JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this...
authorBen Soares <bsoares@dundee.ac.uk>
Thu, 25 Apr 2019 16:25:50 +0000 (17:25 +0100)
committerBen Soares <bsoares@dundee.ac.uk>
Thu, 25 Apr 2019 16:25:50 +0000 (17:25 +0100)
commit44d68d55d9c85bf7b28853feeebc4b901c4a8392
treeeafcd88173b6c54b90c8e9ff2b9943b72e0c3db0
parent6f9d7b98943ecba292a9c0dd65b30c4d8150c98f
JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this in to eclipse classpath generation
200 files changed:
build.gradle
gradle.properties
help/help/help.hs [moved from help/help.hs with 100% similarity]
help/help/help.jhm [moved from help/help.jhm with 100% similarity]
help/help/helpTOC.xml [moved from help/helpTOC.xml with 100% similarity]
help/help/html/.cvsignore [moved from help/html/.cvsignore with 100% similarity]
help/help/html/Jalview_Logo.png [moved from help/html/Jalview_Logo.png with 100% similarity]
help/help/html/align.jpg [moved from help/html/align.jpg with 100% similarity]
help/help/html/calculations/calculatedialog.png [moved from help/html/calculations/calculatedialog.png with 100% similarity]
help/help/html/calculations/calculations.html [moved from help/html/calculations/calculations.html with 100% similarity]
help/help/html/calculations/consensus.html [moved from help/html/calculations/consensus.html with 100% similarity]
help/help/html/calculations/conservation.html [moved from help/html/calculations/conservation.html with 100% similarity]
help/help/html/calculations/pairwise.html [moved from help/html/calculations/pairwise.html with 100% similarity]
help/help/html/calculations/pca.html [moved from help/html/calculations/pca.html with 100% similarity]
help/help/html/calculations/pcaviewer.gif [moved from help/html/calculations/pcaviewer.gif with 100% similarity]
help/help/html/calculations/quality.html [moved from help/html/calculations/quality.html with 100% similarity]
help/help/html/calculations/recoverInputdata.html [moved from help/html/calculations/recoverInputdata.html with 100% similarity]
help/help/html/calculations/redundancy.html [moved from help/html/calculations/redundancy.html with 100% similarity]
help/help/html/calculations/referenceseq.html [moved from help/html/calculations/referenceseq.html with 100% similarity]
help/help/html/calculations/scorematrices.html [moved from help/html/calculations/scorematrices.html with 100% similarity]
help/help/html/calculations/sorting.html [moved from help/html/calculations/sorting.html with 100% similarity]
help/help/html/calculations/structureconsensus.html [moved from help/html/calculations/structureconsensus.html with 100% similarity]
help/help/html/calculations/tree.html [moved from help/html/calculations/tree.html with 100% similarity]
help/help/html/calculations/treeviewer.html [moved from help/html/calculations/treeviewer.html with 100% similarity]
help/help/html/colourSchemes/.cvsignore [moved from help/html/colourSchemes/.cvsignore with 100% similarity]
help/help/html/colourSchemes/abovePID.html [moved from help/html/colourSchemes/abovePID.html with 100% similarity]
help/help/html/colourSchemes/annotationColourSetting.gif [moved from help/html/colourSchemes/annotationColourSetting.gif with 100% similarity]
help/help/html/colourSchemes/annotationColouring.html [moved from help/html/colourSchemes/annotationColouring.html with 100% similarity]
help/help/html/colourSchemes/annotationColours.gif [moved from help/html/colourSchemes/annotationColours.gif with 100% similarity]
help/help/html/colourSchemes/blosum.html [moved from help/html/colourSchemes/blosum.html with 100% similarity]
help/help/html/colourSchemes/buried.html [moved from help/html/colourSchemes/buried.html with 100% similarity]
help/help/html/colourSchemes/clustal.html [moved from help/html/colourSchemes/clustal.html with 100% similarity]
help/help/html/colourSchemes/colbytcoffee.png [moved from help/html/colourSchemes/colbytcoffee.png with 100% similarity]
help/help/html/colourSchemes/conservation.html [moved from help/html/colourSchemes/conservation.html with 100% similarity]
help/help/html/colourSchemes/helix.html [moved from help/html/colourSchemes/helix.html with 100% similarity]
help/help/html/colourSchemes/hydrophobic.html [moved from help/html/colourSchemes/hydrophobic.html with 100% similarity]
help/help/html/colourSchemes/index.html [moved from help/html/colourSchemes/index.html with 100% similarity]
help/help/html/colourSchemes/nucleotide.html [moved from help/html/colourSchemes/nucleotide.html with 100% similarity]
help/help/html/colourSchemes/pid.html [moved from help/html/colourSchemes/pid.html with 100% similarity]
help/help/html/colourSchemes/purinepyrimidine.html [moved from help/html/colourSchemes/purinepyrimidine.html with 100% similarity]
help/help/html/colourSchemes/rnahelicesColouring.html [moved from help/html/colourSchemes/rnahelicesColouring.html with 100% similarity]
help/help/html/colourSchemes/rnahelicescoloring.png [moved from help/html/colourSchemes/rnahelicescoloring.png with 100% similarity]
help/help/html/colourSchemes/strand.html [moved from help/html/colourSchemes/strand.html with 100% similarity]
help/help/html/colourSchemes/taylor.html [moved from help/html/colourSchemes/taylor.html with 100% similarity]
help/help/html/colourSchemes/textcolour.gif [moved from help/html/colourSchemes/textcolour.gif with 100% similarity]
help/help/html/colourSchemes/textcolour.html [moved from help/html/colourSchemes/textcolour.html with 100% similarity]
help/help/html/colourSchemes/turn.html [moved from help/html/colourSchemes/turn.html with 100% similarity]
help/help/html/colourSchemes/user.html [moved from help/html/colourSchemes/user.html with 100% similarity]
help/help/html/colourSchemes/userDefined.gif [moved from help/html/colourSchemes/userDefined.gif with 100% similarity]
help/help/html/colourSchemes/userDefined_java7.gif [moved from help/html/colourSchemes/userDefined_java7.gif with 100% similarity]
help/help/html/colourSchemes/zappo.html [moved from help/html/colourSchemes/zappo.html with 100% similarity]
help/help/html/editing/.cvsignore [moved from help/html/editing/.cvsignore with 100% similarity]
help/help/html/editing/editing.jpg [moved from help/html/editing/editing.jpg with 100% similarity]
help/help/html/editing/index.html [moved from help/html/editing/index.html with 100% similarity]
help/help/html/features/.cvsignore [moved from help/html/features/.cvsignore with 100% similarity]
help/help/html/features/AnnotationColumnSelectionWithSM.png [moved from help/html/features/AnnotationColumnSelectionWithSM.png with 100% similarity]
help/help/html/features/AnnotationColumnSelectionWithoutSM.gif [moved from help/html/features/AnnotationColumnSelectionWithoutSM.gif with 100% similarity]
help/help/html/features/amendfeature.gif [moved from help/html/features/amendfeature.gif with 100% similarity]
help/help/html/features/annotation.html [moved from help/html/features/annotation.html with 100% similarity]
help/help/html/features/annotationsFormat.html [moved from help/html/features/annotationsFormat.html with 100% similarity]
help/help/html/features/bioJsonFormat.html [moved from help/html/features/bioJsonFormat.html with 100% similarity]
help/help/html/features/biojsmsa.html [moved from help/html/features/biojsmsa.html with 100% similarity]
help/help/html/features/chimera.html [moved from help/html/features/chimera.html with 100% similarity]
help/help/html/features/clarguments.html [moved from help/html/features/clarguments.html with 100% similarity]
help/help/html/features/codingfeatures.html [moved from help/html/features/codingfeatures.html with 100% similarity]
help/help/html/features/columnFilterByAnnotation.html [moved from help/html/features/columnFilterByAnnotation.html with 100% similarity]
help/help/html/features/commandline.html [moved from help/html/features/commandline.html with 100% similarity]
help/help/html/features/creatinFeatures.html [moved from help/html/features/creatinFeatures.html with 100% similarity]
help/help/html/features/crnewfeature.gif [moved from help/html/features/crnewfeature.gif with 100% similarity]
help/help/html/features/cursorMode.html [moved from help/html/features/cursorMode.html with 100% similarity]
help/help/html/features/editingFeatures.html [moved from help/html/features/editingFeatures.html with 100% similarity]
help/help/html/features/ensemblsequencefetcher.html [moved from help/html/features/ensemblsequencefetcher.html with 100% similarity]
help/help/html/features/fcsgtthan.gif [moved from help/html/features/fcsgtthan.gif with 100% similarity]
help/help/html/features/fcsltthan.gif [moved from help/html/features/fcsltthan.gif with 100% similarity]
help/help/html/features/fcsminmax.gif [moved from help/html/features/fcsminmax.gif with 100% similarity]
help/help/html/features/fcsntlabel.gif [moved from help/html/features/fcsntlabel.gif with 100% similarity]
help/help/html/features/featureSettings.gif [moved from help/html/features/featureSettings.gif with 100% similarity]
help/help/html/features/featurecoloursettings.gif [moved from help/html/features/featurecoloursettings.gif with 100% similarity]
help/help/html/features/featuresFormat.html [moved from help/html/features/featuresFormat.html with 100% similarity]
help/help/html/features/featureschemes.html [moved from help/html/features/featureschemes.html with 100% similarity]
help/help/html/features/featuresettings.html [moved from help/html/features/featuresettings.html with 100% similarity]
help/help/html/features/groovy.html [moved from help/html/features/groovy.html with 100% similarity]
help/help/html/features/hiddenRegions.html [moved from help/html/features/hiddenRegions.html with 100% similarity]
help/help/html/features/jalarchive.html [moved from help/html/features/jalarchive.html with 100% similarity]
help/help/html/features/jmol.html [moved from help/html/features/jmol.html with 100% similarity]
help/help/html/features/mmcif.html [moved from help/html/features/mmcif.html with 100% similarity]
help/help/html/features/multipleViews.html [moved from help/html/features/multipleViews.html with 100% similarity]
help/help/html/features/newkeystrokes.html [moved from help/html/features/newkeystrokes.html with 100% similarity]
help/help/html/features/overview.html [moved from help/html/features/overview.html with 100% similarity]
help/help/html/features/overview.png [moved from help/html/features/overview.png with 100% similarity]
help/help/html/features/pdbseqfetcher.png [moved from help/html/features/pdbseqfetcher.png with 100% similarity]
help/help/html/features/pdbsequencefetcher.html [moved from help/html/features/pdbsequencefetcher.html with 100% similarity]
help/help/html/features/pdbviewer.html [moved from help/html/features/pdbviewer.html with 100% similarity]
help/help/html/features/preferences.html [moved from help/html/features/preferences.html with 100% similarity]
help/help/html/features/schooser_enter-id.png [moved from help/html/features/schooser_enter-id.png with 100% similarity]
help/help/html/features/schooser_main.png [moved from help/html/features/schooser_main.png with 100% similarity]
help/help/html/features/search.html [moved from help/html/features/search.html with 100% similarity]
help/help/html/features/search.png [moved from help/html/features/search.png with 100% similarity]
help/help/html/features/searchclearhist.png [moved from help/html/features/searchclearhist.png with 100% similarity]
help/help/html/features/searchhist.png [moved from help/html/features/searchhist.png with 100% similarity]
help/help/html/features/selectfetchdb.gif [moved from help/html/features/selectfetchdb.gif with 100% similarity]
help/help/html/features/seqfeatures.html [moved from help/html/features/seqfeatures.html with 100% similarity]
help/help/html/features/seqfetch.html [moved from help/html/features/seqfetch.html with 100% similarity]
help/help/html/features/seqfetcher.gif [moved from help/html/features/seqfetcher.gif with 100% similarity]
help/help/html/features/seqmappings.html [moved from help/html/features/seqmappings.html with 100% similarity]
help/help/html/features/sifts_mapping_output.png [moved from help/html/features/sifts_mapping_output.png with 100% similarity]
help/help/html/features/siftsmapping.html [moved from help/html/features/siftsmapping.html with 100% similarity]
help/help/html/features/splitView.html [moved from help/html/features/splitView.html with 100% similarity]
help/help/html/features/structurechooser.html [moved from help/html/features/structurechooser.html with 100% similarity]
help/help/html/features/uniprotqueryfields.html [moved from help/html/features/uniprotqueryfields.html with 100% similarity]
help/help/html/features/uniprotseqfetcher.png [moved from help/html/features/uniprotseqfetcher.png with 100% similarity]
help/help/html/features/uniprotsequencefetcher.html [moved from help/html/features/uniprotsequencefetcher.html with 100% similarity]
help/help/html/features/varna.html [moved from help/html/features/varna.html with 100% similarity]
help/help/html/features/viewingpdbs.html [moved from help/html/features/viewingpdbs.html with 100% similarity]
help/help/html/features/wrap.html [moved from help/html/features/wrap.html with 100% similarity]
help/help/html/features/xsspannotation.html [moved from help/html/features/xsspannotation.html with 100% similarity]
help/help/html/groovy/featuresCounter.html [moved from help/html/groovy/featuresCounter.html with 100% similarity]
help/help/html/index.html [moved from help/html/index.html with 100% similarity]
help/help/html/io/.cvsignore [moved from help/html/io/.cvsignore with 100% similarity]
help/help/html/io/export.html [moved from help/html/io/export.html with 100% similarity]
help/help/html/io/exportseqreport.html [moved from help/html/io/exportseqreport.html with 100% similarity]
help/help/html/io/file.png [moved from help/html/io/file.png with 100% similarity]
help/help/html/io/fileformats.html [moved from help/html/io/fileformats.html with 100% similarity]
help/help/html/io/index.html [moved from help/html/io/index.html with 100% similarity]
help/help/html/io/modellerpir.html [moved from help/html/io/modellerpir.html with 100% similarity]
help/help/html/io/seqreport.gif [moved from help/html/io/seqreport.gif with 100% similarity]
help/help/html/io/tcoffeescores.html [moved from help/html/io/tcoffeescores.html with 100% similarity]
help/help/html/keys.html [moved from help/html/keys.html with 100% similarity]
help/help/html/memory.html [moved from help/html/memory.html with 100% similarity]
help/help/html/menus/alignmentMenu.html [moved from help/html/menus/alignmentMenu.html with 100% similarity]
help/help/html/menus/alwannotation.html [moved from help/html/menus/alwannotation.html with 100% similarity]
help/help/html/menus/alwannotationpanel.html [moved from help/html/menus/alwannotationpanel.html with 100% similarity]
help/help/html/menus/alwcalculate.html [moved from help/html/menus/alwcalculate.html with 100% similarity]
help/help/html/menus/alwcolour.html [moved from help/html/menus/alwcolour.html with 100% similarity]
help/help/html/menus/alwedit.html [moved from help/html/menus/alwedit.html with 100% similarity]
help/help/html/menus/alwfile.html [moved from help/html/menus/alwfile.html with 100% similarity]
help/help/html/menus/alwformat.html [moved from help/html/menus/alwformat.html with 100% similarity]
help/help/html/menus/alwselect.html [moved from help/html/menus/alwselect.html with 100% similarity]
help/help/html/menus/alwview.html [moved from help/html/menus/alwview.html with 100% similarity]
help/help/html/menus/desktopMenu.html [moved from help/html/menus/desktopMenu.html with 100% similarity]
help/help/html/menus/index.html [moved from help/html/menus/index.html with 100% similarity]
help/help/html/menus/popupMenu.html [moved from help/html/menus/popupMenu.html with 100% similarity]
help/help/html/menus/wsmenu.html [moved from help/html/menus/wsmenu.html with 100% similarity]
help/help/html/misc/.cvsignore [moved from help/html/misc/.cvsignore with 100% similarity]
help/help/html/misc/aaproperties.html [moved from help/html/misc/aaproperties.html with 100% similarity]
help/help/html/misc/ala.jpg [moved from help/html/misc/ala.jpg with 100% similarity]
help/help/html/misc/aminoAcids.html [moved from help/html/misc/aminoAcids.html with 100% similarity]
help/help/html/misc/arg.jpg [moved from help/html/misc/arg.jpg with 100% similarity]
help/help/html/misc/asparagine.jpg [moved from help/html/misc/asparagine.jpg with 100% similarity]
help/help/html/misc/aspartate.jpg [moved from help/html/misc/aspartate.jpg with 100% similarity]
help/help/html/misc/cys.jpg [moved from help/html/misc/cys.jpg with 100% similarity]
help/help/html/misc/geneticCode.html [moved from help/html/misc/geneticCode.html with 100% similarity]
help/help/html/misc/glutamate.jpg [moved from help/html/misc/glutamate.jpg with 100% similarity]
help/help/html/misc/glutamine.jpg [moved from help/html/misc/glutamine.jpg with 100% similarity]
help/help/html/misc/gly.jpg [moved from help/html/misc/gly.jpg with 100% similarity]
help/help/html/misc/his.jpg [moved from help/html/misc/his.jpg with 100% similarity]
help/help/html/misc/iso.jpg [moved from help/html/misc/iso.jpg with 100% similarity]
help/help/html/misc/leu.jpg [moved from help/html/misc/leu.jpg with 100% similarity]
help/help/html/misc/lys.jpg [moved from help/html/misc/lys.jpg with 100% similarity]
help/help/html/misc/met.jpg [moved from help/html/misc/met.jpg with 100% similarity]
help/help/html/misc/phe.jpg [moved from help/html/misc/phe.jpg with 100% similarity]
help/help/html/misc/pro.jpg [moved from help/html/misc/pro.jpg with 100% similarity]
help/help/html/misc/properties.gif [moved from help/html/misc/properties.gif with 100% similarity]
help/help/html/misc/ser.jpg [moved from help/html/misc/ser.jpg with 100% similarity]
help/help/html/misc/thr.jpg [moved from help/html/misc/thr.jpg with 100% similarity]
help/help/html/misc/tryp.jpg [moved from help/html/misc/tryp.jpg with 100% similarity]
help/help/html/misc/tyr.jpg [moved from help/html/misc/tyr.jpg with 100% similarity]
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help/help/html/na/index.html [moved from help/html/na/index.html with 100% similarity]
help/help/html/privacy.html [moved from help/html/privacy.html with 100% similarity]
help/help/html/releases.html [moved from help/html/releases.html with 100% similarity]
help/help/html/vamsas/index.html [moved from help/html/vamsas/index.html with 100% similarity]
help/help/html/webServices/.cvsignore [moved from help/html/webServices/.cvsignore with 100% similarity]
help/help/html/webServices/AACon.html [moved from help/html/webServices/AACon.html with 100% similarity]
help/help/html/webServices/JABAWS.html [moved from help/html/webServices/JABAWS.html with 100% similarity]
help/help/html/webServices/RNAalifold.html [moved from help/html/webServices/RNAalifold.html with 100% similarity]
help/help/html/webServices/RNAalifoldAnnotationRows.png [moved from help/html/webServices/RNAalifoldAnnotationRows.png with 100% similarity]
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help/help/html/webServices/dbreffetcher.html [moved from help/html/webServices/dbreffetcher.html with 100% similarity]
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