From 58965a746aea4d6fc34e101a0958ecdc46493acb Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Tue, 18 Dec 2012 18:02:19 -0600
Subject: Changed html for the marker regression tab

Created file show_trait_mapping_tools.coffee to handle
submitting the form to the marker regression page

Changed form name/id in show_trait.html to "trait_data_form"
---
 .../new/javascript/show_trait_mapping_tools.coffee |  8 +++
 .../new/javascript/show_trait_mapping_tools.js     | 16 ++++++
 wqflask/wqflask/templates/show_trait.html          |  3 +-
 .../templates/show_trait_mapping_tools.html        | 57 ++++++++++------------
 4 files changed, 51 insertions(+), 33 deletions(-)
 create mode 100644 wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
 create mode 100644 wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js

diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
new file mode 100644
index 00000000..cd6dc1d8
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -0,0 +1,8 @@
+$ ->
+    run_marker_regression = ->
+        console.log("In marker regression")
+        url = "/marker_regression"
+        $("#trait_data_form").attr("action", url);
+        $("#trait_data_form").submit()
+    
+    $("#marker_regression_btn").click(run_marker_regression)
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
new file mode 100644
index 00000000..cca396a9
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -0,0 +1,16 @@
+// Generated by CoffeeScript 1.3.3
+(function() {
+
+  $(function() {
+    var run_marker_regression;
+    run_marker_regression = function() {
+      var url;
+      console.log("In marker regression");
+      url = "/marker_regression";
+      $("#trait_data_form").attr("action", url);
+      return $("#trait_data_form").submit();
+    };
+    return $("#marker_regression_btn").click(run_marker_regression);
+  });
+
+}).call(this);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 28341186..6d1a3d4b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -11,7 +11,7 @@
         </div>
     </header>
 
-    <form method="post" action="/corr_compute" name="dataInput" id="trait_data_form">
+    <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form">
             {% for key in hddn %}
                 <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}">
             {% endfor %}
@@ -48,5 +48,6 @@
 
     <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
     <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
+    <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
     <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 1109ded3..d584a774 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -49,43 +49,36 @@
                     <input type="checkbox" name="use_weighted" /> Use Weighted
                 </label>
                 <br>
-                <input type="button" id="interval_mapping" class="btn" value="Compute">
+                    
+                <div class="well well-small">
+                    <strong>Composite Mapping</strong>
+                    - Control for a marker as a co-factor (e.g.: rs12345):
+                    <!--Prefer a <strong>composite</strong>? Tell us the control locus (e.g.: rs12345):-->
+                    <INPUT TYPE="text" NAME="control_locus" default="" />
+                </div>
+                <input type="button" name="interval_mapping_btn" class="btn" value="Compute">
             </div>
+            
             <div class="tab-pane" id="marker_regression">
-                <table cellpadding="0" cellspacing="0" width="100%">
-                  <tr>
-                    <td class="fs12 fwn" nowrap="on" valign="top">
-                      <table cellpadding="2" cellspacing="0" width="263px">
-                        <tr>
-                          <td><span class="ffl fwb fs12"><strong>Display LRS greater than:</strong></span></td>
-
-                          <td><input type="text" name="suggestive" size="5" maxlength="8"></td>
-                        </tr>
-
-                        <tr>
-                          <td><input type="checkbox" name="displayAllLRS" class="checkbox"> <span class="ffl fs12">Display all LRS</span></td>
-                        </tr>
-
-                        <tr>
-                          <td><input type="checkbox" name="parentsf14regression2" class="checkbox"> <span class="ffl fs12">Use Parents</span></td>
-                        </tr>
-
-                        <tr>
-                          <td><input type="checkbox" name="applyVarianceSE2" class="checkbox"> <span class="ffl fs12">Use Weighted</span></td>
-                        </tr>
-                      </table><br>
-                      <input type="button" name="marker" class="btn" value=" Compute "><br>
-                      <br>
-                    </td>
-                  </tr>
-
-                  <tr>
-                    <td valign="top"><span class="fs12"><a href="/glossary.html#" target="_blank">Marker regression</a> computes and displays LRS
+                <label for="suggestive_lrs">Display LRS greater than:
+                    <input name="suggestive_lrs" />
+                </label>
+                <label class="checkbox">
+                    <input type="checkbox" name="display_all_lrs" /> Display All LRS
+                </label>
+                <label class="checkbox">
+                    <input type="checkbox" name="use_parents" /> Use Parents
+                </label>                   
+                <label class="checkbox">
+                    <input type="checkbox" name="use_weighted" /> Use Weighted
+                </label>                
+                <input type="button" id="marker_regression_btn" name="marker_regression_btn" class="btn" value="Compute">
+
+<!--                    <td valign="top"><span class="fs12"><a href="/glossary.html#" target="_blank">Marker regression</a> computes and displays LRS
                     values for individual markers.<br>
                     This function also lists additive effects (phenotype units per allele) and<br>
                     dominance deviations for some datasets.<br></span><br></td>
-                  </tr>
-                </table>
+-->
             </div>
             
             <div class="tab-pane" id="pair_scan">
-- 
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