Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
authorJim Procter <jprocter@compbio.dundee.ac.uk>
Mon, 3 Feb 2014 17:17:52 +0000 (17:17 +0000)
committerJim Procter <jprocter@compbio.dundee.ac.uk>
Mon, 3 Feb 2014 17:17:52 +0000 (17:17 +0000)
commit2f4f1d8fb6878271b64f327bc58c895f458137af
tree3d35ea3717465874924e9d797ae6a34aaa9d700e
parentdd1aed40cf00d837d1643918c380546a1dd2d39a
parent4cf0508ac56ebb01fbd51b547ea9f4a682ca97fb
Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
updating 2.8.1 with source formatting, branding, and new examples build mechanism
Conflicts:
build.xml
examples/linkedapplets_ng.html
help/helpTOC.xml
src/jalview/appletgui/AlignFrame.java
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
100 files changed:
build.xml
examples/linkedapplets_ng.html
help/help.jhm
help/helpTOC.xml
help/html/menus/alignmentMenu.html
help/html/menus/alwselect.html
help/html/menus/popupMenu.html
resources/lang/Messages.properties
schemas/jalview.xsd
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/PDBViewer.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/StructureFrequency.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/JalviewLite.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.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/AppVarnaBinding.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/BlogReader.java
src/jalview/gui/Console.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EPSOptions.java
src/jalview/gui/EditNameDialog.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JalviewDialog.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsPreferences.java
src/jalview/io/FileLoader.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GRestServiceEditorPane.java
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/jws2/AAConClient.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/JabaWsServerQuery.java
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/ParameterUtils.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/jws2/dm/JabaOption.java
src/jalview/ws/jws2/jabaws2/Jws2Instance.java