From cf59eaf9fe5d9f515083b0ff4e927d704568c552 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 11 Dec 2014 17:54:40 +0000
Subject: Fixed some weirdness with the navbar and jumbotron and aligned
 everything to the left

---
 wqflask/wqflask/correlation_matrix/show_corr_matrix.py      | 4 +++-
 wqflask/wqflask/show_trait/show_trait.py                    | 9 +++++++--
 wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css | 3 ---
 wqflask/wqflask/static/packages/bootstrap/css/docs.css      | 8 ++++----
 wqflask/wqflask/templates/base.html                         | 9 ++++-----
 wqflask/wqflask/templates/index_page.html                   | 4 ++--
 6 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 38b7de4b..8bd5919b 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -191,7 +191,9 @@ class CorrelationMatrix(object):
         print("corr_results:",  pf(corr_results_to_list))
 
         m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
-        pca = stats.princomp(m, cor = "TRUE")
+        eigen = base.eigen(m)
+        print("eigen:", eigen)
+        #pca = stats.princomp(m, cor = "TRUE")
         print("pca:", pca)
 
         return pca
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 04cde060..62411640 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -37,9 +37,14 @@ class ShowTrait(object):
 
     def __init__(self, kw):
         print("in ShowTrait, kw are:", kw)
-        self.trait_id = kw['trait_id']
         
-        helper_functions.get_species_dataset_trait(self, kw)
+        if kw['trait_id'] != None:
+            self.temp_trait = False
+            self.trait_id = kw['trait_id']
+            helper_functions.get_species_dataset_trait(self, kw)
+        else:
+            self.temp_trait = True
+            self.create_temp_trait()
 
         #self.dataset.group.read_genotype_file()
 
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
index cf6b33f4..2c93dac8 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
@@ -1390,8 +1390,6 @@ pre code {
 .container {
   padding-right: 15px;
   padding-left: 15px;
-  margin-right: auto;
-  margin-left: auto;
 }
 /*
 @media (min-width: 768px) {
@@ -3875,7 +3873,6 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
 .navbar {
   position: relative;
   min-height: 50px;
-  margin-bottom: 20px;
   border: 1px solid transparent;
 }
 /*
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
index 186ec051..50710348 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
@@ -12,7 +12,7 @@
 
 body {
   position: relative;
-  padding-top: 40px;
+  padding-top: 0px;
 }
 
 /* Code in headings */
@@ -36,7 +36,7 @@ body > .navbar .brand {
   padding-right: 0;
   padding-left: 0;
   margin-left: 20px;
-  float: right;
+  float: left;
   font-weight: bold;
   color: #336699;
   text-shadow: 0 1px 0 rgba(255,255,255,.1), 0 0 30px rgba(255,255,255,.125);
@@ -92,7 +92,7 @@ hr.soften {
   position: relative;
   padding: 0px 0;
   color: #336699;
-  text-align: center;
+  text-align: left;
   text-shadow: 0 1px 3px rgba(0,0,0,.4), 0 0 30px rgba(0,0,0,.075);
   background: #d5d5d5; /* Old browsers */
 
@@ -931,7 +931,7 @@ form.bs-docs-example {
   /* center align subhead text like the masthead */
   .subhead h1,
   .subhead p {
-    text-align: center;
+    text-align: left;
   }
 
   /* Marketing on home */
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 3f89e7a1..240481cc 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -57,13 +57,12 @@
 {% endmacro %}
 
 
-<body style="width: 98% !important;">
-    <!-- Navbar
-    ================================================== -->
+<body style="width: 1500px !important;">
+    <!-- Navbar ================================================== -->
 
-    <div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
+    <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation">
 
-            <div class="container">
+            <div class="container-fluid" style="width: 1500px !important;">
                 <!-- Brand and toggle get grouped for better mobile display -->
                 <div class="navbar-header">
                 <a class="navbar-brand" href="/">GeneNetwork</a>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index df8fc5bb..b3fd3f6f 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -4,13 +4,13 @@
 <!-- Start of body -->
 
     <header class="jumbotron subhead" id="overview">
-        <div class="container" style="width: 1200px !important;">
+        <div class="container">
             <h1>GeneNetwork</h1>
             <p class="lead">Open source bioinformatics for systems genetics</p>   
         </div>
     </header>
 
-    <div class="container" style="width: 1200px !important;">
+    <div class="container-fluid">
         
         {{ flash_me() }}
         
-- 
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