takes files that are uploaded to BNW and creates output % files that can be used for structure and parameter learning. @@ -74,6 +75,11 @@ for i = 1:ncases end end +% Remove all rows that have missing data from data file +remove_count = sum(any(strcmp(data,"NA"),2)); +data(any(strcmp(data,"NA"),2),:)=[]; +ncases = ncases - remove_count; + % Determine whether or not the nodes are continuous or discrete. % First, treat them as all discrete and get the states and number of stats(levels). levels = cell(1,nnodes); @@ -242,6 +248,7 @@ dout = fopen(descfile,'w'); fprintf(dout,['As loaded, the input file had the following properties:\n\n']); dout = fopen(descfile,'a'); fprintf(dout,'There are %i variables and %i cases(rows).\n',size(labels,2),ncases); +fprintf(dout,'%i cases(rows) have been removed because they contained NA (missing data).\n',remove_count); fprintf(dout,'The variable names are:\n'); fprintf(dout,'%s\t',labels{1:end-1}); fprintf(dout,'%s\n\n',labels{end}); diff --git a/sourcecodes/parameter_learning/removeNodes.m b/sourcecodes/parameter_learning/removeNodes.m new file mode 100644 index 00000000..8740d999 --- /dev/null +++ b/sourcecodes/parameter_learning/removeNodes.m @@ -0,0 +1,94 @@ +function [ ] = removeNodes( pre_old, pre_new ) + % This function will allow users to delete variables from uploaded input file. + % For example, if an input file contains 20 variables, but the user is + % only interested in using 10 of these variables in a particular model, + % they can use this function to delete the variable. + % + % + % Input: + % 1) pre_oldcontinuous_input_orig.txt + % This is the original input file that is uploaded to BNW. + % It is directly written out by the BNW php code with no modification. + % The file format is a header line containing the variable names + % followed by the data, with each case in a row. + % 2) pre_olddel_var.txt + % This is a list of the names of the variables that should be delete. + % + % Output: + % pre_newcontinuous_input_orig.txt-- input file with variables deleted. + % + + +% open file for input, include error handling +dfile=strcat(pre_old,'continuous_input_orig.txt'); + +fin = fopen(dfile,'r'); +if fin < 0 + error(['Could not open ',dfile,' for input']); +end + +% Get the number of cases (the number of rows in the file excluding the header) +ncases = fskipl(fin,Inf) - 1; + +frewind(fin); + +% Read in first line to get the number of nodes and the node labels. +buffer = fgetl(fin); %get header line as a string +nnodes = numel(strfind(buffer,"\t")) + 1; +labels = cell(1,nnodes); +for j=1:nnodes + [next,buffer] = strtok(buffer); + labels{j} = next; +end + +% Read in the data +data = cell(ncases,nnodes); +for i = 1:ncases + buffer = fgetl(fin); + for j = 1:nnodes + [next,buffer] = strtok(buffer); + data{i,j} = next; + end +end + + +% open file for input, include error handling +dvarfile=strcat(pre_old,'del_var.txt'); +fin2 = fopen(dvarfile,'r'); +if fin2 < 0 + dellabels = {}; + ndel = 0; +else + buffer = fgetl(fin2); %get header line as a string + ndel = numel(strfind(buffer," ")) + 1; + dellabels = cell(1,ndel); + for j=1:ndel + [next,buffer] = strtok(buffer); + dellabels{j} = next; + end +end + +%get index of variables to delete +delindex = []; +for j=1:nnodes + for k = 1:ndel + if strcmp(labels{j},dellabels{k}) + delindex = [delindex;j]; + endif + end +end + +labels(:,[delindex])=[]; +data(:,[delindex])=[]; + +outfile = strcat(pre_new,'continuous_input_orig.txt'); +fout = fopen(outfile,'w'); +fprintf(fout,'%s\t',labels{1:end-1}); +fprintf(fout,'%s\n',labels{end}); +for i = 1:ncases + fprintf(fout,'%s\t',data{i,1:end-1}); + fprintf(fout,'%s\n',data{i,end}); +end +fclose(fout); + +end diff --git a/sourcecodes/parameter_learning/testSetPredictions.m b/sourcecodes/parameter_learning/testSetPredictions.m index 0fff197d..23a50868 100644 --- a/sourcecodes/parameter_learning/testSetPredictions.m +++ b/sourcecodes/parameter_learning/testSetPredictions.m @@ -273,6 +273,8 @@ for i = 1:ntestcases fprintf(fileID,'%6.4f\t%6.4f\n',predictions(i,:)); end +fflush(fileID); +fclose(fileID); end @@ -353,7 +355,8 @@ for i = 1:ntestcases fprintf(fileID,'%6.4f\n',predictions(i,end)); end - +fflush(fileID); +fclose(fileID); diff --git a/sourcecodes/remove_variables.php~ b/sourcecodes/remove_variables.php~ deleted file mode 100644 index e4cdd91e..00000000 --- a/sourcecodes/remove_variables.php~ +++ /dev/null @@ -1,977 +0,0 @@ -<?php - -///////This code will allow users to group variables in tier. getcombineDescription() function combined all data and take you to "tier_description_processing_gom.php" for preparation of ban and whitelist ////////// - -include("header_new.inc"); -include("runtime_check.php"); -include("input_validate.php"); -$keyval=$_GET["My_key"]; - -$dir="./data/"; - -$type_n=array(); - -//Get number of tier data and key value for changes in number of tier - -if(isset($_POST["nm_tier"])) -{ - $type_n=explode("|",$_POST["nm_tier"]); -} -else if(isset($_POST["nm_parent"])) -{ - $type_n=explode("|",$_POST["nm_parent"]); -} -else if(isset($_POST["nm_k"])) -{ - $type_n=explode("|",$_POST["nm_k"]); -} -else if(isset($_POST["nm_thr"])) -{ - $type_n=explode("|",$_POST["nm_thr"]); -} - -$parent_number=trim($type_n[0]); -$k_number=trim($type_n[1]); -$tier_number=trim($type_n[2]); -$structure_thr=trim($type_n[3]); - - -if($keyval=="") - $keyval=$type_n[4]; - - -if($parent_number=="") -{ - $parent_number=4; -} - -if($k_number=="") -{ - $k_number=1; -} - -if($tier_number=="") -{ - $tier_number=3; -} -if($structure_thr=="") -{ - $structure_thr=0.5; -} - - - -$nf=$dir.$keyval."nnode.txt"; -$node=trim(file_get_contents("$nf")); -$maxplist=$node-1; - -//print default number of parents -$pfile=$dir.$keyval."parent.txt"; -$parentf=fopen($pfile,"w"); -fwrite($parentf,"$parent_number\n"); - -//print default number of k for model averaging -$kfile=$dir.$keyval."k.txt"; -$kf=fopen($kfile,"w"); -fwrite($kf,"$k_number\n"); - -//print model averaging threshold -$thrfile=$dir.$keyval."thr.txt"; -$kf=fopen($thrfile,"w"); -fwrite($kf,"$structure_thr\n"); - -//////////////////Check execution time////////////////////////////////////////////// -$keyval=valid_keyval($keyval); -$runtime=exe_time($keyval,$parent_number,$k_number); - -//print("Runtime is $runtime"); - -?> -<!-- Site navigation menu --> -<ul class="navbar2"> - <li><p onClick="getcombineDescriptionDefault(ntiers,'ban_from','ban_to','white_from','white_to','<?php print($keyval);?>')"><a href="javascript:void(0)" >Remove variables and continue</a></p> - <li><a href="javascript:void(0);" -NAME="InputCheck" title="InputCheck" - onClick=window.open("input_check.php?My_key=<?php print($keyval);?>","Ratting","width=950,height=270,0,status=0,");>View uploaded variables and data</a> -</ul> -<ul class="navbar"> - <li><a href="help.php#constraint_interface" target="_blank">How to use this page</a> - <li><a href="help.php" target="_blank">Help</a> - <li><a href="home.php">Home</a> - -</ul> - -<div id="outernew"> - -<?php - - -if(isset($HTTP_POST_VARS["bantext"])) -{ - $ban_search=$HTTP_POST_VARS["searchkey"]; -} - -if(isset($HTTP_POST_VARS["whitetext"])) -{ - $white_search=$HTTP_POST_VARS["searchkey"]; -} - -?> - -<!DOCTYPE html> -<html> -<head> -<title>Drag and Drop test</title> -<style type="text/css"> - #nodelist{ - width:200px; - font-weight:bold; - border: 2px solid; - } - #tiers{ - position:absolute; - left:215px; - white-space: nowrap; - min-width: 3000px; - float:top; - } - - #int_box1{ - white-space: nowrap; - min-width: 10000px; - } - #int_box2{ - white-space: nowrap; - min-width: 10000px; - } - #int_box3{ - white-space: nowrap; - min-width: 10000px; - } - #int_box4{ - white-space: nowrap; - min-width: 10000px; - } - - #outer_tier_desc{ - margin-top: 100px; - } - - #outer_tier_desc1{ - width:2000px; - margin-top: 20px; - } - - #outer_box_lists{ - margin-top: 100px; - } - #nodelist2{ - width:200px; - font-weight:bold; - border: 2px solid; - float:left; - } - #ban_outer { - position:absolute; - left: 215px; - width:449px; - border: 2px solid; - background-color:#C0C0C0; - font-weight:bold; - margin-left:15px; - } - #ban_from { - width:200px; - border:2px solid; - margin-left:15px; - } - #ban_to { - width:200px; - border:2px solid; - margin-left:15px; - } - #white_outer { - position:absolute; - left:700px; - width:449px; - border: 2px solid; - background-color:#C0C0C0; - font-weight:bold; - } - #white_from { - width:200px; - border:2px solid; - margin-left:15px; - } - #white_to { - width:200px; - border:2px solid; - margin-left:15px; - } - - - .tier { - width:200px; - border: 2px solid; - font-weight:bold; - float:left; - background-color:#FFFFFF; - margin-left:5px; - display: inline-block; - } - .int { - border: 2px solid; - font-weight:bold; - float:left; - background-color:#FFFFFF; - margin-left:0px; - display: inline-block; - } - .int1 { - border: 2px solid; - background-color:#FFFFFF; - clear: left; - float:left; - margin-left:0px; - display: inline-block; - } - .node1 { - width:150px; - height:30px; - float:left; - margin-left:10px; - margin-top:10px; - border: 2px dashed; - background-color:#C0C0C0; - } - .node2 { - width:150px; - height:30px; - float:left; - margin-left:10px; - margin-top:10px; - border: 2px dashed; - background-color:#EAE822; - } - -</style> - -<script type="text/javascript"> - -//There are three groups of functions here: -//The first group is involved with dragging and dropping nodes -// between different locations. -//The second group is involved with creating the divs that are needed -// based on the number of nodes and number of tiers and organizing -// them on the webpage. -//The third group determines which divs the nodes are located in -// to group the nodes into tiers and make ban and white lists. - - -//Drag and drop functions: -function drag(drop_target, e) { - e.dataTransfer.setData('Text', drop_target.id); - } - -function drop(drop_target, e) { - var id = e.dataTransfer.getData('Text'); - drop_target.appendChild(document.getElementById(id)); - e.preventDefault(); - } - -function dropCopy(ev) { - ev.stopPropagation(); - ev.preventDefault(); - var src = ev.dataTransfer.getData("Text"); - var orig = document.getElementById(src); - var pid = orig.parentNode.id; - var target_id = ev.target.id; - //document.write(pid); - if (pid != target_id){ - var origclone = orig.cloneNode(true); - var newid = src+"a"; - origclone.setAttribute('id',newid); - document.getElementById(pid).appendChild(origclone); - ev.target.appendChild(orig); - } - else { - document.write(pid,target_id); - } - return false; -} - - - - -function loadFunction(nnodes,ntiers) { - makeNodeList(nnodes,'nodelist','tr'); - makeNodes(nnodes,'nodelist'); - makeTiers(nnodes,ntiers); - makeNodes(nnodes,'nodelist2','bw'); - makeTierDesc1(ntiers); - makeTierDesc2(ntiers); - makeTierDesc3(ntiers); - makeTierDesc4(ntiers); - makeBWLists(nnodes); -} - - -//Function to make the NodeList. It is similar to the above function. -function makeNodeList(nnodes,nlist) { - var element1 = document.createElement('div'); - var newheight = 45*nnodes + 40; - newheight = newheight+'px'; - element1.setAttribute('id',nlist); - element1.setAttribute('ondrop','drop(this, event)'); - element1.setAttribute('ondragenter','return false'); - element1.setAttribute('ondragover','return false'); - element1.style.height=(newheight); - element1.innerHTML = "Variables to use<br>"; - document.getElementById('tier_box').appendChild(element1); -} - - -//This is the function that makes the nodes. It is called when the -// page loads. The nodes are placed in the "nodelist" div. -//Will need to mofidy this function to pass it a list of the node -// names. The inner html is what is used in the later functions -// that make the tier list, banlist, and white list. -function makeNodes(nnodes,nlist,suffix) { - -<?php $xyz=1; -$nm=$dir."$keyval"."name.txt"; - -$namelist=file_get_contents("$nm"); -$str_arrname=array(); -$str_arrname=explode("\n",$namelist); -$dataname=array(); -$dataname=explode("\t",$str_arrname[0]); - for ($i=1;$i<=$node;$i++){ -$ii=$i-1; -$npr=trim($dataname[$ii]); -?> - i="<?php print($i);?>"; - var newname = 'node'+i; - var element1 = document.createElement('div'); - element1.setAttribute('draggable','true'); - element1.setAttribute('class','node1'); - element1.setAttribute('ondragstart','drag(this, event)'); - element1.setAttribute('id',newname+suffix); - element1.setAttribute('ondragover','return false'); - element1.innerHTML = "<?php print($npr);?>"; - document.getElementById(nlist).appendChild(element1); - <?php } - ?> - } - - -//Function to make the Tiers. It is similar to the above function. -function makeTiers(nnodes,ntiers) { - //ntiers = 1; - // for (i=1;i<=ntiers;i++){ - i = 1; - //var newname = 'Tier'+i; - var newname = 'Variables to remove'; - var element1 = document.createElement('div'); - //var newpos = i*205; - //newpos = 'left: '+newpos+'px'; - var newheight = nnodes*45 + 40; - newheight = newheight+'px'; - //var newstyle = newpos + newheight; - element1.setAttribute('class','tier'); - element1.setAttribute('id',newname); - element1.setAttribute('ondrop','drop(this, event)'); - element1.setAttribute('ondragenter','return false'); - element1.setAttribute('ondragover','return false'); - //element1.setAttribute('style',newpos); - element1.style.height=(newheight); - element1.innerHTML = newname +"<br>"; - document.getElementById('tiers').appendChild(element1); - // } - var newwidth = ntiers*205 + 20; - newwidth = newwidth+'px'; - document.getElementById('tiers').style.width=newwidth; -} - - - -function makeTierDesc1(ntiers) { - var element1 = document.createElement('div'); - var newheight = '20px'; - var newwidth = '220px'; - element1.setAttribute('id','int_box1_first'); - element1.setAttribute('class','int'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - //element1.innerHTML = "st<br>"; - document.getElementById('int_box1').appendChild(element1); - //for (i=1;i<=ntiers;i++) { - i = 1; - var newname = 'int_box1'+i; - var newheight = '20px'; - var newwidth = '205px'; - //var newwidth = ntiers*65 + 20; - //newwidth = newwidth+'px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "  Tier"+i+"<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box1').appendChild(element1); - //} - -} -function makeTierDesc2(ntiers) { - var element1 = document.createElement('div'); - var newheight = '50px'; - var newwidth = '220px'; - element1.setAttribute('id','int_box2_first'); - element1.setAttribute('class','int1'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - element1.innerHTML = "Are within tier <br>interactions allowed?<br>"; - document.getElementById('int_box2').appendChild(element1); - //for (i=1;i<=ntiers;i++) { - i = 1; - var newname = 'int_box2'+i; - var newheight = '50px'; - var newwidth = '205px'; - //var newwidth = ntiers*65 + 20; - //newwidth = newwidth+'px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box2').appendChild(element1); - //create form to hold yes/no radio boxes - var form1 = document.createElement('form'); - //form1.innerHTML = "Allow edges between nodes in Tier"+i+"?<br>"; - var radio_yes = document.createElement('input'); - radio_yes.setAttribute('type','radio'); - radio_yes.setAttribute('name',"r_yes_no_"+newname); - radio_yes.setAttribute('id',"r_yes_"+newname); - - radio_yes.value = "r_yes_"+newname; - radio_yes.setAttribute('checked','checked'); - form1.appendChild(radio_yes); - var yes_label = document.createElement('label'); - yes_label.setAttribute('for',radio_yes.id); - yes_label.innerHTML = "Yes     "; - form1.appendChild(yes_label); - var radio_no = document.createElement('input'); - radio_no.setAttribute('type','radio'); - radio_no.setAttribute('name',"r_yes_no_"+newname); - radio_no.setAttribute('id',"r_no_"+newname); - radio_no.value = "r_no_"+newname; - form1.appendChild(radio_no); - var no_label = document.createElement('label'); - no_label.setAttribute('for',radio_no.id); - no_label.innerHTML = "No<br>"; - form1.appendChild(no_label); - element1.appendChild(form1); - // alert(radio_yes.value); - // alert(radio_yes.checked); - // alert(radio_no.value); - // alert(radio_no.checked); - //} - -} - -function makeTierDesc3(ntiers) { - var element1 = document.createElement('div'); - var newwidth = '220px'; - var newheight = ntiers*10 + 25; - newheight = newheight + 'px'; - //var newheight = '50px'; - //var newwidth = '250px'; - element1.setAttribute('id','int_box3_first'); - element1.setAttribute('class','int1'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - element1.innerHTML = "Which tiers contain nodes that <br>can be the parents of this tier?<br>"; - document.getElementById('int_box3').appendChild(element1); - //for (i=1;i<=ntiers;i++) { - i = 1; - var newname = 'int_box3'+i; - //var newheight = '50px'; - var newwidth = '205px'; - //newwidth = newwidth+'px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box3').appendChild(element1); - //create form to hold allowed parents - var form2 = document.createElement('form'); - //form2.innerHTML = "Which tiers can be the "+ - // "parents of the nodes in Tier"+i+"?<br>"; - var k = 0; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - k = k + 1; - var pbox = document.createElement('input'); - pbox.setAttribute('type','checkbox'); - // pbox.setAttribute('name',"par_"+i); - pbox.setAttribute('name',"par_"+i+"_"+j); - pbox.setAttribute('id',"par_"+i+"_"+j); - pbox.value = "par_"+i+"_"+j; - if (j<i) { - pbox.setAttribute('checked','checked'); - } - var plabel = document.createElement('label'); - plabel.setAttribute('for',pbox.id); - if (k%2 == 0) { - plabel.innerHTML = "Tier"+j+"  <br>"; - } else { - plabel.innerHTML = "Tier"+j+"  "; - } - form2.appendChild(pbox); - form2.appendChild(plabel); - } - } - element1.appendChild(form2); - //} -} - -function makeTierDesc4(ntiers) { - var element1 = document.createElement('div'); - //var newheight = '50px'; - var newwidth = '220px'; - var newheight = ntiers*10 + 25; - newheight = newheight + 'px'; - element1.setAttribute('id','int_box4_first'); - element1.setAttribute('class','int1'); - element1.style.height=(newheight); - element1.style.width=(newwidth); - element1.innerHTML = "Which tiers contain nodes that<br> can be the children of this tier?<br>"; - document.getElementById('int_box4').appendChild(element1); - //for (i=1;i<=ntiers;i++) { - i = 1; - var newname = 'int_box4'+i; - //var newheight = '50px'; - //var newwidth = ntiers*65 + 20; - var newwidth = '205px'; - var element1 = document.createElement('div'); - element1.setAttribute('id',newname); - element1.setAttribute('class','int'); - element1.innerHTML = "<br>"; - element1.style.height=(newheight); - element1.style.width=(newwidth); - document.getElementById('int_box4').appendChild(element1); - //create form to hold allowed children - var form3 = document.createElement('form'); - //form3.innerHTML = "Nodes in which tiers can be <br>the children of this tier?<br>"; - var k = 0; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - k = k + 1; - var cbox = document.createElement('input'); - cbox.setAttribute('type','checkbox'); - //cbox.setAttribute('name',"child_"+i); - cbox.setAttribute('name',"child_"+i+"_"+j); - cbox.setAttribute('id',"child_"+i+"_"+j); - - cbox.value = "child_"+i+"_"+j; - if (j>i) { - cbox.setAttribute('checked','checked'); - } - var clabel = document.createElement('label'); - clabel.setAttribute('for',cbox.id); - if (k%2 == 0) { - clabel.innerHTML = "Tier"+j+"  <br>"; - } - else - { - clabel.innerHTML = "Tier"+j+"  "; - } - form3.appendChild(cbox); - form3.appendChild(clabel); - } - } - element1.appendChild(form3); - //} -} - - - -//Old function to make section of page that allows for tier description. -//Replaced by the four functions above. -function makeTierDesc(ntiers) { - i = 1; - // for (i=1;i<=ntiers;i++) { - //var i = 2; - var newname = 'desc_tier'+i; - - //create the outer division to hold the other boxes - var out_div = document.createElement('div'); - out_div.setAttribute('id',newname); - if (i==1) { - out_div.innerHTML = "Tier"+i+"<br>"; - } else { - out_div.innerHTML = "<br><br>Tier"+i+"<br>"; - } - document.getElementById('outer_tier_desc').appendChild(out_div); - - //create form to hold yes/no radio boxes - var form1 = document.createElement('form'); - form1.innerHTML = "Allow edges between nodes in Tier"+i+"?<br>"; - var radio_yes = document.createElement('input'); - radio_yes.setAttribute('type','radio'); - radio_yes.setAttribute('name',"r_yes_no_"+newname); - radio_yes.setAttribute('id',"r_yes_"+newname); - - radio_yes.value = "r_yes_"+newname; - radio_yes.setAttribute('checked','checked'); - form1.appendChild(radio_yes); - var yes_label = document.createElement('label'); - yes_label.setAttribute('for',radio_yes.id); - yes_label.innerHTML = "Yes "; - form1.appendChild(yes_label); - var radio_no = document.createElement('input'); - radio_no.setAttribute('type','radio'); - radio_no.setAttribute('name',"r_yes_no_"+newname); - radio_no.setAttribute('id',"r_no_"+newname); - radio_no.value = "r_no_"+newname; - form1.appendChild(radio_no); - var no_label = document.createElement('label'); - no_label.setAttribute('for',radio_no.id); - no_label.innerHTML = "No<br>"; - form1.appendChild(no_label); - out_div.appendChild(form1); - // alert(radio_yes.value); - // alert(radio_yes.checked); - // alert(radio_no.value); - // alert(radio_no.checked); - - - //create form to hold allowed parents - var form2 = document.createElement('form'); - form2.innerHTML = "Which tiers can be the "+ - "parents of the nodes in Tier"+i+"?<br>"; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - var pbox = document.createElement('input'); - pbox.setAttribute('type','checkbox'); - // pbox.setAttribute('name',"par_"+i); - pbox.setAttribute('name',"par_"+i+"_"+j); - pbox.setAttribute('id',"par_"+i+"_"+j); - pbox.value = "par_"+i+"_"+j; - if (j<i) { - pbox.setAttribute('checked','checked'); - } - var plabel = document.createElement('label'); - plabel.setAttribute('for',pbox.id); - plabel.innerHTML = "Tier"+j; - form2.appendChild(pbox); - form2.appendChild(plabel); - } - } - out_div.appendChild(form2); - - // alert(pbox.value); - // alert(pbox.checked); - - - - //create form to hold allowed children - var form3 = document.createElement('form'); - form3.innerHTML = "Which tiers can be the "+ - "children of the nodes in Tier"+i+"?<br>"; - for (j=1;j<=ntiers;j++) { - if (j!=i) { - var cbox = document.createElement('input'); - cbox.setAttribute('type','checkbox'); - //cbox.setAttribute('name',"child_"+i); - cbox.setAttribute('name',"child_"+i+"_"+j); - cbox.setAttribute('id',"child_"+i+"_"+j); - - cbox.value = "child_"+i+"_"+j; - if (j>i) { - cbox.setAttribute('checked','checked'); - } - var clabel = document.createElement('label'); - clabel.setAttribute('for',cbox.id); - clabel.innerHTML = "Tier"+j; - form3.appendChild(cbox); - form3.appendChild(clabel); - } - } - out_div.appendChild(form3); - //var break = document.createElement('div'); - //break.innerHTML = "<br>"; - //out_div.appendChild(break); - //out_div.appendChild(break); - // alert(cbox.value); - // alert(cbox.checked); - - // } -} - -//Function to give the divs for the ban and white lists the correct -// dimensions. -function makeBWLists(nnodes) { - var newheight = 45*nnodes + 40; - var nlheight = newheight+'px'; - document.getElementById('nodelist2').style.height=nlheight; - var inheight = newheight*2; - var outheight = inheight + 50; - inheight=inheight+'px'; - outheight = outheight+'px'; - document.getElementById('ban_outer').style.height=outheight; - document.getElementById('white_outer').style.height=outheight; - document.getElementById('ban_from').style.height=inheight; - document.getElementById('ban_to').style.height=inheight; - document.getElementById('white_from').style.height=inheight; - document.getElementById('white_to').style.height=inheight; - -} - - -//Functions that get the locations of the nodes to group the -// nodes into tiers and make ban and white lists. -//Will probably need to add a function to get the tier description information. -//Might be able to do that with just php though? -function getNodesInTiers(ntiers) { - //output = ntiers+",\n"; - i = 1; - //for (i=1;i<=ntiers;i++){ - //var newname = 'Tier'+i; - var newname = 'Variables to remove'; - children = document.getElementById(newname).childNodes; - //temp = children.length - 2; - var temp = []; - //temp = newname + ",\t" +temp+ ",\t" - for (j=2;j<children.length;j++){ - //temp = temp + "\\t" + children[j].innerHTML; - temp.push(children[j].innerHTML); - } - //output = output + temp +"\n" - //} - - output = temp.join(' '); - return output; - - // window.open("http://compbio.uthsc.edu/BNServer/tier.php?tier="+output,"Ratting","width=950,height=270,0,status=0,"); - -} - -function getNodesInList(from_div,to_div) { - children_from = document.getElementById(from_div).childNodes; - children_to = document.getElementById(to_div).childNodes; - if(children_from.length == children_to.length){ - temp = ""; - for (i=2;i<children_from.length;i++){ - temp = temp+children_from[i].innerHTML; - temp = temp+",\t"+children_to[i].innerHTML+",\n"; - } - - - - } - else - { - alert('Error in node list'); - temp=""; - } - return temp; -} - - -//Functions that get the description of the tiers. -function getDescribeTiers(ntiers) { - output = ""; - // for (i=1;i<=ntiers;i++) { - i = 1; - temp=""; - var newname = 'int_box2'+i; - - var temp_id_yes="r_yes_"+newname; - var temp_id_no="r_no_"+newname; - - temp_yes = document.getElementById(temp_id_yes); - temp_no = document.getElementById(temp_id_no); - - // temp = temp + temp_yes.value + ",\t" - temp = temp + temp_yes.checked + ",\t" - - // temp = temp + temp_no.value + ",\t" - temp = temp + temp_no.checked + ",\t" - - //for (j=1;j<=ntiers;j++) { - j = 1; - if(j!=i) - { - var pbox_id="par_"+i+"_"+j; - var cbox_id="child_"+i+"_"+j; - temp_p = document.getElementById(pbox_id); - temp_c = document.getElementById(cbox_id); - - temp = temp + temp_p.checked + ",\t" - - temp = temp + temp_c.checked + ",\t" - - - } - //} - // alert(temp); - - output = output + temp +"\n" - - //} - - - // window.open("http://compbio.uthsc.edu/BNServer/tierdescription.php?tierdesc="+output,"Ratting","width=950,height=270,0,status=0,"); - return output; - -} - - -//Combined all three function together and then execute structure learning - -function getcombineDescription(ntiers,ban_from,ban_to,white_from,white_to,keyv) -{ - ntiers = 1; - var tier=getNodesInTiers(ntiers); - var txtFile="./data/"+keyv+"del_var.txt"; - //var file = new File(txtFile); - //file.open("w"); - //file.write(tier); - //file.close(); - // var tierdesc=getDescribeTiers(ntiers); - // var ban=getNodesInList(ban_from,ban_to); - // var white=getNodesInList(white_from,white_to); - var tierdesc = ""; - var ban = ""; - var white = ""; - window.open("remove_variables_processing.php?tier="+tier+"&My_key="+keyv,'_self',false); -} -function getcombineDescriptionDefault(ntiers,ban_from,ban_to,white_from,white_to,keyv) -{ - ntiers = 1; - var tier=getNodesInTiers(ntiers); - var txtFile="./data/"+keyv+"del_var.txt"; - //var file = new File(txtFile); - //file.open("w"); - //file.write(tier); - //file.close(); - // var tierdesc=getDescribeTiers(ntiers); - // var ban=getNodesInList(ban_from,ban_to); - // var white=getNodesInList(white_from,white_to); - var tierdesc = ""; - var ban = ""; - var white = ""; - window.open("remove_variables_processing_default.php?tier="+tier+"&My_key="+keyv,'_self',false); -} - -function clearBWLists() -{ - var element = document.getElementById('ban_from'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } - var element = document.getElementById('ban_to'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } - var element = document.getElementById('white_from'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } - var element = document.getElementById('white_to'); - var children = element.childNodes; - while (children.length>2) { - element.removeChild(element.lastChild); - var children = element.childNodes; - } -} - - - - - -</script> -</head> - - -<script type="text/javascript"> - var nnodes =<?php print($node);?>; - var ntiers = <?php print($tier_number);?>; -</script> - -<body onload="loadFunction(nnodes,ntiers)"> -</br> - <p><h3>Select variables to remove:<br></h3> - </p> - <br> - <div id="tier_box"> - <div id="tiers"></div> - - </div> - -<!-- - - <div id="outer_tier_desc1"> - <p><h3>3. Define interactions allowed between tiers:<br></h3> - </p> - <br> - <div id="int_box1"> - </div> - <br> - <div id="int_box2"> - </div> - <br> - <div id="int_box3"> - </div> - <br> - <div id="int_box4"> - </div> - </div> - <br> - <br> - <br> - - <div id="outer_box_lists"> - <p><h3>4. Specify additional constraints:<br></h3> - </p> - <br> - <div><input type="button" value="Clear lists of banned and required edges" onClick="clearBWLists()"/></div><br> - <div id="nodelist2" ondrop="return false" - ondragcenter="return false" ondragover="return false" >Nodes<br> - </div> - - <div id="ban_outer">Banned edges<br> - <div id="ban_from" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">From<br></div> - <div id="ban_to" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">To<br></div> - </div> - <div id="white_outer">Required edges<br> - <div id="white_from" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">From<br></div> - <div id="white_to" class="tier" ondrop="return dropCopy(event)" - ondragenter="return false" ondragover="return false">To<br></div> - </div> ---> - - </div> - - <br> - <br> - - - -</body> -</div> -</html> - diff --git a/sourcecodes/run_scripts/run_del_var b/sourcecodes/run_scripts/run_del_var new file mode 100644 index 00000000..0b1bdfdc --- /dev/null +++ b/sourcecodes/run_scripts/run_del_var @@ -0,0 +1,8 @@ +#!/usr/bin/octave -qf +cd ./data +arg_list = argv(); +addpath("../bnt-master"); +addpath(genpathKPM("../bnt-master")); +addpath("../parameter_learning"); +removeNodes(arg_list{1},arg_list{2}); +prepareInput(arg_list{2}); \ No newline at end of file diff --git a/sourcecodes/run_kfold b/sourcecodes/run_scripts/run_kfold index ad87b5d1..f90a5428 100644 --- a/sourcecodes/run_kfold +++ b/sourcecodes/run_scripts/run_kfold @@ -4,11 +4,15 @@ arg_list = argv(); addpath("../bnt-master"); addpath(genpathKPM("../bnt-master")); addpath("../parameter_learning"); -filename=strcat(arg_list{1},"kfoldCV.txt"); -delete(filename); +fileout=strcat(arg_list{1},"kfoldCV.txt"); +delete(fileout); filename=strcat(arg_list{1},"kfoldCV_temp.txt"); fout_temp=fopen(filename,'w'); fprintf(fout_temp,arg_list{2}); kfoldCrossValid(arg_list{1},arg_list{2},arg_list{3}); fclose(fout_temp); -delete(filename); \ No newline at end of file +delete(filename); + + +command=strcat({"/home/jziebart/python/Python-2.7.15/python ../kfold_plotly.py "},arg_list{1}); +test=system(command); diff --git a/sourcecodes/run_loo b/sourcecodes/run_scripts/run_loo index 8c164651..3ff4f4db 100644 --- a/sourcecodes/run_loo +++ b/sourcecodes/run_scripts/run_loo @@ -9,6 +9,9 @@ delete(filename); filename=strcat(arg_list{1},"looCV_temp.txt"); fout_temp=fopen(filename,'w'); fprintf(fout_temp,arg_list{2}); -looCrossValid(arg_list{1},arg_list{2}); fclose(fout_temp); -delete(filename); \ No newline at end of file +looCrossValid(arg_list{1},arg_list{2}); +delete(filename); + +command=strcat({"/home/jziebart/python/Python-2.7.15/python ../cv_plotly.py "},arg_list{1}); +test=system(command); diff --git a/sourcecodes/run_scripts/run_mod_edges b/sourcecodes/run_scripts/run_mod_edges new file mode 100644 index 00000000..30176e9c --- /dev/null +++ b/sourcecodes/run_scripts/run_mod_edges @@ -0,0 +1,24 @@ +#!/usr/bin/octave -qf +cd ./data +arg_list = argv(); +addpath("../bnt-master"); +addpath(genpathKPM("../bnt-master")); +addpath("../parameter_learning"); +modifyEdges(arg_list{1},arg_list{2}); + +fname1=strcat(arg_list{1},"continuous_input.txt"); +fname2=strcat(arg_list{2},"continuous_input.txt"); +copyfile(fname1,fname2); + +fname1=strcat(arg_list{1},"continuous_input_orig.txt"); +fname2=strcat(arg_list{2},"continuous_input_orig.txt"); +copyfile(fname1,fname2); + +fname1=strcat(arg_list{1},"nnode.txt"); +fname2=strcat(arg_list{2},"nnode.txt"); +copyfile(fname1,fname2); + +fname1=strcat(arg_list{1},"name.txt"); +fname2=strcat(arg_list{2},"name.txt"); +copyfile(fname1,fname2); + diff --git a/sourcecodes/run_scripts/run_mod_str b/sourcecodes/run_scripts/run_mod_str new file mode 100644 index 00000000..63439afd --- /dev/null +++ b/sourcecodes/run_scripts/run_mod_str @@ -0,0 +1,11 @@ +#!/usr/bin/octave -qf +cd ./data +arg_list = argv(); +addpath("../bnt-master"); +addpath(genpathKPM("../bnt-master")); +addpath("../parameter_learning"); + +fname1=strcat(arg_list{1},"continuous_input_orig.txt"); +fname2=strcat(arg_list{2},"continuous_input_orig.txt"); +copyfile(fname1,fname2); + diff --git a/sourcecodes/run_scripts/run_mod_str~ b/sourcecodes/run_scripts/run_mod_str~ new file mode 100644 index 00000000..30176e9c --- /dev/null +++ b/sourcecodes/run_scripts/run_mod_str~ @@ -0,0 +1,24 @@ +#!/usr/bin/octave -qf +cd ./data +arg_list = argv(); +addpath("../bnt-master"); +addpath(genpathKPM("../bnt-master")); +addpath("../parameter_learning"); +modifyEdges(arg_list{1},arg_list{2}); + +fname1=strcat(arg_list{1},"continuous_input.txt"); +fname2=strcat(arg_list{2},"continuous_input.txt"); +copyfile(fname1,fname2); + +fname1=strcat(arg_list{1},"continuous_input_orig.txt"); +fname2=strcat(arg_list{2},"continuous_input_orig.txt"); +copyfile(fname1,fname2); + +fname1=strcat(arg_list{1},"nnode.txt"); +fname2=strcat(arg_list{2},"nnode.txt"); +copyfile(fname1,fname2); + +fname1=strcat(arg_list{1},"name.txt"); +fname2=strcat(arg_list{2},"name.txt"); +copyfile(fname1,fname2); + diff --git a/sourcecodes/run_octave b/sourcecodes/run_scripts/run_octave index 3879280e..3879280e 100644 --- a/sourcecodes/run_octave +++ b/sourcecodes/run_scripts/run_octave diff --git a/sourcecodes/run_octave_evd b/sourcecodes/run_scripts/run_octave_evd index 9f661925..9f661925 100644 --- a/sourcecodes/run_octave_evd +++ b/sourcecodes/run_scripts/run_octave_evd diff --git a/sourcecodes/run_octave_inv b/sourcecodes/run_scripts/run_octave_inv index f9e568e3..f9e568e3 100644 --- a/sourcecodes/run_octave_inv +++ b/sourcecodes/run_scripts/run_octave_inv diff --git a/sourcecodes/run_prep_input b/sourcecodes/run_scripts/run_prep_input index 4611d880..4611d880 100644 --- a/sourcecodes/run_prep_input +++ b/sourcecodes/run_scripts/run_prep_input diff --git a/sourcecodes/run_test_set b/sourcecodes/run_scripts/run_test_set index 503032f0..dbf929f8 100644 --- a/sourcecodes/run_test_set +++ b/sourcecodes/run_scripts/run_test_set @@ -7,5 +7,9 @@ addpath("../parameter_learning"); filename=strcat(arg_list{1},"ts_output.txt"); delete(filename); testSetPredictions(arg_list{1}); +fclose(filename); filename=strcat(arg_list{1},"ts_upload.txt"); -delete(filename); \ No newline at end of file +delete(filename); + +command=strcat({"/home/jziebart/python/Python-2.7.15/python ../ts_plotly.py "},arg_list{1}); +test=system(command); |