Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop
authorJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Mar 2015 14:44:39 +0000 (14:44 +0000)
committerJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Mar 2015 14:44:39 +0000 (14:44 +0000)
131 files changed:
1  2 
build.xml
examples/applets.html
examples/embedded.html
examples/embeddedWJmol.html
examples/formComplete.html
examples/javascriptLaunch.html
examples/linkedapplets_ng.html
help/help.jhm
help/helpTOC.xml
help/html/features/annotationsFormat.html
help/html/menus/alwselect.html
help/html/releases.html
src/MCview/AppletPDBCanvas.java
src/MCview/PDBCanvas.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/Finder.java
src/jalview/analysis/Grouping.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/api/AlignViewControllerGuiI.java
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/SequenceRenderer.java
src/jalview/api/SequenceStructureBinding.java
src/jalview/api/structures/JalviewStructureDisplayI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SequenceRenderer.java
src/jalview/appletgui/TreePanel.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/ext/varna/JalviewVarnaBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/IdwidthAdjuster.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/ScriptWindow.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/StructureViewer.java
src/jalview/gui/TreePanel.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HTMLOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/structures/models/SequenceStructureBindingModel.java
src/jalview/util/ColorUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/AWSThread.java
src/jalview/ws/HttpClientUtils.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/rest/params/AnnotationFile.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
test/jalview/ws/jabaws/RNAStructExportImport.java

diff --cc build.xml
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diff --cc help/help.jhm
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                        </td>
                </tr>
                <tr>
+                       <td width="60" nowrap>
+                               <div align="center">
+                                       <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
+                               </div>
+                       </td>
+                       <td>
+                               <div align="center">
+                               </div>
+                       </td>
+                       <td>
+                               <div align="center">
+                                       <ul><li>Reinstated the display of default example file on startup</li>
+                                       <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
+                                       </ul>
+                               </div>
+                       </td>
+               </tr>
+               <tr>
                        <td><div align="center">
 +                                      <strong><a name="Jalview.2.9">2.9</a><br /> <em>23/2/2015</em></strong>
 +                              </div></td>
 +                      <td><em>General</em>
 +                              <ul>
 +                              </ul> <em>Application</em>
 +                              <ul>
 +                              </ul>
 +        <em>Applet</em>
 +                              <ul>
 +                              </ul>
 +                </td>
 +                      <td>
 +                              <em>General</em>
 +                              <ul>
 +                                      <li>Make selection for columns now works on marked columns
 +                                              rather than columns in rubber-band selection region.</li>
 +                              </ul>
 +                              <!--  issues resolved --> <em>Application</em>
 +                              <ul>
 +                              </ul> <!--  <em>Applet</em>
 +                              <ul>
 +                              </ul> <em>General</em>
 +                              <ul> 
 +                              </ul>--> <em>Deployment and Documentation</em>
 +                              <ul>
 +                              </ul> <em>Application Known issues</em>
 +                              <ul>
 +                              </ul> <em>Applet Known Issues</em>
 +                              <ul>
 +                              </ul>
 +                      </td>
 +              </tr>
 +              <tr>
 +                      <td><div align="center">
                                        <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
                                </div></td>
                        <td><em>General</em>
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