Merge pull request #117 from AliTVTeam/develop

Develop
AliTVTeam · Aug 5, 2016 · 41513e8 · 41513e8
2 parents 5678b30 + 9585f1f
commit 41513e8
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Showing 10 changed files with 1,053 additions and 238 deletions.
diff --git a/README.org b/README.org
@@ -72,6 +72,14 @@ The licenses of included libraries might differ, please see [[LICENSES/README.or
 [[https://travis-ci.org/AliTVTeam/AliTV/][https://travis-ci.org/AliTVTeam/AliTV.svg?branch=master]]
 [[https://coveralls.io/github/AliTVTeam/AliTV?branch=master][https://coveralls.io/repos/github/AliTVTeam/AliTV/badge.svg?branch=master]]
 ** Changelog
+*** 0.4.1
+ - Fix corner cases for move chromosome left/right
+ - Fix corner cases for move genome up/down
+ - Add linkOpacity setting (#104)
+ - Remove circular from headline (#102)
+ - Fix special characters in id bug (#108)
+ - Add feature labels
+ - Update perl part to version 0.1.7
 *** 0.4.0 <2016-06-18 Sa>
  - Include new perl interface
  - Update documentation

diff --git a/d3/AliTV.html b/d3/AliTV.html
@@ -56,14 +56,19 @@
 
  });
 
+ // https://learn.jquery.com/using-jquery-core/faq/how-do-i-select-an-element-by-an-id-that-has-characters-used-in-css-notation/
+ function jq(myid) {
+ return "#" + myid.replace(/(:|\.|\[|\]|,)/g, "\\$1");
+ }
+
  function initialize() {
  setJSONEditorFromAli();
  ali.onDataChange(setJSONEditorFromAli);
  addFeatureGroupTemplates();
  ali.onDataChange(addFeatureGroupTemplates);
  setParameters();
  ali.onDataChange(setParameters);
- showHideCircularWarning()
+ showHideCircularWarning();
  ali.onDataChange(showHideCircularWarning);
  setSlider();
  ali.drawLinear();
@@ -382,6 +387,16 @@
  }
  }
 
+ function changeLinkOpacity() {
+ var opacity = $("#linkOpacity").val();
+ try {
+ ali.setLinkOpacity(opacity);
+ } catch (err) {
+ bootbox.alert(err);
+ $("#linkOpacity").val(ali.getLinkOpacity());
+ }
+ }
+
  function changeGenomeLabelColor() {
  var color = $("#genomeLabelColor").val();
  try {
@@ -423,7 +438,7 @@
  }
 
  function changeOffset(karyoId) {
- var offset = Number($('#offset-' + karyoId).val());
+ var offset = Number($(jq('offset-' + karyoId)).val());
  try {
  ali.setOffset(offset, karyoId);
  $("#offset-" + karyoId).val(ali.getOffset(karyoId));
@@ -467,6 +482,7 @@
  $('#drawTree').attr('checked', function() {
  return ali.conf.tree.drawTree;
  });
+ $("#linkOpacity").val(ali.getLinkOpacity());
  setOffsetGroup();
  setSlider();
  }
@@ -488,6 +504,7 @@
  changeTickDistance();
  changeGenomeColor();
  changeLinkColor();
+ changeLinkOpacity();
  changeGenomeLabelColor();
  changeGenomeLabelSize();
  changeTickLabelColor();
@@ -861,7 +878,7 @@
 <body>
 
  <div class="page-header">
- <h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="margin:0px 20px"/><b>AliTV <sup id="version-placeholder"></sup></b><small>&nbsp;Visualize multiple whole genome alignments as circular or linear maps</small></h1>
+ <h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="margin:0px 20px"/><b>AliTV <sup id="version-placeholder"></sup></b><small>&nbsp;Visualize multiple whole genome alignments as linear maps</small></h1>
  <div>
  <ul class="nav nav-tabs" role="tablist">
 
@@ -1239,6 +1256,10 @@ <h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="mar
  <input id="maxLinkColor" type="text" class="form-control" />
  <span class="input-group-addon"><i></i></span>
  </div>
+ <div class="input-group" style="margin: 10px 10px">
+ Link opacity:
+ <input type="text" id="linkOpacity" placeholder="Opacity (0-1)">
+ </div>
  </div>
  </div>
  </div>