[jalview] branch master updated (7c4c6df -> 066da38)

Fri Sep 12 12:56:46 UTC 2014

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ebourg-guest pushed a change to branch master
in repository jalview.

      from  7c4c6df   Removed the unused build dependency on libgnujaf-java Updated Standards-Version to 3.9.5 (no changes)
      adds  90f861a   Initial upstream branch.
      adds  1bf52fe   Imported Upstream version 2.7.dfsg
       new  80665ce   Merge tag 'upstream/2.7.dfsg'
       new  dfad943   Moved the package to Git
       new  abe1d5b   Switch to debhelper level 9
       new  60aeb35   Wrap and sort
       new  23fe84a   Fixed a compilation error with Java 8
       new  38e9dee   debian/copyright: Fixed a license short name
       new  9011fa3   Removed the unused build dependencies on libgnumail-java, libxalan2-java and libxerces2-java
       new  066da38   Upload to unstable

The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.

Summary of changes:
 JalviewApplet.jpx                                  |   75 +
 JalviewX.jpx                                       |   47 +
 LICENSE                                            |  621 +++
 README                                             |   39 +
 build.xml                                          |  595 +++
 debian/changelog                                   |   12 +-
 debian/compat                                      |    2 +-
 debian/control                                     |   50 +-
 debian/copyright                                   |    2 +-
 debian/patches/java8-compatibility.patch           |   20 +
 debian/patches/series                              |    1 +
 doc/AddingGroovySupport.html                       |   60 +
 doc/building.html                                  |   99 +
 doc/developing.html                                |   41 +
 doc/index.html                                     |  153 +
 doc/newdmobj.html                                  |   36 +
 help/help.hs                                       |   43 +
 help/help.jhm                                      |  106 +
 help/helpTOC.html                                  |   97 +
 help/helpTOC.xml                                   |  131 +
 help/html/align.jpg                                |  Bin 0 -> 14648 bytes
 help/html/calculations/consensus.html              |   35 +
 help/html/calculations/conservation.html           |   44 +
 help/html/calculations/pairwise.html               |   37 +
 help/html/calculations/pca.html                    |   84 +
 help/html/calculations/quality.html                |   49 +
 help/html/calculations/recoverInputdata.html       |   30 +
 help/html/calculations/redundancy.html             |   33 +
 help/html/calculations/sorting.html                |   72 +
 help/html/calculations/tree.html                   |   85 +
 help/html/calculations/treeviewer.html             |  117 +
 help/html/colourSchemes/abovePID.html              |   37 +
 .../html/colourSchemes/annotationColourSetting.jpg |  Bin 0 -> 43293 bytes
 help/html/colourSchemes/annotationColouring.html   |   61 +
 help/html/colourSchemes/annotationColours.jpg      |  Bin 0 -> 107885 bytes
 help/html/colourSchemes/blosum.html                |   37 +
 help/html/colourSchemes/buried.html                |   69 +
 help/html/colourSchemes/clustal.html               |   62 +
 help/html/colourSchemes/conservation.html          |   44 +
 help/html/colourSchemes/helix.html                 |   69 +
 help/html/colourSchemes/hydrophobic.html           |   72 +
 help/html/colourSchemes/index.html                 |  297 ++
 help/html/colourSchemes/nucleotide.html            |   42 +
 help/html/colourSchemes/pid.html                   |   50 +
 help/html/colourSchemes/strand.html                |   69 +
 help/html/colourSchemes/taylor.html                |   68 +
 help/html/colourSchemes/textcolour.gif             |  Bin 0 -> 21788 bytes
 help/html/colourSchemes/textcolour.html            |   37 +
 help/html/colourSchemes/turn.html                  |   69 +
 help/html/colourSchemes/user.html                  |   39 +
 help/html/colourSchemes/userDefined.gif            |  Bin 0 -> 35269 bytes
 help/html/colourSchemes/zappo.html                 |   67 +
 help/html/editing/editing.jpg                      |  Bin 0 -> 42427 bytes
 help/html/editing/index.html                       |   73 +
 help/html/features/amendfeature.gif                |  Bin 0 -> 28030 bytes
 help/html/features/annotation.html                 |  108 +
 help/html/features/annotationsFormat.html          |  209 +
 help/html/features/clarguments.html                |  196 +
 help/html/features/codingfeatures.html             |   33 +
 help/html/features/commandline.html                |   52 +
 help/html/features/creatinFeatures.html            |   55 +
 help/html/features/crnewfeature.gif                |  Bin 0 -> 24348 bytes
 help/html/features/cursorMode.html                 |   72 +
 help/html/features/das.gif                         |  Bin 0 -> 37535 bytes
 help/html/features/dasfeatures.html                |   62 +
 help/html/features/dassettings.html                |   54 +
 help/html/features/editingFeatures.html            |   43 +
 help/html/features/exportannot.gif                 |  Bin 0 -> 8555 bytes
 help/html/features/fcsgtthan.gif                   |  Bin 0 -> 136 bytes
 help/html/features/fcsltthan.gif                   |  Bin 0 -> 136 bytes
 help/html/features/fcsminmax.gif                   |  Bin 0 -> 104 bytes
 help/html/features/fcsntlabel.gif                  |  Bin 0 -> 121 bytes
 help/html/features/featureSettings.gif             |  Bin 0 -> 23195 bytes
 help/html/features/featurecoloursettings.gif       |  Bin 0 -> 8518 bytes
 help/html/features/featuresFormat.html             |  215 +
 help/html/features/featureschemes.html             |   73 +
 help/html/features/featuresettings.html            |   79 +
 help/html/features/groovy.html                     |   94 +
 help/html/features/hiddenRegions.html              |   98 +
 help/html/features/jalarchive.html                 |   38 +
 help/html/features/jmol.html                       |  214 +
 help/html/features/multipleViews.html              |   76 +
 help/html/features/newkeystrokes.html              |   50 +
 help/html/features/overview.gif                    |  Bin 0 -> 10356 bytes
 help/html/features/overview.html                   |   29 +
 help/html/features/pdbviewer.html                  |  160 +
 help/html/features/preferences.html                |  177 +
 help/html/features/search.gif                      |  Bin 0 -> 5043 bytes
 help/html/features/search.html                     |  116 +
 help/html/features/seqfeatures.html                |   81 +
 help/html/features/seqfetch.html                   |   72 +
 help/html/features/seqfetcher.gif                  |  Bin 0 -> 8702 bytes
 help/html/features/seqmappings.html                |   39 +
 help/html/features/viewingpdbs.html                |  121 +
 help/html/features/wrap.html                       |  335 ++
 help/html/index.html                               |   36 +
 help/html/io/export.html                           |   57 +
 help/html/io/file.png                              |  Bin 0 -> 590 bytes
 help/html/io/fileformats.html                      |   72 +
 help/html/io/index.html                            |   74 +
 help/html/io/modellerpir.html                      |   62 +
 help/html/jalviewjnlp.html                         |   78 +
 help/html/keys.html                                |  264 +
 help/html/memory.html                              |  118 +
 help/html/menus/alignmentMenu.html                 |  567 +++
 help/html/menus/alwannotations.html                |   87 +
 help/html/menus/alwcalculate.html                  |   93 +
 help/html/menus/alwcolour.html                     |   61 +
 help/html/menus/alwedit.html                       |  101 +
 help/html/menus/alwfile.html                       |  111 +
 help/html/menus/alwformat.html                     |   79 +
 help/html/menus/alwselect.html                     |   48 +
 help/html/menus/alwview.html                       |   91 +
 help/html/menus/desktopMenu.html                   |  126 +
 help/html/menus/index.html                         |   39 +
 help/html/menus/popupMenu.html                     |  166 +
 help/html/menus/wsmenu.html                        |   90 +
 help/html/misc/aaproperties.html                   |   48 +
 help/html/misc/ala.jpg                             |  Bin 0 -> 2039 bytes
 help/html/misc/aminoAcids.html                     |  308 ++
 help/html/misc/arg.jpg                             |  Bin 0 -> 4445 bytes
 help/html/misc/asparagine.jpg                      |  Bin 0 -> 3212 bytes
 help/html/misc/aspartate.jpg                       |  Bin 0 -> 2824 bytes
 help/html/misc/cys.jpg                             |  Bin 0 -> 2360 bytes
 help/html/misc/geneticCode.html                    |   92 +
 help/html/misc/glutamate.jpg                       |  Bin 0 -> 3341 bytes
 help/html/misc/glutamine.jpg                       |  Bin 0 -> 3546 bytes
 help/html/misc/gly.jpg                             |  Bin 0 -> 1823 bytes
 help/html/misc/his.jpg                             |  Bin 0 -> 3673 bytes
 help/html/misc/iso.jpg                             |  Bin 0 -> 3613 bytes
 help/html/misc/leu.jpg                             |  Bin 0 -> 3483 bytes
 help/html/misc/lys.jpg                             |  Bin 0 -> 3912 bytes
 help/html/misc/met.jpg                             |  Bin 0 -> 3365 bytes
 help/html/misc/phe.jpg                             |  Bin 0 -> 3148 bytes
 help/html/misc/pro.jpg                             |  Bin 0 -> 3037 bytes
 help/html/misc/properties.gif                      |  Bin 0 -> 29022 bytes
 help/html/misc/ser.jpg                             |  Bin 0 -> 2203 bytes
 help/html/misc/thr.jpg                             |  Bin 0 -> 2850 bytes
 help/html/misc/tryp.jpg                            |  Bin 0 -> 4450 bytes
 help/html/misc/tyr.jpg                             |  Bin 0 -> 3500 bytes
 help/html/misc/val.jpg                             |  Bin 0 -> 3024 bytes
 help/html/privacy.html                             |   76 +
 help/html/releases.html                            | 1139 +++++
 help/html/vamsas/index.html                        |  136 +
 help/html/webServices/JABAWS.html                  |   61 +
 help/html/webServices/clwqueued.gif                |  Bin 0 -> 5619 bytes
 help/html/webServices/dbreffetcher.html            |   77 +
 help/html/webServices/index.html                   |   97 +
 help/html/webServices/invalidurldialog.gif         |  Bin 0 -> 9370 bytes
 help/html/webServices/jalviewrssreader.gif         |  Bin 0 -> 24576 bytes
 help/html/webServices/jnet.html                    |  116 +
 help/html/webServices/jnetprediction.gif           |  Bin 0 -> 14715 bytes
 help/html/webServices/msaclient.html               |   75 +
 help/html/webServices/multimafftjbs.gif            |  Bin 0 -> 7301 bytes
 help/html/webServices/newsreader.html              |   28 +
 help/html/webServices/shmr.html                    |   65 +
 help/html/webServices/urllinks.html                |   89 +
 help/html/webServices/webServicesParams.html       |   86 +
 help/html/webServices/webServicesPrefs.html        |   79 +
 help/html/webServices/wsparams.gif                 |  Bin 0 -> 19287 bytes
 help/html/webServices/wsprefs.gif                  |  Bin 0 -> 18473 bytes
 help/html/whatsNew.html                            |  103 +
 help/icons/Home.png                                |  Bin 0 -> 1598 bytes
 help/icons/back.png                                |  Bin 0 -> 1315 bytes
 help/icons/forward.png                             |  Bin 0 -> 1303 bytes
 help/icons/print.png                               |  Bin 0 -> 1405 bytes
 help/icons/setup.png                               |  Bin 0 -> 1514 bytes
 jalview-jalopy.xml                                 |  393 ++
 nbbuild.xml                                        |   98 +
 nbproject/genfiles.properties                      |   25 +
 nbproject/project.properties                       |  143 +
 nbproject/project.xml                              |   30 +
 resources/embl_mapping.xml                         |  158 +
 resources/images/file.png                          |  Bin 0 -> 590 bytes
 resources/images/idwidth.gif                       |  Bin 0 -> 166 bytes
 resources/images/link.gif                          |  Bin 0 -> 320 bytes
 resources/images/logo.gif                          |  Bin 0 -> 615 bytes
 resources/images/logo_big.gif                      |  Bin 0 -> 6804 bytes
 resources/uniprot_mapping.xml                      |   96 +
 schemas/JalviewUserColours.xsd                     |   50 +
 schemas/JalviewWsParamSet.xsd                      |   74 +
 schemas/castor-mapping.xsd                         |  314 ++
 schemas/jalview.nodesc.properties                  |   30 +
 schemas/jalview.properties                         |   30 +
 schemas/jalview.xsd                                |  304 ++
 schemas/jalviewJvV1.xsd                            |  162 +
 schemas/vamsas.xsd                                 |  268 +
 schemas/vamsasJvV1.xsd                             |   91 +
 src/MCview/AppletPDBCanvas.java                    | 1202 +++++
 src/MCview/AppletPDBViewer.java                    |  255 +
 src/MCview/Atom.java                               |  105 +
 src/MCview/Bond.java                               |   79 +
 src/MCview/MCMatrix.java                           |  174 +
 src/MCview/PDBCanvas.java                          | 1167 +++++
 src/MCview/PDBChain.java                           |  514 ++
 src/MCview/PDBViewer.java                          |  694 +++
 src/MCview/PDBfile.java                            |  266 +
 src/MCview/Residue.java                            |   51 +
 src/MCview/Zsort.java                              |   72 +
 src/com/stevesoft/pat/AmpersandRule.java           |   30 +
 src/com/stevesoft/pat/Any.java                     |   55 +
 src/com/stevesoft/pat/BackG.java                   |   47 +
 src/com/stevesoft/pat/BackMatch.java               |   57 +
 src/com/stevesoft/pat/BackRefRule.java             |   40 +
 src/com/stevesoft/pat/Backup.java                  |   54 +
 src/com/stevesoft/pat/BasicStringBufferLike.java   |   23 +
 src/com/stevesoft/pat/Bits.java                    | 3040 ++++++++++++
 src/com/stevesoft/pat/Boundary.java                |   89 +
 src/com/stevesoft/pat/Bracket.java                 |   88 +
 src/com/stevesoft/pat/CaseMgr.java                 | 4409 +++++++++++++++++
 src/com/stevesoft/pat/ChangeRule.java              |   50 +
 src/com/stevesoft/pat/CodeRule.java                |   33 +
 src/com/stevesoft/pat/Ctrl.java                    |   61 +
 src/com/stevesoft/pat/Custom.java                  |   64 +
 src/com/stevesoft/pat/CustomEndpoint.java          |   44 +
 src/com/stevesoft/pat/DirFileRegex.java            |   31 +
 src/com/stevesoft/pat/DotMulti.java                |  209 +
 src/com/stevesoft/pat/End.java                     |   71 +
 src/com/stevesoft/pat/FastBracket.java             |  256 +
 src/com/stevesoft/pat/FastMulti.java               |  169 +
 src/com/stevesoft/pat/FileRegex.java               |  323 ++
 src/com/stevesoft/pat/Group.java                   |   77 +
 src/com/stevesoft/pat/LeftRule.java                |   31 +
 src/com/stevesoft/pat/Multi.java                   |   90 +
 src/com/stevesoft/pat/MultiMin.java                |   21 +
 src/com/stevesoft/pat/Multi_stage2.java            |  157 +
 src/com/stevesoft/pat/NoPattern.java               |   33 +
 src/com/stevesoft/pat/NonDirFileRegex.java         |   31 +
 src/com/stevesoft/pat/NotImplementedError.java     |   16 +
 src/com/stevesoft/pat/NullPattern.java             |   37 +
 src/com/stevesoft/pat/NullRule.java                |   30 +
 src/com/stevesoft/pat/Or.java                      |  130 +
 src/com/stevesoft/pat/OrMark.java                  |   73 +
 src/com/stevesoft/pat/PartialBuffer.java           |  109 +
 src/com/stevesoft/pat/Pattern.java                 |  294 ++
 src/com/stevesoft/pat/PatternSub.java              |   16 +
 src/com/stevesoft/pat/PopRule.java                 |   24 +
 src/com/stevesoft/pat/Prop.java                    |   75 +
 src/com/stevesoft/pat/Pthings.java                 |   47 +
 src/com/stevesoft/pat/PushRule.java                |   50 +
 src/com/stevesoft/pat/RBuffer.java                 |   52 +
 src/com/stevesoft/pat/Range.java                   |   97 +
 src/com/stevesoft/pat/RegOpt.java                  |  448 ++
 src/com/stevesoft/pat/RegRes.java                  |  299 ++
 src/com/stevesoft/pat/RegSyntax.java               |   30 +
 src/com/stevesoft/pat/RegSyntaxError.java          |   40 +
 src/com/stevesoft/pat/Regex.java                   | 2085 ++++++++
 src/com/stevesoft/pat/RegexReader.java             |  309 ++
 src/com/stevesoft/pat/RegexTokenizer.java          |  171 +
 src/com/stevesoft/pat/RegexWriter.java             |  276 ++
 src/com/stevesoft/pat/ReplaceRule.java             |  400 ++
 src/com/stevesoft/pat/Replacer.java                |  367 ++
 src/com/stevesoft/pat/RightRule.java               |   31 +
 src/com/stevesoft/pat/Rthings.java                 |   68 +
 src/com/stevesoft/pat/RuleHolder.java              |   43 +
 src/com/stevesoft/pat/Skip.java                    |  196 +
 src/com/stevesoft/pat/Skip2.java                   |   57 +
 src/com/stevesoft/pat/SkipBMH.java                 |  279 ++
 src/com/stevesoft/pat/Skipped.java                 |   56 +
 src/com/stevesoft/pat/SpecialRule.java             |   19 +
 src/com/stevesoft/pat/Start.java                   |   56 +
 src/com/stevesoft/pat/StrPos.java                  |  192 +
 src/com/stevesoft/pat/StringBufferLike.java        |   92 +
 src/com/stevesoft/pat/StringLike.java              |   47 +
 src/com/stevesoft/pat/StringRule.java              |   39 +
 src/com/stevesoft/pat/SubMark.java                 |   32 +
 src/com/stevesoft/pat/TransPat.java                |   51 +
 src/com/stevesoft/pat/Transformer.java             |  233 +
 src/com/stevesoft/pat/UniValidator.java            |   24 +
 src/com/stevesoft/pat/Validator.java               |   75 +
 src/com/stevesoft/pat/WantMoreTextReplaceRule.java |   29 +
 src/com/stevesoft/pat/lookAhead.java               |   99 +
 src/com/stevesoft/pat/oneChar.java                 |   76 +
 src/com/stevesoft/pat/parsePerl.java               |  373 ++
 src/com/stevesoft/pat/patInf.java                  |   16 +
 src/com/stevesoft/pat/patInt.java                  |  180 +
 .../stevesoft/pat/wrap/CharArrayBufferWrap.java    |   54 +
 src/com/stevesoft/pat/wrap/CharArrayWrap.java      |   75 +
 .../stevesoft/pat/wrap/RandomAccessFileWrap.java   |  170 +
 src/com/stevesoft/pat/wrap/StringBufferWrap.java   |   49 +
 src/com/stevesoft/pat/wrap/StringWrap.java         |   59 +
 src/com/stevesoft/pat/wrap/WriterWrap.java         |   61 +
 src/ext/vamsas/IRegistry.java                      |   24 +
 src/ext/vamsas/IRegistryService.java               |   29 +
 src/ext/vamsas/IRegistryServiceLocator.java        |  183 +
 src/ext/vamsas/Jpred.java                          |   34 +
 src/ext/vamsas/JpredService.java                   |   28 +
 src/ext/vamsas/JpredServiceLocator.java            |  181 +
 src/ext/vamsas/JpredSoapBindingStub.java           |  413 ++
 src/ext/vamsas/MuscleWS.java                       |   34 +
 src/ext/vamsas/MuscleWSService.java                |   29 +
 src/ext/vamsas/MuscleWSServiceLocator.java         |  190 +
 src/ext/vamsas/MuscleWSSoapBindingStub.java        |  458 ++
 src/ext/vamsas/RegistryServiceSoapBindingStub.java |  230 +
 src/ext/vamsas/SeqSearchI.java                     |   37 +
 src/ext/vamsas/SeqSearchServiceLocator.java        |  183 +
 src/ext/vamsas/SeqSearchServiceService.java        |   29 +
 .../vamsas/SeqSearchServiceSoapBindingStub.java    |  488 ++
 src/ext/vamsas/ServiceHandle.java                  |  254 +
 src/ext/vamsas/ServiceHandles.java                 |  154 +
 src/jalview/analysis/AAFrequency.java              |  336 ++
 src/jalview/analysis/AlignSeq.java                 |  921 ++++
 src/jalview/analysis/AlignmentSorter.java          |  949 ++++
 src/jalview/analysis/Conservation.java             |  698 +++
 src/jalview/analysis/CrossRef.java                 |  598 +++
 src/jalview/analysis/Dna.java                      |  716 +++
 src/jalview/analysis/Finder.java                   |  358 ++
 src/jalview/analysis/Grouping.java                 |  207 +
 src/jalview/analysis/NJTree.java                   | 1377 ++++++
 src/jalview/analysis/PCA.java                      |  255 +
 src/jalview/analysis/ParseProperties.java          |  180 +
 src/jalview/analysis/SeqsetUtils.java              |  300 ++
 src/jalview/analysis/SequenceIdMatcher.java        |  312 ++
 src/jalview/api/AlignmentViewPanel.java            |   34 +
 src/jalview/api/FeatureRenderer.java               |   37 +
 src/jalview/api/SequenceRenderer.java              |   29 +
 src/jalview/api/SequenceStructureBinding.java      |   31 +
 .../api/StructureSelectionManagerProvider.java     |   27 +
 src/jalview/appletgui/APopupMenu.java              | 1066 ++++
 src/jalview/appletgui/AlignFrame.java              | 3583 ++++++++++++++
 src/jalview/appletgui/AlignViewport.java           | 1761 +++++++
 src/jalview/appletgui/AlignmentPanel.java          |  983 ++++
 src/jalview/appletgui/AnnotationColourChooser.java |  546 +++
 src/jalview/appletgui/AnnotationLabels.java        |  713 +++
 src/jalview/appletgui/AnnotationPanel.java         | 1287 +++++
 src/jalview/appletgui/AppletJmol.java              |  656 +++
 src/jalview/appletgui/AppletJmolBinding.java       |  181 +
 src/jalview/appletgui/CutAndPasteTransfer.java     |  277 ++
 src/jalview/appletgui/EditNameDialog.java          |   76 +
 src/jalview/appletgui/EmbmenuFrame.java            |  314 ++
 src/jalview/appletgui/ExtJmol.java                 |  195 +
 src/jalview/appletgui/FeatureColourChooser.java    |  439 ++
 src/jalview/appletgui/FeatureRenderer.java         | 1266 +++++
 src/jalview/appletgui/FeatureSettings.java         |  834 ++++
 src/jalview/appletgui/Finder.java                  |  260 +
 src/jalview/appletgui/FontChooser.java             |  281 ++
 src/jalview/appletgui/IdCanvas.java                |  373 ++
 src/jalview/appletgui/IdPanel.java                 |  480 ++
 src/jalview/appletgui/IdwidthAdjuster.java         |  107 +
 src/jalview/appletgui/JVDialog.java                |   77 +
 src/jalview/appletgui/OverviewPanel.java           |  453 ++
 src/jalview/appletgui/PCAPanel.java                |  324 ++
 src/jalview/appletgui/PaintRefresher.java          |  249 +
 src/jalview/appletgui/PairwiseAlignPanel.java      |  170 +
 src/jalview/appletgui/RedundancyPanel.java         |  325 ++
 src/jalview/appletgui/RotatableCanvas.java         |  643 +++
 src/jalview/appletgui/ScalePanel.java              |  456 ++
 src/jalview/appletgui/SeqCanvas.java               |  815 ++++
 src/jalview/appletgui/SeqPanel.java                | 1815 +++++++
 src/jalview/appletgui/SequenceRenderer.java        |  362 ++
 src/jalview/appletgui/SliderPanel.java             |  376 ++
 src/jalview/appletgui/Tooltip.java                 |  233 +
 src/jalview/appletgui/TreeCanvas.java              |  679 +++
 src/jalview/appletgui/TreePanel.java               |  381 ++
 src/jalview/appletgui/UserDefinedColours.java      |  687 +++
 src/jalview/bin/Cache.java                         |  805 +++
 src/jalview/bin/Jalview.java                       | 1024 ++++
 src/jalview/bin/JalviewLite.java                   | 2686 ++++++++++
 src/jalview/bin/JalviewLiteURLRetrieve.java        |  144 +
 src/jalview/binding/Alignment.java                 |  186 +
 src/jalview/binding/Annotation.java                |  449 ++
 src/jalview/binding/AnnotationElement.java         |  308 ++
 src/jalview/binding/Colour.java                    |  500 ++
 src/jalview/binding/Feature.java                   |  307 ++
 src/jalview/binding/FeatureSettings.java           |  292 ++
 src/jalview/binding/Features.java                  |  133 +
 src/jalview/binding/JGroup.java                    |  756 +++
 src/jalview/binding/JSeq.java                      |  640 +++
 src/jalview/binding/JalviewModel.java              |  237 +
 src/jalview/binding/JalviewModelSequence.java      |  939 ++++
 src/jalview/binding/JalviewUserColours.java        |  347 ++
 src/jalview/binding/Pdbentry.java                  |  343 ++
 src/jalview/binding/PdbentryItem.java              |  209 +
 src/jalview/binding/Pdbids.java                    |  133 +
 src/jalview/binding/Property.java                  |  186 +
 src/jalview/binding/Sequence.java                  |  133 +
 src/jalview/binding/SequenceSet.java               |  531 ++
 src/jalview/binding/SequenceType.java              |  211 +
 src/jalview/binding/Setting.java                   |  267 +
 src/jalview/binding/Tree.java                      |  837 ++++
 src/jalview/binding/UserColourScheme.java          |  133 +
 src/jalview/binding/UserColours.java               |  186 +
 src/jalview/binding/VAMSAS.java                    |  598 +++
 src/jalview/binding/VamsasModel.java               |  133 +
 src/jalview/binding/Viewport.java                  | 1449 ++++++
 src/jalview/commands/ChangeCaseCommand.java        |  137 +
 src/jalview/commands/CommandI.java                 |   29 +
 src/jalview/commands/EditCommand.java              |  923 ++++
 src/jalview/commands/OrderCommand.java             |   61 +
 src/jalview/commands/RemoveGapColCommand.java      |  116 +
 src/jalview/commands/RemoveGapsCommand.java        |  129 +
 src/jalview/commands/SlideSequencesCommand.java    |   85 +
 src/jalview/commands/TrimRegionCommand.java        |  171 +
 src/jalview/datamodel/AlignedCodonFrame.java       |  318 ++
 src/jalview/datamodel/Alignment.java               | 1285 +++++
 src/jalview/datamodel/AlignmentAnnotation.java     |  826 ++++
 src/jalview/datamodel/AlignmentI.java              |  425 ++
 src/jalview/datamodel/AlignmentOrder.java          |  326 ++
 src/jalview/datamodel/AlignmentView.java           | 1175 +++++
 src/jalview/datamodel/Annotation.java              |  120 +
 src/jalview/datamodel/BinaryNode.java              |  299 ++
 src/jalview/datamodel/BinarySequence.java          |  168 +
 src/jalview/datamodel/CigarArray.java              |  379 ++
 src/jalview/datamodel/CigarBase.java               |  646 +++
 src/jalview/datamodel/CigarCigar.java              |   61 +
 src/jalview/datamodel/CigarSimple.java             |   32 +
 src/jalview/datamodel/ColumnSelection.java         | 1245 +++++
 src/jalview/datamodel/DBRefEntry.java              |  183 +
 src/jalview/datamodel/DBRefSource.java             |  133 +
 src/jalview/datamodel/FeatureProperties.java       |   48 +
 src/jalview/datamodel/GraphLine.java               |   54 +
 src/jalview/datamodel/HiddenSequences.java         |  280 ++
 src/jalview/datamodel/Mapping.java                 |  455 ++
 src/jalview/datamodel/NodeTransformI.java          |   27 +
 src/jalview/datamodel/PDBEntry.java                |  112 +
 src/jalview/datamodel/Provenance.java              |   47 +
 src/jalview/datamodel/ProvenanceEntry.java         |   53 +
 src/jalview/datamodel/SearchResults.java           |  190 +
 src/jalview/datamodel/SeqCigar.java                |  770 +++
 src/jalview/datamodel/Sequence.java                | 1175 +++++
 src/jalview/datamodel/SequenceFeature.java         |  299 ++
 src/jalview/datamodel/SequenceGroup.java           | 1170 +++++
 src/jalview/datamodel/SequenceI.java               |  352 ++
 src/jalview/datamodel/SequenceNode.java            |  184 +
 src/jalview/datamodel/SequencePoint.java           |   50 +
 src/jalview/datamodel/UniprotEntry.java            |   97 +
 src/jalview/datamodel/UniprotFile.java             |   35 +
 src/jalview/datamodel/UniprotProteinName.java      |   37 +
 src/jalview/datamodel/UniprotSequence.java         |   45 +
 src/jalview/datamodel/xdb/embl/BasePosition.java   |   59 +
 src/jalview/datamodel/xdb/embl/EmblEntry.java      |  823 ++++
 src/jalview/datamodel/xdb/embl/EmblError.java      |   40 +
 src/jalview/datamodel/xdb/embl/EmblFeature.java    |  100 +
 .../datamodel/xdb/embl/EmblFeatureLocElement.java  |  116 +
 .../datamodel/xdb/embl/EmblFeatureLocations.java   |  168 +
 src/jalview/datamodel/xdb/embl/EmblFile.java       |  143 +
 src/jalview/datamodel/xdb/embl/EmblSequence.java   |   78 +
 src/jalview/datamodel/xdb/embl/Qualifier.java      |  108 +
 src/jalview/ext/jmol/JalviewJmolBinding.java       | 1546 ++++++
 src/jalview/ext/jmol/JmolCommands.java             |  166 +
 src/jalview/gui/AlignFrame.java                    | 5109 ++++++++++++++++++++
 src/jalview/gui/AlignViewport.java                 | 2285 +++++++++
 src/jalview/gui/AlignmentPanel.java                | 1453 ++++++
 src/jalview/gui/AnnotationColourChooser.java       |  579 +++
 src/jalview/gui/AnnotationExporter.java            |  303 ++
 src/jalview/gui/AnnotationLabels.java              |  878 ++++
 src/jalview/gui/AnnotationPanel.java               | 1503 ++++++
 src/jalview/gui/AppJmol.java                       | 1331 +++++
 src/jalview/gui/AppJmolBinding.java                |  230 +
 src/jalview/gui/AssociatePdbFileWithSeq.java       |   78 +
 src/jalview/gui/BlogReader.java                    |  851 ++++
 src/jalview/gui/ConservationThread.java            |  103 +
 src/jalview/gui/Console.java                       |  649 +++
 src/jalview/gui/CutAndPasteTransfer.java           |  260 +
 src/jalview/gui/DasSourceBrowser.java              |  962 ++++
 src/jalview/gui/Desktop.java                       | 2504 ++++++++++
 src/jalview/gui/EPSOptions.java                    |  148 +
 src/jalview/gui/EditNameDialog.java                |   82 +
 src/jalview/gui/FeatureColourChooser.java          |  545 +++
 src/jalview/gui/FeatureRenderer.java               | 1462 ++++++
 src/jalview/gui/FeatureSettings.java               | 1741 +++++++
 src/jalview/gui/Finder.java                        |  264 +
 src/jalview/gui/FontChooser.java                   |  270 ++
 src/jalview/gui/IProgressIndicator.java            |   49 +
 src/jalview/gui/IProgressIndicatorHandler.java     |   35 +
 src/jalview/gui/IdCanvas.java                      |  488 ++
 src/jalview/gui/IdPanel.java                       |  514 ++
 src/jalview/gui/IdwidthAdjuster.java               |  171 +
 src/jalview/gui/Jalview2XML.java                   | 3917 +++++++++++++++
 src/jalview/gui/Jalview2XML_V1.java                |  468 ++
 src/jalview/gui/JalviewAppender.java               |   60 +
 src/jalview/gui/JalviewChangeSupport.java          |   87 +
 src/jalview/gui/JalviewDialog.java                 |  171 +
 src/jalview/gui/JvSwingUtils.java                  |  194 +
 src/jalview/gui/OOMWarning.java                    |   88 +
 src/jalview/gui/OptsAndParamsPage.java             |  883 ++++
 src/jalview/gui/OptsParametersContainerI.java      |   30 +
 src/jalview/gui/OverviewPanel.java                 |  458 ++
 src/jalview/gui/PCAPanel.java                      |  588 +++
 src/jalview/gui/PaintRefresher.java                |  245 +
 src/jalview/gui/PairwiseAlignPanel.java            |  154 +
 src/jalview/gui/PopupMenu.java                     | 1897 ++++++++
 src/jalview/gui/Preferences.java                   |  678 +++
 src/jalview/gui/PromptUserConfig.java              |  249 +
 src/jalview/gui/RedundancyPanel.java               |  341 ++
 src/jalview/gui/RestInputParamEditDialog.java      |  266 +
 src/jalview/gui/RestServiceEditorPane.java         |  506 ++
 src/jalview/gui/RotatableCanvas.java               |  835 ++++
 src/jalview/gui/ScalePanel.java                    |  511 ++
 src/jalview/gui/ScriptWindow.java                  |  732 +++
 src/jalview/gui/SeqCanvas.java                     |  946 ++++
 src/jalview/gui/SeqPanel.java                      | 1970 ++++++++
 src/jalview/gui/SequenceFetcher.java               |  834 ++++
 src/jalview/gui/SequenceRenderer.java              |  494 ++
 src/jalview/gui/SliderPanel.java                   |  372 ++
 src/jalview/gui/SplashScreen.java                  |  221 +
 src/jalview/gui/TextColourChooser.java             |  207 +
 src/jalview/gui/TreeCanvas.java                    |  995 ++++
 src/jalview/gui/TreePanel.java                     |  830 ++++
 src/jalview/gui/UserDefinedColours.java            |  932 ++++
 src/jalview/gui/UserQuestionnaireCheck.java        |  158 +
 src/jalview/gui/VamsasApplication.java             | 1114 +++++
 src/jalview/gui/ViewSelectionMenu.java             |  308 ++
 src/jalview/gui/WebserviceInfo.java                |  842 ++++
 src/jalview/gui/WsJobParameters.java               | 1388 ++++++
 src/jalview/gui/WsParamSetManager.java             |  315 ++
 src/jalview/gui/WsPreferences.java                 |  525 ++
 src/jalview/io/AMSAFile.java                       |  102 +
 src/jalview/io/AlignFile.java                      |  290 ++
 src/jalview/io/AlignmentProperties.java            |  147 +
 src/jalview/io/AnnotationFile.java                 | 1487 ++++++
 src/jalview/io/AppletFormatAdapter.java            |  718 +++
 src/jalview/io/BLCFile.java                        |  282 ++
 src/jalview/io/ClansFile.java                      |   27 +
 src/jalview/io/ClustalFile.java                    |  219 +
 src/jalview/io/DBRefFile.java                      |   44 +
 src/jalview/io/FastaFile.java                      |  241 +
 src/jalview/io/FeaturesFile.java                   | 1002 ++++
 src/jalview/io/FileLoader.java                     |  463 ++
 src/jalview/io/FileParse.java                      |  410 ++
 src/jalview/io/FormatAdapter.java                  |  245 +
 src/jalview/io/HTMLOutput.java                     |  381 ++
 src/jalview/io/IdentifyFile.java                   |  300 ++
 src/jalview/io/JPredFile.java                      |  431 ++
 src/jalview/io/JalviewFileChooser.java             |  286 ++
 src/jalview/io/JalviewFileFilter.java              |  172 +
 src/jalview/io/JalviewFileView.java                |  110 +
 src/jalview/io/JnetAnnotationMaker.java            |  200 +
 src/jalview/io/MSFfile.java                        |  414 ++
 src/jalview/io/MatrixFile.java                     |   34 +
 src/jalview/io/ModellerDescription.java            |  421 ++
 src/jalview/io/NewickFile.java                     |  975 ++++
 src/jalview/io/PIRFile.java                        |  198 +
 src/jalview/io/PfamFile.java                       |  177 +
 src/jalview/io/PileUpfile.java                     |  200 +
 src/jalview/io/SimpleBlastFile.java                |  294 ++
 src/jalview/io/StockholmFile.java                  |  583 +++
 src/jalview/io/VamsasAppDatastore.java             | 2778 +++++++++++
 src/jalview/io/WSWUBlastClient.java                |  304 ++
 src/jalview/io/packed/DataProvider.java            |   78 +
 src/jalview/io/packed/JalviewDataset.java          |  272 ++
 src/jalview/io/packed/ParsePackedSet.java          |  297 ++
 src/jalview/io/packed/SimpleDataProvider.java      |   66 +
 src/jalview/io/vamsas/Datasetsequence.java         |  275 ++
 src/jalview/io/vamsas/DatastoreItem.java           |  582 +++
 src/jalview/io/vamsas/DatastoreRegistry.java       |  176 +
 src/jalview/io/vamsas/Dbref.java                   |  236 +
 src/jalview/io/vamsas/LocalDocSyncObject.java      |  124 +
 src/jalview/io/vamsas/Rangetype.java               |  336 ++
 src/jalview/io/vamsas/Sequencefeature.java         |  359 ++
 src/jalview/io/vamsas/Sequencemapping.java         |  465 ++
 src/jalview/io/vamsas/Tree.java                    |  643 +++
 src/jalview/javascript/JSFunctionExec.java         |  273 ++
 src/jalview/javascript/JalviewLiteJsApi.java       |  511 ++
 src/jalview/javascript/JsCallBack.java             |   25 +
 src/jalview/javascript/JsSelectionSender.java      |  147 +
 src/jalview/javascript/MouseOverListener.java      |  101 +
 .../javascript/MouseOverStructureListener.java     |  322 ++
 src/jalview/jbgui/GAlignFrame.java                 | 2420 +++++++++
 src/jalview/jbgui/GAlignmentPanel.java             |  125 +
 src/jalview/jbgui/GCutAndPasteTransfer.java        |  233 +
 src/jalview/jbgui/GDasSourceBrowser.java           |  221 +
 src/jalview/jbgui/GDesktop.java                    |  528 ++
 src/jalview/jbgui/GFinder.java                     |  197 +
 src/jalview/jbgui/GFontChooser.java                |  275 ++
 src/jalview/jbgui/GPCAPanel.java                   |  306 ++
 src/jalview/jbgui/GPairwiseAlignPanel.java         |   93 +
 src/jalview/jbgui/GPreferences.java                |  896 ++++
 src/jalview/jbgui/GRestInputParamEditDialog.java   |  110 +
 src/jalview/jbgui/GRestServiceEditorPane.java      |  517 ++
 src/jalview/jbgui/GSequenceLink.java               |  158 +
 src/jalview/jbgui/GSliderPanel.java                |  207 +
 src/jalview/jbgui/GStructureViewer.java            |  398 ++
 src/jalview/jbgui/GTreePanel.java                  |  278 ++
 src/jalview/jbgui/GUserDefinedColours.java         |  283 ++
 src/jalview/jbgui/GWebserviceInfo.java             |  124 +
 src/jalview/jbgui/GWsPreferences.java              |  499 ++
 src/jalview/math/Matrix.java                       |  856 ++++
 src/jalview/math/RotatableMatrix.java              |  343 ++
 src/jalview/schemabinding/version2/.castor.cdr     |   45 +
 src/jalview/schemabinding/version2/AlcodMap.java   |  201 +
 src/jalview/schemabinding/version2/Alcodon.java    |  280 ++
 .../schemabinding/version2/AlcodonFrame.java       |  449 ++
 src/jalview/schemabinding/version2/Annotation.java | 1102 +++++
 .../schemabinding/version2/AnnotationColours.java  |  379 ++
 .../schemabinding/version2/AnnotationElement.java  |  357 ++
 src/jalview/schemabinding/version2/Colour.java     |  500 ++
 src/jalview/schemabinding/version2/DBRef.java      |  236 +
 src/jalview/schemabinding/version2/Feature.java    |  536 ++
 .../schemabinding/version2/FeatureSettings.java    |  449 ++
 src/jalview/schemabinding/version2/Features.java   |  133 +
 src/jalview/schemabinding/version2/Group.java      |  219 +
 .../schemabinding/version2/HiddenColumns.java      |  233 +
 src/jalview/schemabinding/version2/JGroup.java     | 1167 +++++
 src/jalview/schemabinding/version2/JSeq.java       |  831 ++++
 .../schemabinding/version2/JalviewModel.java       |  238 +
 .../version2/JalviewModelSequence.java             |  942 ++++
 .../schemabinding/version2/JalviewUserColours.java |  348 ++
 .../schemabinding/version2/MapListFrom.java        |  233 +
 src/jalview/schemabinding/version2/MapListTo.java  |  233 +
 .../schemabinding/version2/MapListType.java        |  599 +++
 src/jalview/schemabinding/version2/Mapping.java    |  182 +
 .../schemabinding/version2/MappingChoice.java      |  187 +
 src/jalview/schemabinding/version2/OtherData.java  |  187 +
 src/jalview/schemabinding/version2/Pdbentry.java   |  369 ++
 .../schemabinding/version2/PdbentryItem.java       |  209 +
 src/jalview/schemabinding/version2/Pdbids.java     |  297 ++
 src/jalview/schemabinding/version2/Property.java   |  187 +
 src/jalview/schemabinding/version2/Sequence.java   |  328 ++
 .../schemabinding/version2/SequenceSet.java        |  824 ++++
 .../version2/SequenceSetProperties.java            |  187 +
 .../schemabinding/version2/SequenceType.java       |  237 +
 src/jalview/schemabinding/version2/Setting.java    |  683 +++
 .../schemabinding/version2/StructureState.java     |  693 +++
 .../schemabinding/version2/ThresholdLine.java      |  258 +
 src/jalview/schemabinding/version2/Tree.java       |  869 ++++
 .../schemabinding/version2/UserColourScheme.java   |  134 +
 .../schemabinding/version2/UserColours.java        |  187 +
 src/jalview/schemabinding/version2/VAMSAS.java     |  446 ++
 .../schemabinding/version2/VamsasModel.java        |  133 +
 src/jalview/schemabinding/version2/Viewport.java   | 2451 ++++++++++
 .../version2/WebServiceParameterSet.java           |  456 ++
 .../version2/descriptors/AlcodMapDescriptor.java   |  251 +
 .../version2/descriptors/AlcodonDescriptor.java    |  297 ++
 .../descriptors/AlcodonFrameDescriptor.java        |  261 +
 .../descriptors/AnnotationColoursDescriptor.java   |  420 ++
 .../version2/descriptors/AnnotationDescriptor.java |  943 ++++
 .../descriptors/AnnotationElementDescriptor.java   |  422 ++
 .../version2/descriptors/ColourDescriptor.java     |  534 ++
 .../version2/descriptors/DBRefDescriptor.java      |  321 ++
 .../version2/descriptors/FeatureDescriptor.java    |  498 ++
 .../descriptors/FeatureSettingsDescriptor.java     |  261 +
 .../version2/descriptors/FeaturesDescriptor.java   |  168 +
 .../version2/descriptors/GroupDescriptor.java      |  254 +
 .../descriptors/HiddenColumnsDescriptor.java       |  260 +
 .../version2/descriptors/JGroupDescriptor.java     |  967 ++++
 .../version2/descriptors/JSeqDescriptor.java       |  520 ++
 .../descriptors/JalviewModelDescriptor.java        |  329 ++
 .../JalviewModelSequenceDescriptor.java            |  421 ++
 .../descriptors/JalviewUserColoursDescriptor.java  |  293 ++
 .../descriptors/MapListFromDescriptor.java         |  260 +
 .../version2/descriptors/MapListToDescriptor.java  |  260 +
 .../descriptors/MapListTypeDescriptor.java         |  345 ++
 .../descriptors/MappingChoiceDescriptor.java       |  247 +
 .../version2/descriptors/MappingDescriptor.java    |  213 +
 .../version2/descriptors/OtherDataDescriptor.java  |  252 +
 .../version2/descriptors/PdbentryDescriptor.java   |  329 ++
 .../descriptors/PdbentryItemDescriptor.java        |  219 +
 .../version2/descriptors/PdbidsDescriptor.java     |  220 +
 .../version2/descriptors/PropertyDescriptor.java   |  252 +
 .../version2/descriptors/SequenceDescriptor.java   |  257 +
 .../descriptors/SequenceSetDescriptor.java         |  421 ++
 .../SequenceSetPropertiesDescriptor.java           |  248 +
 .../descriptors/SequenceTypeDescriptor.java        |  327 ++
 .../version2/descriptors/SettingDescriptor.java    |  637 +++
 .../descriptors/StructureStateDescriptor.java      |  583 +++
 .../descriptors/ThresholdLineDescriptor.java       |  297 ++
 .../version2/descriptors/TreeDescriptor.java       |  832 ++++
 .../descriptors/UserColourSchemeDescriptor.java    |  168 +
 .../descriptors/UserColoursDescriptor.java         |  249 +
 .../version2/descriptors/VAMSASDescriptor.java     |  266 +
 .../descriptors/VamsasModelDescriptor.java         |  168 +
 .../version2/descriptors/ViewportDescriptor.java   | 1975 ++++++++
 .../WebServiceParameterSetDescriptor.java          |  371 ++
 src/jalview/schemes/AnnotationColourGradient.java  |  226 +
 src/jalview/schemes/Blosum62ColourScheme.java      |   88 +
 src/jalview/schemes/BuriedColourScheme.java        |   51 +
 src/jalview/schemes/ClustalxColourScheme.java      |  334 ++
 src/jalview/schemes/ColourSchemeI.java             |   42 +
 src/jalview/schemes/ColourSchemeProperty.java      |  525 ++
 src/jalview/schemes/Consensus.java                 |   94 +
 src/jalview/schemes/GraduatedColor.java            |  295 ++
 src/jalview/schemes/HelixColourScheme.java         |   34 +
 src/jalview/schemes/HydrophobicColourScheme.java   |   51 +
 src/jalview/schemes/NucleotideColourScheme.java    |   87 +
 src/jalview/schemes/PIDColourScheme.java           |   92 +
 src/jalview/schemes/ResidueColourScheme.java       |  281 ++
 src/jalview/schemes/ResidueProperties.java         | 1310 +++++
 src/jalview/schemes/ScoreColourScheme.java         |  125 +
 src/jalview/schemes/ScoreMatrix.java               |   86 +
 src/jalview/schemes/StrandColourScheme.java        |   51 +
 src/jalview/schemes/TaylorColourScheme.java        |   26 +
 src/jalview/schemes/TurnColourScheme.java          |   51 +
 src/jalview/schemes/UserColourScheme.java          |  238 +
 src/jalview/schemes/ZappoColourScheme.java         |   35 +
 .../structure/AlignmentViewPanelListener.java      |   33 +
 src/jalview/structure/SelectionListener.java       |   39 +
 src/jalview/structure/SelectionSource.java         |   28 +
 src/jalview/structure/SequenceListener.java        |   29 +
 src/jalview/structure/StructureListener.java       |   68 +
 src/jalview/structure/StructureMapping.java        |   98 +
 .../structure/StructureMappingcommandSet.java      |   51 +
 .../structure/StructureSelectionManager.java       |  813 ++++
 src/jalview/structure/VamsasListener.java          |   34 +
 src/jalview/structure/VamsasSource.java            |   31 +
 src/jalview/util/AWTConsole.java                   |  249 +
 src/jalview/util/BrowserLauncher.java              |  889 ++++
 src/jalview/util/Comparison.java                   |  259 +
 src/jalview/util/DBRefUtils.java                   |  449 ++
 src/jalview/util/Format.java                       |  938 ++++
 src/jalview/util/GroupUrlLink.java                 |  911 ++++
 src/jalview/util/ImageMaker.java                   |  185 +
 src/jalview/util/MapList.java                      | 1000 ++++
 src/jalview/util/ParseHtmlBodyAndLinks.java        |  156 +
 src/jalview/util/Platform.java                     |   54 +
 src/jalview/util/QuickSort.java                    |  229 +
 src/jalview/util/ShiftList.java                    |  143 +
 src/jalview/util/TableSorter.java                  |  597 +++
 src/jalview/util/UrlLink.java                      |  398 ++
 src/jalview/util/jarInputStreamProvider.java       |   45 +
 src/jalview/ws/AWSThread.java                      |  369 ++
 src/jalview/ws/AWsJob.java                         |  227 +
 src/jalview/ws/DBRefFetcher.java                   |  721 +++
 src/jalview/ws/DasSequenceFeatureFetcher.java      |  898 ++++
 src/jalview/ws/EnfinEnvision2OneWay.java           |  709 +++
 src/jalview/ws/JobStateSummary.java                |  165 +
 src/jalview/ws/SequenceFetcher.java                |  407 ++
 src/jalview/ws/WSClient.java                       |   74 +
 src/jalview/ws/WSClientI.java                      |   46 +
 src/jalview/ws/WSMenuEntryProviderI.java           |   36 +
 src/jalview/ws/dbsources/DasSequenceSource.java    |  176 +
 .../ws/dbsources/EbiFileRetrievedProxy.java        |   64 +
 src/jalview/ws/dbsources/EmblCdsSouce.java         |   88 +
 src/jalview/ws/dbsources/EmblSource.java           |  127 +
 src/jalview/ws/dbsources/EmblXmlSource.java        |  162 +
 src/jalview/ws/dbsources/GeneDbSource.java         |  130 +
 src/jalview/ws/dbsources/Pdb.java                  |  218 +
 src/jalview/ws/dbsources/Pfam.java                 |  154 +
 src/jalview/ws/dbsources/PfamFull.java             |   63 +
 src/jalview/ws/dbsources/PfamSeed.java             |   65 +
 src/jalview/ws/dbsources/Uniprot.java              |  297 ++
 src/jalview/ws/dbsources/UnprotName.java           |   41 +
 .../dbsources/das/DasSequenceSourceListener.java   |  165 +
 src/jalview/ws/ebi/EBIFetchClient.java             |  242 +
 src/jalview/ws/io/mime/HttpContentHandler.java     |   34 +
 .../ws/io/mime/JalviewMimeContentHandler.java      |  173 +
 src/jalview/ws/io/mime/MimeTypes.java              |   78 +
 src/jalview/ws/jws1/Discoverer.java                |  433 ++
 src/jalview/ws/jws1/JPredClient.java               |  354 ++
 src/jalview/ws/jws1/JPredThread.java               |  574 +++
 src/jalview/ws/jws1/JWS1Thread.java                |   48 +
 src/jalview/ws/jws1/MsaWSClient.java               |  235 +
 src/jalview/ws/jws1/MsaWSThread.java               |  702 +++
 src/jalview/ws/jws1/SeqSearchWSClient.java         |  316 ++
 src/jalview/ws/jws1/SeqSearchWSThread.java         |  661 +++
 src/jalview/ws/jws1/WS1Client.java                 |  129 +
 src/jalview/ws/jws1/WSJob.java                     |  147 +
 src/jalview/ws/jws2/AWS2Thread.java                |   33 +
 src/jalview/ws/jws2/JWs2Job.java                   |  158 +
 src/jalview/ws/jws2/JabaParamStore.java            |  338 ++
 src/jalview/ws/jws2/JabaPreset.java                |   97 +
 src/jalview/ws/jws2/JabaWsServerQuery.java         |  128 +
 src/jalview/ws/jws2/Jws2Client.java                |   70 +
 src/jalview/ws/jws2/Jws2Discoverer.java            |  804 +++
 src/jalview/ws/jws2/MsaWSClient.java               |  365 ++
 src/jalview/ws/jws2/MsaWSThread.java               |  975 ++++
 src/jalview/ws/jws2/ParameterUtils.java            |  205 +
 src/jalview/ws/jws2/dm/JabaOption.java             |  105 +
 src/jalview/ws/jws2/dm/JabaParameter.java          |   55 +
 src/jalview/ws/jws2/dm/JabaValueConstrain.java     |   59 +
 src/jalview/ws/jws2/dm/JabaWsParamSet.java         |  204 +
 src/jalview/ws/params/ArgumentI.java               |   40 +
 .../ws/params/InvalidArgumentException.java        |   50 +
 src/jalview/ws/params/OptionI.java                 |   36 +
 src/jalview/ws/params/ParamDatastoreI.java         |   89 +
 src/jalview/ws/params/ParamManager.java            |   71 +
 src/jalview/ws/params/ParameterI.java              |   31 +
 src/jalview/ws/params/ValueConstrainI.java         |   40 +
 src/jalview/ws/params/WsParamSetI.java             |   80 +
 src/jalview/ws/params/simple/BooleanOption.java    |   35 +
 src/jalview/ws/params/simple/IntegerParameter.java |   99 +
 src/jalview/ws/params/simple/Option.java           |  118 +
 src/jalview/ws/params/simple/Parameter.java        |   42 +
 .../ws/params/simple/StringChoiceParameter.java    |   23 +
 src/jalview/ws/rest/AlignmentProcessor.java        |   29 +
 src/jalview/ws/rest/HttpResultSet.java             |  232 +
 src/jalview/ws/rest/InputType.java                 |  266 +
 src/jalview/ws/rest/NoValidInputDataException.java |   38 +
 src/jalview/ws/rest/RestClient.java                |  451 ++
 src/jalview/ws/rest/RestJob.java                   |  473 ++
 src/jalview/ws/rest/RestJobThread.java             | 1311 +++++
 src/jalview/ws/rest/RestServiceDescription.java    | 1096 +++++
 src/jalview/ws/rest/params/Alignment.java          |  205 +
 src/jalview/ws/rest/params/AnnotationFile.java     |  124 +
 src/jalview/ws/rest/params/JobConstant.java        |  115 +
 .../ws/rest/params/SeqGroupIndexVector.java        |  302 ++
 src/jalview/ws/rest/params/SeqIdVector.java        |  138 +
 src/jalview/ws/rest/params/SeqVector.java          |  128 +
 src/jalview/ws/rest/params/Tree.java               |   81 +
 src/jalview/ws/seqfetcher/ASequenceFetcher.java    |  334 ++
 src/jalview/ws/seqfetcher/DbSourceProxy.java       |  131 +
 src/jalview/ws/seqfetcher/DbSourceProxyImpl.java   |  139 +
 .../biojava/dasobert/das/DAS_FeatureRetrieve.java  |  287 ++
 .../biojava/dasobert/das/DAS_Feature_Handler.java  |  314 ++
 .../biojava/dasobert/das/DAS_Sequence_Handler.java |  161 +
 src/org/biojava/dasobert/das/FeatureThread.java    |  198 +
 src/org/biojava/dasobert/das/SequenceThread.java   |  299 ++
 src/org/biojava/dasobert/das2/Das2Capability.java  |   51 +
 .../biojava/dasobert/das2/Das2CapabilityImpl.java  |  131 +
 src/org/biojava/dasobert/das2/Das2Source.java      |   42 +
 src/org/biojava/dasobert/das2/Das2SourceImpl.java  |  157 +
 .../biojava/dasobert/das2/DasSourceConverter.java  |   92 +
 .../dasobert/das2/io/DAS2SourceHandler.java        |  216 +
 .../biojava/dasobert/das2/io/DasSourceReader.java  |   33 +
 .../dasobert/das2/io/DasSourceReaderImpl.java      |  183 +
 .../biojava/dasobert/dasregistry/Das1Source.java   |  305 ++
 .../dasobert/dasregistry/Das2Validator.java        |   44 +
 .../dasregistry/DasCoordSysComparator.java         |  128 +
 .../dasobert/dasregistry/DasCoordinateSystem.java  |  233 +
 .../biojava/dasobert/dasregistry/DasSource.java    |  130 +
 .../dasobert/dasregistry/DasSourceComparator.java  |  190 +
 .../dasobert/eventmodel/AbstractDasEvent.java      |   43 +
 .../biojava/dasobert/eventmodel/FeatureEvent.java  |   96 +
 .../dasobert/eventmodel/FeatureListener.java       |   48 +
 .../dasobert/eventmodel/ObjectListener.java        |   51 +
 .../biojava/dasobert/eventmodel/SequenceEvent.java |   62 +
 .../dasobert/eventmodel/SequenceListener.java      |   64 +
 .../dasobert/feature/AbstractFeatureTrack.java     |  278 ++
 .../biojava/dasobert/feature/AbstractSegment.java  |  256 +
 .../dasobert/feature/FeatureComparator.java        |   87 +
 .../dasobert/feature/FeatureMapComparator.java     |   68 +
 src/org/biojava/dasobert/feature/FeatureTrack.java |  127 +
 .../dasobert/feature/FeatureTrackConverter.java    |  526 ++
 .../biojava/dasobert/feature/FeatureTrackImpl.java |   68 +
 .../biojava/dasobert/feature/HistogramFeature.java |   95 +
 .../biojava/dasobert/feature/HistogramSegment.java |   67 +
 src/org/biojava/dasobert/feature/Segment.java      |   84 +
 .../dasobert/feature/SegmentComparator.java        |   45 +
 src/org/biojava/dasobert/feature/SegmentImpl.java  |   83 +
 src/org/jibble/epsgraphics/EpsDocument.java        |  267 +
 src/org/jibble/epsgraphics/EpsException.java       |   27 +
 src/org/jibble/epsgraphics/EpsGraphics2D.java      | 1444 ++++++
 src/uk/ac/ebi/picr/model/CrossReference.java       |  330 ++
 .../ac/ebi/picr/model/CrossReference_Helper.java   |  125 +
 src/uk/ac/ebi/picr/model/UPEntry.java              |  290 ++
 src/uk/ac/ebi/picr/model/UPEntry_Helper.java       |  106 +
 src/uk/ac/ebi/www/Data.java                        |  154 +
 src/uk/ac/ebi/www/InputParams.java                 |  466 ++
 src/uk/ac/ebi/www/WSFile.java                      |  154 +
 src/uk/ac/ebi/www/WSWUBlast.java                   |   42 +
 src/uk/ac/ebi/www/WSWUBlastService.java            |   29 +
 src/uk/ac/ebi/www/WSWUBlastServiceLocator.java     |  132 +
 src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java    |  487 ++
 .../AccessionMapperBindingStub.java                |  397 ++
 .../AccessionMapperInterface.java                  |   34 +
 .../AccessionMapperService.java                    |   29 +
 .../AccessionMapperServiceLocator.java             |  189 +
 src/vamsas/IMsaWS.java                             |   31 +
 src/vamsas/objects/simple/Alignment.java           |  162 +
 src/vamsas/objects/simple/Alignment_Helper.java    |   80 +
 src/vamsas/objects/simple/JpredResult.java         |  131 +
 src/vamsas/objects/simple/JpredResult_Helper.java  |   74 +
 src/vamsas/objects/simple/MsaResult.java           |  131 +
 src/vamsas/objects/simple/MsaResult_Helper.java    |   86 +
 src/vamsas/objects/simple/Msfalignment.java        |  130 +
 src/vamsas/objects/simple/Msfalignment_Helper.java |   74 +
 src/vamsas/objects/simple/Object.java              |   63 +
 src/vamsas/objects/simple/Object_Helper.java       |   62 +
 src/vamsas/objects/simple/Result.java              |  349 ++
 src/vamsas/objects/simple/Result_Helper.java       |  128 +
 src/vamsas/objects/simple/Secstructpred.java       |  100 +
 .../objects/simple/Secstructpred_Helper.java       |   68 +
 src/vamsas/objects/simple/SeqSearchResult.java     |  185 +
 .../objects/simple/SeqSearchResult_Helper.java     |   86 +
 src/vamsas/objects/simple/Sequence.java            |  124 +
 src/vamsas/objects/simple/SequenceSet.java         |  101 +
 src/vamsas/objects/simple/SequenceSet_Helper.java  |   68 +
 src/vamsas/objects/simple/Sequence_Helper.java     |   74 +
 src/vamsas/objects/simple/WsJobId.java             |  120 +
 src/vamsas/objects/simple/WsJobId_Helper.java      |   74 +
 870 files changed, 263042 insertions(+), 23 deletions(-)
 create mode 100644 JalviewApplet.jpx
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 create mode 100644 LICENSE
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 create mode 100644 help/html/features/newkeystrokes.html
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 create mode 100644 help/html/io/modellerpir.html
 create mode 100644 help/html/jalviewjnlp.html
 create mode 100644 help/html/keys.html
 create mode 100644 help/html/memory.html
 create mode 100644 help/html/menus/alignmentMenu.html
 create mode 100644 help/html/menus/alwannotations.html
 create mode 100644 help/html/menus/alwcalculate.html
 create mode 100644 help/html/menus/alwcolour.html
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 create mode 100644 help/html/menus/alwview.html
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 create mode 100644 help/html/menus/wsmenu.html
 create mode 100644 help/html/misc/aaproperties.html
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 create mode 100644 help/html/misc/aminoAcids.html
 create mode 100644 help/html/misc/arg.jpg
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 create mode 100644 help/html/webServices/JABAWS.html
 create mode 100644 help/html/webServices/clwqueued.gif
 create mode 100644 help/html/webServices/dbreffetcher.html
 create mode 100644 help/html/webServices/index.html
 create mode 100644 help/html/webServices/invalidurldialog.gif
 create mode 100644 help/html/webServices/jalviewrssreader.gif
 create mode 100644 help/html/webServices/jnet.html
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 create mode 100644 src/com/stevesoft/pat/AmpersandRule.java
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 create mode 100644 src/jalview/analysis/AAFrequency.java
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 create mode 100644 src/jalview/api/AlignmentViewPanel.java
 create mode 100644 src/jalview/api/FeatureRenderer.java
 create mode 100644 src/jalview/api/SequenceRenderer.java
 create mode 100644 src/jalview/api/SequenceStructureBinding.java
 create mode 100644 src/jalview/api/StructureSelectionManagerProvider.java
 create mode 100644 src/jalview/appletgui/APopupMenu.java
 create mode 100644 src/jalview/appletgui/AlignFrame.java
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 create mode 100644 src/jalview/appletgui/AnnotationColourChooser.java
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