From 44d68d55d9c85bf7b28853feeebc4b901c4a8392 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 25 Apr 2019 17:25:50 +0100 Subject: [PATCH] JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this in to eclipse classpath generation --- build.gradle | 180 ++++++++++---------- gradle.properties | 1 + help/{ => help}/help.hs | 0 help/{ => help}/help.jhm | 0 help/{ => help}/helpTOC.xml | 0 help/{ => help}/html/.cvsignore | 0 help/{ => help}/html/Jalview_Logo.png | Bin 15420 -> 15420 bytes help/{ => help}/html/align.jpg | Bin 14648 -> 14648 bytes .../html/calculations/calculatedialog.png | Bin 23917 -> 23917 bytes .../{ => help}/html/calculations/calculations.html | 0 help/{ => help}/html/calculations/consensus.html | 0 .../{ => help}/html/calculations/conservation.html | 0 help/{ => help}/html/calculations/pairwise.html | 0 help/{ => help}/html/calculations/pca.html | 0 help/{ => help}/html/calculations/pcaviewer.gif | Bin 27629 -> 27629 bytes help/{ => help}/html/calculations/quality.html | 0 .../html/calculations/recoverInputdata.html | 0 help/{ => help}/html/calculations/redundancy.html | 0 .../{ => help}/html/calculations/referenceseq.html | 0 .../html/calculations/scorematrices.html | 0 help/{ => help}/html/calculations/sorting.html | 0 .../html/calculations/structureconsensus.html | 0 help/{ => help}/html/calculations/tree.html | 0 help/{ => help}/html/calculations/treeviewer.html | 0 help/{ => help}/html/colourSchemes/.cvsignore | 0 help/{ => help}/html/colourSchemes/abovePID.html | 0 .../html/colourSchemes/annotationColourSetting.gif | Bin 13891 -> 13891 bytes .../html/colourSchemes/annotationColouring.html | 0 .../html/colourSchemes/annotationColours.gif | Bin 23564 -> 23564 bytes help/{ => help}/html/colourSchemes/blosum.html | 0 help/{ => help}/html/colourSchemes/buried.html | 0 help/{ => help}/html/colourSchemes/clustal.html | 0 .../{ => help}/html/colourSchemes/colbytcoffee.png | Bin 137157 -> 137157 bytes .../html/colourSchemes/conservation.html | 0 help/{ => help}/html/colourSchemes/helix.html | 0 .../{ => help}/html/colourSchemes/hydrophobic.html | 0 help/{ => help}/html/colourSchemes/index.html | 0 help/{ => help}/html/colourSchemes/nucleotide.html | 0 help/{ => help}/html/colourSchemes/pid.html | 0 .../html/colourSchemes/purinepyrimidine.html | 0 .../html/colourSchemes/rnahelicesColouring.html | 0 .../html/colourSchemes/rnahelicescoloring.png | Bin 34699 -> 34699 bytes help/{ => help}/html/colourSchemes/strand.html | 0 help/{ => help}/html/colourSchemes/taylor.html | 0 help/{ => help}/html/colourSchemes/textcolour.gif | Bin 21788 -> 21788 bytes help/{ => help}/html/colourSchemes/textcolour.html | 0 help/{ => help}/html/colourSchemes/turn.html | 0 help/{ => help}/html/colourSchemes/user.html | 0 help/{ => help}/html/colourSchemes/userDefined.gif | Bin 35269 -> 35269 bytes .../html/colourSchemes/userDefined_java7.gif | Bin 90049 -> 90049 bytes help/{ => help}/html/colourSchemes/zappo.html | 0 help/{ => help}/html/editing/.cvsignore | 0 help/{ => help}/html/editing/editing.jpg | Bin 42427 -> 42427 bytes help/{ => help}/html/editing/index.html | 0 help/{ => help}/html/features/.cvsignore | 0 .../features/AnnotationColumnSelectionWithSM.png | Bin 37455 -> 37455 bytes .../AnnotationColumnSelectionWithoutSM.gif | Bin 37778 -> 37778 bytes help/{ => help}/html/features/amendfeature.gif | Bin 28030 -> 28030 bytes help/{ => help}/html/features/annotation.html | 0 .../html/features/annotationsFormat.html | 0 help/{ => help}/html/features/bioJsonFormat.html | 0 help/{ => help}/html/features/biojsmsa.html | 0 help/{ => help}/html/features/chimera.html | 0 help/{ => help}/html/features/clarguments.html | 0 help/{ => help}/html/features/codingfeatures.html | 0 .../html/features/columnFilterByAnnotation.html | 0 help/{ => help}/html/features/commandline.html | 0 help/{ => help}/html/features/creatinFeatures.html | 0 help/{ => help}/html/features/crnewfeature.gif | Bin 24348 -> 24348 bytes help/{ => help}/html/features/cursorMode.html | 0 help/{ => help}/html/features/editingFeatures.html | 0 .../html/features/ensemblsequencefetcher.html | 0 help/{ => help}/html/features/fcsgtthan.gif | Bin 136 -> 136 bytes help/{ => help}/html/features/fcsltthan.gif | Bin 136 -> 136 bytes help/{ => help}/html/features/fcsminmax.gif | Bin 104 -> 104 bytes help/{ => help}/html/features/fcsntlabel.gif | Bin 121 -> 121 bytes help/{ => help}/html/features/featureSettings.gif | Bin 23195 -> 23195 bytes .../html/features/featurecoloursettings.gif | Bin 8518 -> 8518 bytes help/{ => help}/html/features/featuresFormat.html | 0 help/{ => help}/html/features/featureschemes.html | 0 help/{ => help}/html/features/featuresettings.html | 0 help/{ => help}/html/features/groovy.html | 0 help/{ => help}/html/features/hiddenRegions.html | 0 help/{ => help}/html/features/jalarchive.html | 0 help/{ => help}/html/features/jmol.html | 0 help/{ => help}/html/features/mmcif.html | 0 help/{ => help}/html/features/multipleViews.html | 0 help/{ => help}/html/features/newkeystrokes.html | 0 help/{ => help}/html/features/overview.html | 0 help/{ => help}/html/features/overview.png | Bin 20667 -> 20667 bytes help/{ => help}/html/features/pdbseqfetcher.png | Bin 254335 -> 254335 bytes .../html/features/pdbsequencefetcher.html | 0 help/{ => help}/html/features/pdbviewer.html | 0 help/{ => help}/html/features/preferences.html | 0 .../{ => help}/html/features/schooser_enter-id.png | Bin 23685 -> 23685 bytes help/{ => help}/html/features/schooser_main.png | Bin 166751 -> 166751 bytes help/{ => help}/html/features/search.html | 0 help/{ => help}/html/features/search.png | Bin 18771 -> 18771 bytes help/{ => help}/html/features/searchclearhist.png | Bin 35172 -> 35172 bytes help/{ => help}/html/features/searchhist.png | Bin 23228 -> 23228 bytes help/{ => help}/html/features/selectfetchdb.gif | Bin 19522 -> 19522 bytes help/{ => help}/html/features/seqfeatures.html | 0 help/{ => help}/html/features/seqfetch.html | 0 help/{ => help}/html/features/seqfetcher.gif | Bin 11434 -> 11434 bytes help/{ => help}/html/features/seqmappings.html | 0 .../html/features/sifts_mapping_output.png | Bin 123157 -> 123157 bytes help/{ => help}/html/features/siftsmapping.html | 0 help/{ => help}/html/features/splitView.html | 0 .../{ => help}/html/features/structurechooser.html | 0 .../html/features/uniprotqueryfields.html | 0 .../{ => help}/html/features/uniprotseqfetcher.png | Bin 313878 -> 313878 bytes .../html/features/uniprotsequencefetcher.html | 0 help/{ => help}/html/features/varna.html | 0 help/{ => help}/html/features/viewingpdbs.html | 0 help/{ => help}/html/features/wrap.html | 0 help/{ => help}/html/features/xsspannotation.html | 0 help/{ => help}/html/groovy/featuresCounter.html | 0 help/{ => help}/html/index.html | 0 help/{ => help}/html/io/.cvsignore | 0 help/{ => help}/html/io/export.html | 0 help/{ => help}/html/io/exportseqreport.html | 0 help/{ => help}/html/io/file.png | Bin 590 -> 590 bytes help/{ => help}/html/io/fileformats.html | 0 help/{ => help}/html/io/index.html | 0 help/{ => help}/html/io/modellerpir.html | 0 help/{ => help}/html/io/seqreport.gif | Bin 25151 -> 25151 bytes help/{ => help}/html/io/tcoffeescores.html | 0 help/{ => help}/html/keys.html | 0 help/{ => help}/html/memory.html | 0 help/{ => help}/html/menus/alignmentMenu.html | 0 help/{ => help}/html/menus/alwannotation.html | 0 help/{ => help}/html/menus/alwannotationpanel.html | 0 help/{ => help}/html/menus/alwcalculate.html | 0 help/{ => help}/html/menus/alwcolour.html | 0 help/{ => help}/html/menus/alwedit.html | 0 help/{ => help}/html/menus/alwfile.html | 0 help/{ => help}/html/menus/alwformat.html | 0 help/{ => help}/html/menus/alwselect.html | 0 help/{ => help}/html/menus/alwview.html | 0 help/{ => help}/html/menus/desktopMenu.html | 0 help/{ => help}/html/menus/index.html | 0 help/{ => help}/html/menus/popupMenu.html | 0 help/{ => help}/html/menus/wsmenu.html | 0 help/{ => help}/html/misc/.cvsignore | 0 help/{ => help}/html/misc/aaproperties.html | 0 help/{ => help}/html/misc/ala.jpg | Bin 2039 -> 2039 bytes help/{ => help}/html/misc/aminoAcids.html | 0 help/{ => help}/html/misc/arg.jpg | Bin 4445 -> 4445 bytes help/{ => help}/html/misc/asparagine.jpg | Bin 3212 -> 3212 bytes help/{ => help}/html/misc/aspartate.jpg | Bin 2824 -> 2824 bytes help/{ => help}/html/misc/cys.jpg | Bin 2360 -> 2360 bytes help/{ => help}/html/misc/geneticCode.html | 0 help/{ => help}/html/misc/glutamate.jpg | Bin 3341 -> 3341 bytes help/{ => help}/html/misc/glutamine.jpg | Bin 3546 -> 3546 bytes help/{ => help}/html/misc/gly.jpg | Bin 1823 -> 1823 bytes help/{ => help}/html/misc/his.jpg | Bin 3673 -> 3673 bytes help/{ => help}/html/misc/iso.jpg | Bin 3613 -> 3613 bytes help/{ => help}/html/misc/leu.jpg | Bin 3483 -> 3483 bytes help/{ => help}/html/misc/lys.jpg | Bin 3912 -> 3912 bytes help/{ => help}/html/misc/met.jpg | Bin 3365 -> 3365 bytes help/{ => help}/html/misc/phe.jpg | Bin 3148 -> 3148 bytes help/{ => help}/html/misc/pro.jpg | Bin 3037 -> 3037 bytes help/{ => help}/html/misc/properties.gif | Bin 29022 -> 29022 bytes help/{ => help}/html/misc/ser.jpg | Bin 2203 -> 2203 bytes help/{ => help}/html/misc/thr.jpg | Bin 2850 -> 2850 bytes help/{ => help}/html/misc/tryp.jpg | Bin 4450 -> 4450 bytes help/{ => help}/html/misc/tyr.jpg | Bin 3500 -> 3500 bytes help/{ => help}/html/misc/val.jpg | Bin 3024 -> 3024 bytes help/{ => help}/html/na/index.html | 0 help/{ => help}/html/privacy.html | 0 help/{ => help}/html/releases.html | 0 help/{ => help}/html/vamsas/index.html | 0 help/{ => help}/html/webServices/.cvsignore | 0 help/{ => help}/html/webServices/AACon.html | 0 help/{ => help}/html/webServices/JABAWS.html | 0 help/{ => help}/html/webServices/RNAalifold.html | 0 .../html/webServices/RNAalifoldAnnotationRows.png | Bin 31732 -> 31732 bytes help/{ => help}/html/webServices/clwqueued.gif | Bin 5619 -> 5619 bytes help/{ => help}/html/webServices/dbreffetcher.html | 0 help/{ => help}/html/webServices/index.html | 0 .../html/webServices/invalidurldialog.gif | Bin 9370 -> 9370 bytes .../html/webServices/jalviewrssreader.gif | Bin 24576 -> 24576 bytes help/{ => help}/html/webServices/jnet.html | 0 .../{ => help}/html/webServices/jnetprediction.gif | Bin 63895 -> 63895 bytes help/{ => help}/html/webServices/msaclient.html | 0 help/{ => help}/html/webServices/multimafftjbs.gif | Bin 7301 -> 7301 bytes help/{ => help}/html/webServices/newsreader.html | 0 .../html/webServices/proteinDisorder.html | 0 help/{ => help}/html/webServices/shmr.html | 0 help/{ => help}/html/webServices/urllinks.html | 0 .../html/webServices/webServicesParams.html | 0 .../html/webServices/webServicesPrefs.html | 0 help/{ => help}/html/webServices/wsparams.gif | Bin 19287 -> 19287 bytes help/{ => help}/html/webServices/wsprefs.gif | Bin 23662 -> 23662 bytes help/{ => help}/html/whatsNew.html | 0 help/{ => help}/icons/Home.png | Bin 1598 -> 1598 bytes help/{ => help}/icons/back.png | Bin 1315 -> 1315 bytes help/{ => help}/icons/forward.png | Bin 1303 -> 1303 bytes help/{ => help}/icons/print.png | Bin 1405 -> 1405 bytes help/{ => help}/icons/setup.png | Bin 1514 -> 1514 bytes 200 files changed, 93 insertions(+), 88 deletions(-) rename help/{ => help}/help.hs (100%) rename help/{ => help}/help.jhm (100%) rename help/{ => help}/helpTOC.xml (100%) rename help/{ => help}/html/.cvsignore (100%) rename help/{ => help}/html/Jalview_Logo.png (100%) rename help/{ => help}/html/align.jpg (100%) rename help/{ => help}/html/calculations/calculatedialog.png (100%) rename help/{ => help}/html/calculations/calculations.html (100%) rename help/{ => help}/html/calculations/consensus.html (100%) rename help/{ => help}/html/calculations/conservation.html (100%) rename help/{ => help}/html/calculations/pairwise.html (100%) rename help/{ => help}/html/calculations/pca.html (100%) rename help/{ => help}/html/calculations/pcaviewer.gif (100%) rename help/{ => help}/html/calculations/quality.html (100%) rename help/{ => help}/html/calculations/recoverInputdata.html (100%) rename help/{ => help}/html/calculations/redundancy.html (100%) rename help/{ => help}/html/calculations/referenceseq.html (100%) rename help/{ => help}/html/calculations/scorematrices.html (100%) rename help/{ => help}/html/calculations/sorting.html (100%) rename help/{ => help}/html/calculations/structureconsensus.html (100%) rename help/{ => help}/html/calculations/tree.html (100%) rename help/{ => help}/html/calculations/treeviewer.html (100%) rename help/{ => help}/html/colourSchemes/.cvsignore (100%) rename help/{ => help}/html/colourSchemes/abovePID.html (100%) rename help/{ => help}/html/colourSchemes/annotationColourSetting.gif (100%) rename help/{ => help}/html/colourSchemes/annotationColouring.html (100%) rename help/{ => help}/html/colourSchemes/annotationColours.gif (100%) rename help/{ => help}/html/colourSchemes/blosum.html (100%) rename help/{ => help}/html/colourSchemes/buried.html (100%) rename help/{ => help}/html/colourSchemes/clustal.html (100%) rename help/{ => help}/html/colourSchemes/colbytcoffee.png (100%) rename help/{ => help}/html/colourSchemes/conservation.html (100%) rename help/{ => help}/html/colourSchemes/helix.html (100%) rename help/{ => help}/html/colourSchemes/hydrophobic.html (100%) rename help/{ => help}/html/colourSchemes/index.html (100%) rename help/{ => help}/html/colourSchemes/nucleotide.html (100%) rename help/{ => help}/html/colourSchemes/pid.html (100%) rename help/{ => help}/html/colourSchemes/purinepyrimidine.html (100%) rename help/{ => help}/html/colourSchemes/rnahelicesColouring.html (100%) rename help/{ => help}/html/colourSchemes/rnahelicescoloring.png (100%) rename help/{ => help}/html/colourSchemes/strand.html (100%) rename help/{ => help}/html/colourSchemes/taylor.html (100%) rename help/{ => help}/html/colourSchemes/textcolour.gif (100%) rename help/{ => help}/html/colourSchemes/textcolour.html (100%) rename help/{ => help}/html/colourSchemes/turn.html (100%) rename help/{ => help}/html/colourSchemes/user.html (100%) rename help/{ => help}/html/colourSchemes/userDefined.gif (100%) rename help/{ => help}/html/colourSchemes/userDefined_java7.gif (100%) rename help/{ => help}/html/colourSchemes/zappo.html (100%) rename help/{ => help}/html/editing/.cvsignore (100%) rename help/{ => help}/html/editing/editing.jpg (100%) rename help/{ => help}/html/editing/index.html (100%) rename help/{ => help}/html/features/.cvsignore (100%) rename help/{ => help}/html/features/AnnotationColumnSelectionWithSM.png (100%) rename help/{ => help}/html/features/AnnotationColumnSelectionWithoutSM.gif (100%) rename help/{ => help}/html/features/amendfeature.gif (100%) rename help/{ => help}/html/features/annotation.html (100%) rename help/{ => help}/html/features/annotationsFormat.html (100%) rename help/{ => help}/html/features/bioJsonFormat.html (100%) rename help/{ => help}/html/features/biojsmsa.html (100%) rename help/{ => help}/html/features/chimera.html (100%) rename help/{ => help}/html/features/clarguments.html (100%) rename help/{ => help}/html/features/codingfeatures.html (100%) rename help/{ => help}/html/features/columnFilterByAnnotation.html (100%) rename help/{ => help}/html/features/commandline.html (100%) rename help/{ => help}/html/features/creatinFeatures.html (100%) rename help/{ => help}/html/features/crnewfeature.gif (100%) rename help/{ => help}/html/features/cursorMode.html (100%) rename help/{ => help}/html/features/editingFeatures.html (100%) rename help/{ => help}/html/features/ensemblsequencefetcher.html (100%) rename help/{ => help}/html/features/fcsgtthan.gif (100%) rename help/{ => help}/html/features/fcsltthan.gif (100%) rename help/{ => help}/html/features/fcsminmax.gif (100%) rename help/{ => help}/html/features/fcsntlabel.gif (100%) rename help/{ => help}/html/features/featureSettings.gif (100%) rename help/{ => help}/html/features/featurecoloursettings.gif (100%) rename help/{ => help}/html/features/featuresFormat.html (100%) rename help/{ => help}/html/features/featureschemes.html (100%) rename help/{ => help}/html/features/featuresettings.html (100%) rename help/{ => help}/html/features/groovy.html (100%) rename help/{ => help}/html/features/hiddenRegions.html (100%) rename help/{ => help}/html/features/jalarchive.html (100%) rename help/{ => help}/html/features/jmol.html (100%) rename help/{ => help}/html/features/mmcif.html (100%) rename help/{ => help}/html/features/multipleViews.html (100%) rename help/{ => help}/html/features/newkeystrokes.html (100%) rename help/{ => help}/html/features/overview.html (100%) rename help/{ => help}/html/features/overview.png (100%) rename help/{ => help}/html/features/pdbseqfetcher.png (100%) rename help/{ => help}/html/features/pdbsequencefetcher.html (100%) rename help/{ => help}/html/features/pdbviewer.html (100%) rename help/{ => help}/html/features/preferences.html (100%) rename help/{ => help}/html/features/schooser_enter-id.png (100%) rename help/{ => help}/html/features/schooser_main.png (100%) rename help/{ => help}/html/features/search.html (100%) rename help/{ => help}/html/features/search.png (100%) rename help/{ => help}/html/features/searchclearhist.png (100%) rename help/{ => help}/html/features/searchhist.png (100%) rename help/{ => help}/html/features/selectfetchdb.gif (100%) rename help/{ => help}/html/features/seqfeatures.html (100%) rename help/{ => help}/html/features/seqfetch.html (100%) rename help/{ => help}/html/features/seqfetcher.gif (100%) rename help/{ => help}/html/features/seqmappings.html (100%) rename help/{ => help}/html/features/sifts_mapping_output.png (100%) rename help/{ => help}/html/features/siftsmapping.html (100%) rename help/{ => help}/html/features/splitView.html (100%) rename help/{ => help}/html/features/structurechooser.html (100%) rename help/{ => help}/html/features/uniprotqueryfields.html (100%) rename help/{ => help}/html/features/uniprotseqfetcher.png (100%) rename help/{ => help}/html/features/uniprotsequencefetcher.html (100%) rename help/{ => help}/html/features/varna.html (100%) rename help/{ => help}/html/features/viewingpdbs.html (100%) rename help/{ => help}/html/features/wrap.html (100%) rename help/{ => help}/html/features/xsspannotation.html (100%) rename help/{ => help}/html/groovy/featuresCounter.html (100%) rename help/{ => help}/html/index.html (100%) rename help/{ => help}/html/io/.cvsignore (100%) rename help/{ => help}/html/io/export.html (100%) rename help/{ => help}/html/io/exportseqreport.html (100%) rename help/{ => help}/html/io/file.png (100%) rename help/{ => help}/html/io/fileformats.html (100%) rename help/{ => help}/html/io/index.html (100%) rename help/{ => help}/html/io/modellerpir.html (100%) rename help/{ => help}/html/io/seqreport.gif (100%) rename help/{ => help}/html/io/tcoffeescores.html (100%) rename help/{ => help}/html/keys.html (100%) rename help/{ => help}/html/memory.html (100%) rename help/{ => help}/html/menus/alignmentMenu.html (100%) rename help/{ => help}/html/menus/alwannotation.html (100%) rename help/{ => help}/html/menus/alwannotationpanel.html (100%) rename help/{ => help}/html/menus/alwcalculate.html (100%) rename help/{ => help}/html/menus/alwcolour.html (100%) rename help/{ => help}/html/menus/alwedit.html (100%) rename help/{ => help}/html/menus/alwfile.html (100%) rename help/{ => help}/html/menus/alwformat.html (100%) rename help/{ => help}/html/menus/alwselect.html (100%) rename help/{ => help}/html/menus/alwview.html (100%) rename help/{ => help}/html/menus/desktopMenu.html (100%) rename help/{ => help}/html/menus/index.html (100%) rename help/{ => help}/html/menus/popupMenu.html (100%) rename help/{ => help}/html/menus/wsmenu.html (100%) rename help/{ => help}/html/misc/.cvsignore (100%) rename help/{ => help}/html/misc/aaproperties.html (100%) rename help/{ => help}/html/misc/ala.jpg (100%) rename help/{ => help}/html/misc/aminoAcids.html (100%) rename help/{ => help}/html/misc/arg.jpg (100%) rename help/{ => help}/html/misc/asparagine.jpg (100%) rename help/{ => help}/html/misc/aspartate.jpg (100%) rename help/{ => help}/html/misc/cys.jpg (100%) rename help/{ => help}/html/misc/geneticCode.html (100%) rename help/{ => help}/html/misc/glutamate.jpg (100%) rename help/{ => help}/html/misc/glutamine.jpg (100%) rename help/{ => help}/html/misc/gly.jpg (100%) rename help/{ => help}/html/misc/his.jpg (100%) rename help/{ => help}/html/misc/iso.jpg (100%) rename help/{ => help}/html/misc/leu.jpg (100%) rename help/{ => help}/html/misc/lys.jpg (100%) rename help/{ => help}/html/misc/met.jpg (100%) rename help/{ => help}/html/misc/phe.jpg (100%) rename help/{ => help}/html/misc/pro.jpg (100%) rename help/{ => help}/html/misc/properties.gif (100%) rename help/{ => help}/html/misc/ser.jpg (100%) rename help/{ => help}/html/misc/thr.jpg (100%) rename help/{ => help}/html/misc/tryp.jpg (100%) rename help/{ => help}/html/misc/tyr.jpg (100%) rename help/{ => help}/html/misc/val.jpg (100%) rename help/{ => help}/html/na/index.html (100%) rename help/{ => help}/html/privacy.html (100%) rename help/{ => help}/html/releases.html (100%) rename help/{ => help}/html/vamsas/index.html (100%) rename help/{ => help}/html/webServices/.cvsignore (100%) rename help/{ => help}/html/webServices/AACon.html (100%) rename help/{ => help}/html/webServices/JABAWS.html (100%) rename help/{ => help}/html/webServices/RNAalifold.html (100%) rename help/{ => help}/html/webServices/RNAalifoldAnnotationRows.png (100%) rename help/{ => help}/html/webServices/clwqueued.gif (100%) rename help/{ => help}/html/webServices/dbreffetcher.html (100%) rename help/{ => help}/html/webServices/index.html (100%) rename help/{ => help}/html/webServices/invalidurldialog.gif (100%) rename help/{ => help}/html/webServices/jalviewrssreader.gif (100%) rename help/{ => help}/html/webServices/jnet.html (100%) rename help/{ => help}/html/webServices/jnetprediction.gif (100%) rename help/{ => help}/html/webServices/msaclient.html (100%) rename help/{ => help}/html/webServices/multimafftjbs.gif (100%) rename help/{ => help}/html/webServices/newsreader.html (100%) rename help/{ => help}/html/webServices/proteinDisorder.html (100%) rename help/{ => help}/html/webServices/shmr.html (100%) rename help/{ => help}/html/webServices/urllinks.html (100%) rename help/{ => help}/html/webServices/webServicesParams.html (100%) rename help/{ => help}/html/webServices/webServicesPrefs.html (100%) rename help/{ => help}/html/webServices/wsparams.gif (100%) rename help/{ => help}/html/webServices/wsprefs.gif (100%) rename help/{ => help}/html/whatsNew.html (100%) rename help/{ => help}/icons/Home.png (100%) rename help/{ => help}/icons/back.png (100%) rename help/{ => help}/icons/forward.png (100%) rename help/{ => help}/icons/print.png (100%) rename help/{ => help}/icons/setup.png (100%) diff --git a/build.gradle b/build.gradle index ed3ace3..f41e2b3 100644 --- a/build.gradle +++ b/build.gradle @@ -3,8 +3,8 @@ import org.gradle.internal.os.OperatingSystem buildscript { dependencies { - classpath 'org.openclover:clover:4.3.1' - classpath 'org.apache.commons:commons-compress:1.18' + classpath 'org.openclover:clover:4.3.1' + classpath 'org.apache.commons:commons-compress:1.18' } } @@ -46,7 +46,7 @@ def compile_source_compatibility def compile_target_compatibility ext { - // where the getdown channel will be built. + // where the getdown channel will be built. // TODO: consider allowing this expression to be overrriden by -P arg getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/' getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir @@ -66,7 +66,7 @@ ext { def JAVA_INTEGER_VERSION def additional_compiler_args = [] -// these are getdown.txt properties defined dependent on the JAVA_VERSION +// these are getdown.txt properties defined dependent on the JAVA_VERSION def getdown_alt_java_min_version // this property is assigned below and expanded to multiple lines in the getdown task def getdown_alt_multi_java_location @@ -116,10 +116,10 @@ sourceSets { } clover { java { - srcDirs = [ cloverInstrDir ] - outputDir = file("${buildDir}/${cloverClassesDir}") + srcDirs = [ cloverInstrDir ] + outputDir = file("${buildDir}/${cloverClassesDir}") } - + resources { srcDirs = sourceSets.main.resources.srcDirs } @@ -131,7 +131,7 @@ sourceSets { runtimeClasspath = compileClasspath } - + test { java { srcDirs "$jalviewDir/$testSourceDir" @@ -142,7 +142,7 @@ sourceSets { srcDirs = sourceSets.main.resources.srcDirs } - compileClasspath = files( sourceSets.test.java.outputDir ) + compileClasspath = files( sourceSets.test.java.outputDir ) if (use_clover) { compileClasspath += sourceSets.clover.compileClasspath @@ -167,8 +167,8 @@ dependencies { } configurations { - cloverRuntime - cloverRuntime.extendsFrom cloverCompile + cloverRuntime + cloverRuntime.extendsFrom cloverCompile } eclipse { @@ -191,7 +191,7 @@ eclipse { } } containers 'org.eclipse.buildship.core.gradleclasspathcontainer' - + minusConfigurations += removeThese plusConfigurations = [ ] file { @@ -201,7 +201,7 @@ eclipse { HashMap addedSrcPath = new HashMap<>(); cp.entries.each { entry -> if (entry.kind == 'src') { - if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test" || entry.path == "resources")) { + if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) { removeTheseToo += entry } else { addedSrcPath.putAt(entry.path, true) @@ -210,7 +210,7 @@ eclipse { } cp.entries.removeAll(removeTheseToo) } - + withXml { def node = it.asNode() def srcTestAttributes @@ -230,8 +230,10 @@ eclipse { if (addTestAttribute) { srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"])) } - + node.appendNode('classpathentry', [kind:"output", path:"bin/main"]) + node.appendNode('classpathentry', [kind:"lib", path:helpParentDir]) + node.appendNode('classpathentry', [kind:"lib", path:resourceDir]) HashMap addedLibPath = new HashMap<>(); def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath sourceSets.main.compileClasspath.each{ @@ -271,8 +273,8 @@ eclipse { } else { //println("Adding entry "+itPath) node.appendNode('classpathentry', [kind:"lib", path:itPath]) - .appendNode('attributes') - .appendNode('attribute', [name:"test", value:"true"]) + .appendNode('attributes') + .appendNode('attribute', [name:"test", value:"true"]) addedLibPath.put(itPath, true) } } @@ -290,14 +292,14 @@ eclipse { file { withProperties { props -> def jalview_prefs = new Properties() - def ins = new FileInputStream(eclipse_extra_jdt_prefs_file) - jalview_prefs.load(ins) - ins.close() - jalview_prefs.forEach { t, v -> - if (props.getAt(t) == null) { - props.putAt(t, v) - } - } + def ins = new FileInputStream(eclipse_extra_jdt_prefs_file) + jalview_prefs.load(ins) + ins.close() + jalview_prefs.forEach { t, v -> + if (props.getAt(t) == null) { + props.putAt(t, v) + } + } } } } @@ -306,42 +308,42 @@ eclipse { task cloverInstr() { // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) - outputs.dir cloverInstrDir - - doFirst { - delete cloverInstrDir - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-d", "${buildDir}/${cloverSourcesInstrDir}"] - argsList.addAll(inputs.files.files.collect({ file -> - file.absolutePath - })) - String[] args = argsList.toArray() - println("About to instrument "+args.length +" files") - com.atlassian.clover.CloverInstr.mainImpl(args) - } + inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) + outputs.dir cloverInstrDir + + doFirst { + delete cloverInstrDir + def argsList = ["--initstring", "${buildDir}/clover/clover.db", + "-d", "${buildDir}/${cloverSourcesInstrDir}"] + argsList.addAll(inputs.files.files.collect({ file -> + file.absolutePath + })) + String[] args = argsList.toArray() + println("About to instrument "+args.length +" files") + com.atlassian.clover.CloverInstr.mainImpl(args) + } } - + task cloverReport { - group = "Verification" - description = "Createst the Clover report" - inputs.dir "${buildDir}/clover" - outputs.dir "${reportsDir}/clover" - onlyIf { - file("${buildDir}/clover/clover.db").exists() - } - doFirst { - def argsList = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover"] - String[] args = argsList.toArray() - com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) - - // and generate ${reportsDir}/clover/clover.xml - args = ["--initstring", "${buildDir}/clover/clover.db", - "-o", "${reportsDir}/clover/clover.xml"].toArray() - com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) - } + group = "Verification" + description = "Createst the Clover report" + inputs.dir "${buildDir}/clover" + outputs.dir "${reportsDir}/clover" + onlyIf { + file("${buildDir}/clover/clover.db").exists() + } + doFirst { + def argsList = ["--initstring", "${buildDir}/clover/clover.db", + "-o", "${reportsDir}/clover"] + String[] args = argsList.toArray() + com.atlassian.clover.reporters.html.HtmlReporter.runReport(args) + + // and generate ${reportsDir}/clover/clover.xml + args = ["--initstring", "${buildDir}/clover/clover.db", + "-o", "${reportsDir}/clover/clover.xml"].toArray() + com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) + } } // end clover bits @@ -442,21 +444,23 @@ task syncDocs(type: Sync) { } def helpFile = "$classes/$helpDir/help.jhm" -task syncHelp(type: Sync) { - inputs.files("$jalviewDir/$helpDir") - outputs.files(helpFile) - - def syncDir = "$classes/$helpDir" - from fileTree("$jalviewDir/$helpDir") - into syncDir -} task copyHelp(type: Copy) { - def inputDir = "$jalviewDir/$helpDir" + def inputDir = "$jalviewDir/$helpParentDir/$helpDir" def outputDir = "$classes/$helpDir" - from inputDir + from(inputDir) { + exclude '**/*.gif' + exclude '**/*.jpg' + exclude '**/*.png' + filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION]) + } + from(inputDir) { + include '**/*.gif' + include '**/*.jpg' + include '**/*.png' + } into outputDir - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"]) + inputs.dir(inputDir) outputs.files(helpFile) outputs.dir(outputDir) @@ -493,14 +497,14 @@ test { dependsOn cloverInstr } - print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") - + print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") + useTestNG() { includeGroups testngGroups preserveOrder true useDefaultListeners=true } - + workingDir = jalviewDir //systemProperties 'clover.jar' System.properties.clover.jar sourceCompatibility = compile_source_compatibility @@ -620,7 +624,7 @@ task cleanDist { shadowJar { dependsOn makeDist from ("$jalviewDir/$libDistDir") { - include("*.jar") + include("*.jar") } mainClassName = shadowJarMainClass mergeServiceFiles() @@ -642,7 +646,7 @@ task getdownWebsite() { def props = project.properties.sort { it.key } props.put("getdown_txt_java_min_version", getdown_alt_java_min_version) props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location) - + props.put("getdown_txt_appbase", getdown_app_base) props.each{ prop, val -> if (prop.startsWith("getdown_txt_") && val != null) { @@ -705,18 +709,18 @@ task getdownWebsite() { // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist /* - if (JAVA_VERSION.equals("11")) { - def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles() - j11libFiles.sort().each{f -> - def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n" - getdownTextString += line - copy { - from f.getPath() - into project.ext.getdownJ11libDir - } - } - } - */ + if (JAVA_VERSION.equals("11")) { + def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles() + j11libFiles.sort().each{f -> + def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n" + getdownTextString += line + copy { + from f.getPath() + into project.ext.getdownJ11libDir + } + } + } + */ getdownTextString += "code = " + file(getdownLauncher).getName() + "\n" getdownTextString += "class = " + mainClass + "\n" @@ -750,7 +754,7 @@ task getdownWebsite() { from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image') from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon') from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon') - into project.ext.getdownFilesDir + '/' + getdown_resource_dir + into project.ext.getdownFilesDir + '/' + getdown_resource_dir } } @@ -806,7 +810,7 @@ def windowsJavaVMTgz def install4jDir = "$jalviewDir/$install4jResourceDir" def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j" install4jConf = "$install4jDir/$install4jConfFile" - + task copyInstall4jTemplate(type: Copy) { macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre" macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz" diff --git a/gradle.properties b/gradle.properties index 7c794f5..45a45f4 100644 --- a/gradle.properties +++ b/gradle.properties @@ -22,6 +22,7 @@ javac_target = 11 j8libDir = j8lib j11libDir = j11lib resourceDir = resources +helpParentDir = help helpDir = help docDir = doc sourceDir = src diff --git a/help/help.hs b/help/help/help.hs similarity index 100% rename from help/help.hs rename to help/help/help.hs diff --git a/help/help.jhm b/help/help/help.jhm similarity index 100% rename from help/help.jhm rename to help/help/help.jhm diff --git a/help/helpTOC.xml b/help/help/helpTOC.xml similarity index 100% rename from help/helpTOC.xml rename to help/help/helpTOC.xml diff --git a/help/html/.cvsignore b/help/help/html/.cvsignore similarity index 100% rename from help/html/.cvsignore rename to help/help/html/.cvsignore diff --git a/help/html/Jalview_Logo.png b/help/help/html/Jalview_Logo.png similarity index 100% rename from help/html/Jalview_Logo.png rename to help/help/html/Jalview_Logo.png diff --git a/help/html/align.jpg b/help/help/html/align.jpg similarity index 100% rename from help/html/align.jpg rename to help/help/html/align.jpg diff --git a/help/html/calculations/calculatedialog.png b/help/help/html/calculations/calculatedialog.png similarity index 100% rename from help/html/calculations/calculatedialog.png rename to help/help/html/calculations/calculatedialog.png diff --git a/help/html/calculations/calculations.html b/help/help/html/calculations/calculations.html similarity index 100% rename from help/html/calculations/calculations.html rename to help/help/html/calculations/calculations.html diff --git a/help/html/calculations/consensus.html b/help/help/html/calculations/consensus.html similarity index 100% rename from help/html/calculations/consensus.html rename to help/help/html/calculations/consensus.html diff --git a/help/html/calculations/conservation.html b/help/help/html/calculations/conservation.html similarity index 100% rename from help/html/calculations/conservation.html rename to help/help/html/calculations/conservation.html diff --git a/help/html/calculations/pairwise.html b/help/help/html/calculations/pairwise.html similarity index 100% rename from help/html/calculations/pairwise.html rename to help/help/html/calculations/pairwise.html diff --git a/help/html/calculations/pca.html b/help/help/html/calculations/pca.html similarity index 100% rename from help/html/calculations/pca.html rename to help/help/html/calculations/pca.html diff --git a/help/html/calculations/pcaviewer.gif b/help/help/html/calculations/pcaviewer.gif similarity index 100% rename from help/html/calculations/pcaviewer.gif rename to help/help/html/calculations/pcaviewer.gif diff --git a/help/html/calculations/quality.html b/help/help/html/calculations/quality.html similarity index 100% rename from help/html/calculations/quality.html rename to help/help/html/calculations/quality.html diff --git a/help/html/calculations/recoverInputdata.html b/help/help/html/calculations/recoverInputdata.html similarity index 100% rename from help/html/calculations/recoverInputdata.html rename to help/help/html/calculations/recoverInputdata.html diff --git a/help/html/calculations/redundancy.html b/help/help/html/calculations/redundancy.html similarity index 100% rename from help/html/calculations/redundancy.html rename to help/help/html/calculations/redundancy.html diff --git a/help/html/calculations/referenceseq.html b/help/help/html/calculations/referenceseq.html similarity index 100% rename from help/html/calculations/referenceseq.html rename to help/help/html/calculations/referenceseq.html diff --git a/help/html/calculations/scorematrices.html b/help/help/html/calculations/scorematrices.html similarity index 100% rename from help/html/calculations/scorematrices.html rename to help/help/html/calculations/scorematrices.html diff --git a/help/html/calculations/sorting.html b/help/help/html/calculations/sorting.html similarity index 100% rename from help/html/calculations/sorting.html rename to help/help/html/calculations/sorting.html diff --git a/help/html/calculations/structureconsensus.html b/help/help/html/calculations/structureconsensus.html similarity index 100% rename from help/html/calculations/structureconsensus.html rename to help/help/html/calculations/structureconsensus.html diff --git a/help/html/calculations/tree.html b/help/help/html/calculations/tree.html similarity index 100% rename from help/html/calculations/tree.html rename to help/help/html/calculations/tree.html diff --git a/help/html/calculations/treeviewer.html b/help/help/html/calculations/treeviewer.html similarity index 100% rename from help/html/calculations/treeviewer.html rename to help/help/html/calculations/treeviewer.html diff --git a/help/html/colourSchemes/.cvsignore b/help/help/html/colourSchemes/.cvsignore similarity index 100% rename from help/html/colourSchemes/.cvsignore rename to help/help/html/colourSchemes/.cvsignore diff --git a/help/html/colourSchemes/abovePID.html b/help/help/html/colourSchemes/abovePID.html similarity index 100% rename from help/html/colourSchemes/abovePID.html rename to help/help/html/colourSchemes/abovePID.html diff --git a/help/html/colourSchemes/annotationColourSetting.gif b/help/help/html/colourSchemes/annotationColourSetting.gif similarity index 100% rename from help/html/colourSchemes/annotationColourSetting.gif rename to help/help/html/colourSchemes/annotationColourSetting.gif diff --git a/help/html/colourSchemes/annotationColouring.html b/help/help/html/colourSchemes/annotationColouring.html similarity index 100% rename from help/html/colourSchemes/annotationColouring.html rename to help/help/html/colourSchemes/annotationColouring.html diff --git a/help/html/colourSchemes/annotationColours.gif b/help/help/html/colourSchemes/annotationColours.gif similarity index 100% rename from help/html/colourSchemes/annotationColours.gif rename to help/help/html/colourSchemes/annotationColours.gif diff --git a/help/html/colourSchemes/blosum.html b/help/help/html/colourSchemes/blosum.html similarity index 100% rename from help/html/colourSchemes/blosum.html rename to help/help/html/colourSchemes/blosum.html diff --git a/help/html/colourSchemes/buried.html b/help/help/html/colourSchemes/buried.html similarity index 100% rename from help/html/colourSchemes/buried.html rename to help/help/html/colourSchemes/buried.html diff --git a/help/html/colourSchemes/clustal.html b/help/help/html/colourSchemes/clustal.html similarity index 100% rename from help/html/colourSchemes/clustal.html rename to help/help/html/colourSchemes/clustal.html diff --git a/help/html/colourSchemes/colbytcoffee.png b/help/help/html/colourSchemes/colbytcoffee.png similarity index 100% rename from help/html/colourSchemes/colbytcoffee.png rename to help/help/html/colourSchemes/colbytcoffee.png diff --git a/help/html/colourSchemes/conservation.html b/help/help/html/colourSchemes/conservation.html similarity index 100% rename from help/html/colourSchemes/conservation.html rename to help/help/html/colourSchemes/conservation.html diff --git a/help/html/colourSchemes/helix.html b/help/help/html/colourSchemes/helix.html similarity index 100% rename from help/html/colourSchemes/helix.html rename to help/help/html/colourSchemes/helix.html diff --git a/help/html/colourSchemes/hydrophobic.html b/help/help/html/colourSchemes/hydrophobic.html similarity index 100% rename from help/html/colourSchemes/hydrophobic.html rename to help/help/html/colourSchemes/hydrophobic.html diff --git a/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html similarity index 100% rename from help/html/colourSchemes/index.html rename to help/help/html/colourSchemes/index.html diff --git a/help/html/colourSchemes/nucleotide.html b/help/help/html/colourSchemes/nucleotide.html similarity index 100% rename from help/html/colourSchemes/nucleotide.html rename to help/help/html/colourSchemes/nucleotide.html diff --git a/help/html/colourSchemes/pid.html b/help/help/html/colourSchemes/pid.html similarity index 100% rename from help/html/colourSchemes/pid.html rename to help/help/html/colourSchemes/pid.html diff --git a/help/html/colourSchemes/purinepyrimidine.html b/help/help/html/colourSchemes/purinepyrimidine.html similarity index 100% rename from help/html/colourSchemes/purinepyrimidine.html rename to help/help/html/colourSchemes/purinepyrimidine.html diff --git a/help/html/colourSchemes/rnahelicesColouring.html b/help/help/html/colourSchemes/rnahelicesColouring.html similarity index 100% rename from help/html/colourSchemes/rnahelicesColouring.html rename to help/help/html/colourSchemes/rnahelicesColouring.html diff --git a/help/html/colourSchemes/rnahelicescoloring.png b/help/help/html/colourSchemes/rnahelicescoloring.png similarity index 100% rename from help/html/colourSchemes/rnahelicescoloring.png rename to help/help/html/colourSchemes/rnahelicescoloring.png diff --git a/help/html/colourSchemes/strand.html b/help/help/html/colourSchemes/strand.html similarity index 100% rename from help/html/colourSchemes/strand.html rename to help/help/html/colourSchemes/strand.html diff --git a/help/html/colourSchemes/taylor.html b/help/help/html/colourSchemes/taylor.html similarity index 100% rename from help/html/colourSchemes/taylor.html rename to help/help/html/colourSchemes/taylor.html diff --git a/help/html/colourSchemes/textcolour.gif b/help/help/html/colourSchemes/textcolour.gif similarity index 100% rename from help/html/colourSchemes/textcolour.gif rename to help/help/html/colourSchemes/textcolour.gif diff --git a/help/html/colourSchemes/textcolour.html b/help/help/html/colourSchemes/textcolour.html similarity index 100% rename from help/html/colourSchemes/textcolour.html rename to help/help/html/colourSchemes/textcolour.html diff --git a/help/html/colourSchemes/turn.html b/help/help/html/colourSchemes/turn.html similarity index 100% rename from help/html/colourSchemes/turn.html rename to help/help/html/colourSchemes/turn.html diff --git a/help/html/colourSchemes/user.html b/help/help/html/colourSchemes/user.html similarity index 100% rename from help/html/colourSchemes/user.html rename to help/help/html/colourSchemes/user.html diff --git a/help/html/colourSchemes/userDefined.gif b/help/help/html/colourSchemes/userDefined.gif similarity index 100% rename from help/html/colourSchemes/userDefined.gif rename to help/help/html/colourSchemes/userDefined.gif diff --git a/help/html/colourSchemes/userDefined_java7.gif b/help/help/html/colourSchemes/userDefined_java7.gif similarity index 100% rename from help/html/colourSchemes/userDefined_java7.gif rename to help/help/html/colourSchemes/userDefined_java7.gif diff --git a/help/html/colourSchemes/zappo.html b/help/help/html/colourSchemes/zappo.html similarity index 100% rename from help/html/colourSchemes/zappo.html rename to help/help/html/colourSchemes/zappo.html diff --git a/help/html/editing/.cvsignore b/help/help/html/editing/.cvsignore similarity index 100% rename from help/html/editing/.cvsignore rename to help/help/html/editing/.cvsignore diff --git a/help/html/editing/editing.jpg b/help/help/html/editing/editing.jpg similarity index 100% rename from help/html/editing/editing.jpg rename to help/help/html/editing/editing.jpg diff --git a/help/html/editing/index.html b/help/help/html/editing/index.html similarity index 100% rename from help/html/editing/index.html rename to help/help/html/editing/index.html diff --git a/help/html/features/.cvsignore b/help/help/html/features/.cvsignore similarity index 100% rename from help/html/features/.cvsignore rename to help/help/html/features/.cvsignore diff --git a/help/html/features/AnnotationColumnSelectionWithSM.png b/help/help/html/features/AnnotationColumnSelectionWithSM.png similarity index 100% rename from help/html/features/AnnotationColumnSelectionWithSM.png rename to help/help/html/features/AnnotationColumnSelectionWithSM.png diff --git a/help/html/features/AnnotationColumnSelectionWithoutSM.gif b/help/help/html/features/AnnotationColumnSelectionWithoutSM.gif similarity index 100% rename from help/html/features/AnnotationColumnSelectionWithoutSM.gif rename to help/help/html/features/AnnotationColumnSelectionWithoutSM.gif diff --git a/help/html/features/amendfeature.gif b/help/help/html/features/amendfeature.gif similarity index 100% rename from help/html/features/amendfeature.gif rename to help/help/html/features/amendfeature.gif diff --git a/help/html/features/annotation.html b/help/help/html/features/annotation.html similarity index 100% rename from help/html/features/annotation.html rename to help/help/html/features/annotation.html diff --git a/help/html/features/annotationsFormat.html b/help/help/html/features/annotationsFormat.html similarity index 100% rename from help/html/features/annotationsFormat.html rename to help/help/html/features/annotationsFormat.html diff --git a/help/html/features/bioJsonFormat.html b/help/help/html/features/bioJsonFormat.html similarity index 100% rename from help/html/features/bioJsonFormat.html rename to help/help/html/features/bioJsonFormat.html diff --git a/help/html/features/biojsmsa.html b/help/help/html/features/biojsmsa.html similarity index 100% rename from help/html/features/biojsmsa.html rename to help/help/html/features/biojsmsa.html diff --git a/help/html/features/chimera.html b/help/help/html/features/chimera.html similarity index 100% rename from help/html/features/chimera.html rename to help/help/html/features/chimera.html diff --git a/help/html/features/clarguments.html b/help/help/html/features/clarguments.html similarity index 100% rename from help/html/features/clarguments.html rename to help/help/html/features/clarguments.html diff --git a/help/html/features/codingfeatures.html b/help/help/html/features/codingfeatures.html similarity index 100% rename from help/html/features/codingfeatures.html rename to help/help/html/features/codingfeatures.html diff --git a/help/html/features/columnFilterByAnnotation.html b/help/help/html/features/columnFilterByAnnotation.html similarity index 100% rename from help/html/features/columnFilterByAnnotation.html rename to help/help/html/features/columnFilterByAnnotation.html diff --git a/help/html/features/commandline.html b/help/help/html/features/commandline.html similarity index 100% rename from help/html/features/commandline.html rename to help/help/html/features/commandline.html diff --git a/help/html/features/creatinFeatures.html b/help/help/html/features/creatinFeatures.html similarity index 100% rename from help/html/features/creatinFeatures.html rename to help/help/html/features/creatinFeatures.html diff --git a/help/html/features/crnewfeature.gif b/help/help/html/features/crnewfeature.gif similarity index 100% rename from help/html/features/crnewfeature.gif rename to help/help/html/features/crnewfeature.gif diff --git a/help/html/features/cursorMode.html b/help/help/html/features/cursorMode.html similarity index 100% rename from help/html/features/cursorMode.html rename to help/help/html/features/cursorMode.html diff --git a/help/html/features/editingFeatures.html b/help/help/html/features/editingFeatures.html similarity index 100% rename from help/html/features/editingFeatures.html rename to help/help/html/features/editingFeatures.html diff --git a/help/html/features/ensemblsequencefetcher.html b/help/help/html/features/ensemblsequencefetcher.html similarity index 100% rename from help/html/features/ensemblsequencefetcher.html rename to help/help/html/features/ensemblsequencefetcher.html diff --git a/help/html/features/fcsgtthan.gif b/help/help/html/features/fcsgtthan.gif similarity index 100% rename from help/html/features/fcsgtthan.gif rename to help/help/html/features/fcsgtthan.gif diff --git a/help/html/features/fcsltthan.gif b/help/help/html/features/fcsltthan.gif similarity index 100% rename from help/html/features/fcsltthan.gif rename to help/help/html/features/fcsltthan.gif diff --git a/help/html/features/fcsminmax.gif b/help/help/html/features/fcsminmax.gif similarity index 100% rename from help/html/features/fcsminmax.gif rename to help/help/html/features/fcsminmax.gif diff --git a/help/html/features/fcsntlabel.gif b/help/help/html/features/fcsntlabel.gif similarity index 100% rename from help/html/features/fcsntlabel.gif rename to help/help/html/features/fcsntlabel.gif diff --git a/help/html/features/featureSettings.gif b/help/help/html/features/featureSettings.gif similarity index 100% rename from help/html/features/featureSettings.gif rename to help/help/html/features/featureSettings.gif diff --git a/help/html/features/featurecoloursettings.gif b/help/help/html/features/featurecoloursettings.gif similarity index 100% rename from help/html/features/featurecoloursettings.gif rename to help/help/html/features/featurecoloursettings.gif diff --git a/help/html/features/featuresFormat.html b/help/help/html/features/featuresFormat.html similarity index 100% rename from help/html/features/featuresFormat.html rename to help/help/html/features/featuresFormat.html diff --git a/help/html/features/featureschemes.html b/help/help/html/features/featureschemes.html similarity index 100% rename from help/html/features/featureschemes.html rename to help/help/html/features/featureschemes.html diff --git a/help/html/features/featuresettings.html b/help/help/html/features/featuresettings.html similarity index 100% rename from help/html/features/featuresettings.html rename to help/help/html/features/featuresettings.html diff --git a/help/html/features/groovy.html b/help/help/html/features/groovy.html similarity index 100% rename from help/html/features/groovy.html rename to help/help/html/features/groovy.html diff --git a/help/html/features/hiddenRegions.html b/help/help/html/features/hiddenRegions.html similarity index 100% rename from help/html/features/hiddenRegions.html rename to help/help/html/features/hiddenRegions.html diff --git a/help/html/features/jalarchive.html b/help/help/html/features/jalarchive.html similarity index 100% rename from help/html/features/jalarchive.html rename to help/help/html/features/jalarchive.html diff --git a/help/html/features/jmol.html b/help/help/html/features/jmol.html similarity index 100% rename from help/html/features/jmol.html rename to help/help/html/features/jmol.html diff --git a/help/html/features/mmcif.html b/help/help/html/features/mmcif.html similarity index 100% rename from help/html/features/mmcif.html rename to help/help/html/features/mmcif.html diff --git a/help/html/features/multipleViews.html b/help/help/html/features/multipleViews.html similarity index 100% rename from help/html/features/multipleViews.html rename to help/help/html/features/multipleViews.html diff --git a/help/html/features/newkeystrokes.html b/help/help/html/features/newkeystrokes.html similarity index 100% rename from help/html/features/newkeystrokes.html rename to help/help/html/features/newkeystrokes.html diff --git a/help/html/features/overview.html b/help/help/html/features/overview.html similarity index 100% rename from help/html/features/overview.html rename to help/help/html/features/overview.html diff --git a/help/html/features/overview.png b/help/help/html/features/overview.png similarity index 100% rename from help/html/features/overview.png rename to help/help/html/features/overview.png diff --git a/help/html/features/pdbseqfetcher.png b/help/help/html/features/pdbseqfetcher.png similarity index 100% rename from help/html/features/pdbseqfetcher.png rename to help/help/html/features/pdbseqfetcher.png diff --git a/help/html/features/pdbsequencefetcher.html b/help/help/html/features/pdbsequencefetcher.html similarity index 100% rename from help/html/features/pdbsequencefetcher.html rename to help/help/html/features/pdbsequencefetcher.html diff --git a/help/html/features/pdbviewer.html b/help/help/html/features/pdbviewer.html similarity index 100% rename from help/html/features/pdbviewer.html rename to help/help/html/features/pdbviewer.html diff --git a/help/html/features/preferences.html b/help/help/html/features/preferences.html similarity index 100% rename from help/html/features/preferences.html rename to help/help/html/features/preferences.html diff --git a/help/html/features/schooser_enter-id.png b/help/help/html/features/schooser_enter-id.png similarity index 100% rename from help/html/features/schooser_enter-id.png rename to help/help/html/features/schooser_enter-id.png diff --git a/help/html/features/schooser_main.png b/help/help/html/features/schooser_main.png similarity index 100% rename from help/html/features/schooser_main.png rename to help/help/html/features/schooser_main.png diff --git a/help/html/features/search.html b/help/help/html/features/search.html similarity index 100% rename from help/html/features/search.html rename to help/help/html/features/search.html diff --git a/help/html/features/search.png b/help/help/html/features/search.png similarity index 100% rename from help/html/features/search.png rename to help/help/html/features/search.png diff --git a/help/html/features/searchclearhist.png b/help/help/html/features/searchclearhist.png similarity index 100% rename from help/html/features/searchclearhist.png rename to help/help/html/features/searchclearhist.png diff --git a/help/html/features/searchhist.png b/help/help/html/features/searchhist.png similarity index 100% rename from help/html/features/searchhist.png rename to help/help/html/features/searchhist.png diff --git a/help/html/features/selectfetchdb.gif b/help/help/html/features/selectfetchdb.gif similarity index 100% rename from help/html/features/selectfetchdb.gif rename to help/help/html/features/selectfetchdb.gif diff --git a/help/html/features/seqfeatures.html b/help/help/html/features/seqfeatures.html similarity index 100% rename from help/html/features/seqfeatures.html rename to help/help/html/features/seqfeatures.html diff --git a/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html similarity index 100% rename from help/html/features/seqfetch.html rename to help/help/html/features/seqfetch.html diff --git a/help/html/features/seqfetcher.gif b/help/help/html/features/seqfetcher.gif similarity index 100% rename from help/html/features/seqfetcher.gif rename to help/help/html/features/seqfetcher.gif diff --git a/help/html/features/seqmappings.html b/help/help/html/features/seqmappings.html similarity index 100% rename from help/html/features/seqmappings.html rename to help/help/html/features/seqmappings.html diff --git a/help/html/features/sifts_mapping_output.png b/help/help/html/features/sifts_mapping_output.png similarity index 100% rename from help/html/features/sifts_mapping_output.png rename to help/help/html/features/sifts_mapping_output.png diff --git a/help/html/features/siftsmapping.html b/help/help/html/features/siftsmapping.html similarity index 100% rename from help/html/features/siftsmapping.html rename to help/help/html/features/siftsmapping.html diff --git a/help/html/features/splitView.html b/help/help/html/features/splitView.html similarity index 100% rename from help/html/features/splitView.html rename to help/help/html/features/splitView.html diff --git a/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html similarity index 100% rename from help/html/features/structurechooser.html rename to help/help/html/features/structurechooser.html diff --git a/help/html/features/uniprotqueryfields.html b/help/help/html/features/uniprotqueryfields.html similarity index 100% rename from help/html/features/uniprotqueryfields.html rename to help/help/html/features/uniprotqueryfields.html diff --git a/help/html/features/uniprotseqfetcher.png b/help/help/html/features/uniprotseqfetcher.png similarity index 100% rename from help/html/features/uniprotseqfetcher.png rename to help/help/html/features/uniprotseqfetcher.png diff --git a/help/html/features/uniprotsequencefetcher.html b/help/help/html/features/uniprotsequencefetcher.html similarity index 100% rename from help/html/features/uniprotsequencefetcher.html rename to help/help/html/features/uniprotsequencefetcher.html diff --git a/help/html/features/varna.html b/help/help/html/features/varna.html similarity index 100% rename from help/html/features/varna.html rename to help/help/html/features/varna.html diff --git a/help/html/features/viewingpdbs.html b/help/help/html/features/viewingpdbs.html similarity index 100% rename from help/html/features/viewingpdbs.html rename to help/help/html/features/viewingpdbs.html diff --git a/help/html/features/wrap.html b/help/help/html/features/wrap.html similarity index 100% rename from help/html/features/wrap.html rename to help/help/html/features/wrap.html diff --git a/help/html/features/xsspannotation.html b/help/help/html/features/xsspannotation.html similarity index 100% rename from help/html/features/xsspannotation.html rename to help/help/html/features/xsspannotation.html diff --git a/help/html/groovy/featuresCounter.html b/help/help/html/groovy/featuresCounter.html similarity index 100% rename from help/html/groovy/featuresCounter.html rename to help/help/html/groovy/featuresCounter.html diff --git a/help/html/index.html b/help/help/html/index.html similarity index 100% rename from help/html/index.html rename to help/help/html/index.html diff --git a/help/html/io/.cvsignore b/help/help/html/io/.cvsignore similarity index 100% rename from help/html/io/.cvsignore rename to help/help/html/io/.cvsignore diff --git a/help/html/io/export.html b/help/help/html/io/export.html similarity index 100% rename from help/html/io/export.html rename to help/help/html/io/export.html diff --git a/help/html/io/exportseqreport.html b/help/help/html/io/exportseqreport.html similarity index 100% rename from help/html/io/exportseqreport.html rename to help/help/html/io/exportseqreport.html diff --git a/help/html/io/file.png b/help/help/html/io/file.png similarity index 100% rename from help/html/io/file.png rename to help/help/html/io/file.png diff --git a/help/html/io/fileformats.html b/help/help/html/io/fileformats.html similarity index 100% rename from help/html/io/fileformats.html rename to help/help/html/io/fileformats.html diff --git a/help/html/io/index.html b/help/help/html/io/index.html similarity index 100% rename from help/html/io/index.html rename to help/help/html/io/index.html diff --git a/help/html/io/modellerpir.html b/help/help/html/io/modellerpir.html similarity index 100% rename from help/html/io/modellerpir.html rename to help/help/html/io/modellerpir.html diff --git a/help/html/io/seqreport.gif b/help/help/html/io/seqreport.gif similarity index 100% rename from help/html/io/seqreport.gif rename to help/help/html/io/seqreport.gif diff --git a/help/html/io/tcoffeescores.html b/help/help/html/io/tcoffeescores.html similarity index 100% rename from help/html/io/tcoffeescores.html rename to help/help/html/io/tcoffeescores.html diff --git a/help/html/keys.html b/help/help/html/keys.html similarity index 100% rename from help/html/keys.html rename to help/help/html/keys.html diff --git a/help/html/memory.html b/help/help/html/memory.html similarity index 100% rename from help/html/memory.html rename to help/help/html/memory.html diff --git a/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html similarity index 100% rename from help/html/menus/alignmentMenu.html rename to help/help/html/menus/alignmentMenu.html diff --git a/help/html/menus/alwannotation.html b/help/help/html/menus/alwannotation.html similarity index 100% rename from help/html/menus/alwannotation.html rename to help/help/html/menus/alwannotation.html diff --git a/help/html/menus/alwannotationpanel.html b/help/help/html/menus/alwannotationpanel.html similarity index 100% rename from help/html/menus/alwannotationpanel.html rename to help/help/html/menus/alwannotationpanel.html diff --git a/help/html/menus/alwcalculate.html b/help/help/html/menus/alwcalculate.html similarity index 100% rename from help/html/menus/alwcalculate.html rename to help/help/html/menus/alwcalculate.html diff --git a/help/html/menus/alwcolour.html b/help/help/html/menus/alwcolour.html similarity index 100% rename from help/html/menus/alwcolour.html rename to help/help/html/menus/alwcolour.html diff --git a/help/html/menus/alwedit.html b/help/help/html/menus/alwedit.html similarity index 100% rename from help/html/menus/alwedit.html rename to help/help/html/menus/alwedit.html diff --git a/help/html/menus/alwfile.html b/help/help/html/menus/alwfile.html similarity index 100% rename from help/html/menus/alwfile.html rename to help/help/html/menus/alwfile.html diff --git a/help/html/menus/alwformat.html b/help/help/html/menus/alwformat.html similarity index 100% rename from help/html/menus/alwformat.html rename to help/help/html/menus/alwformat.html diff --git a/help/html/menus/alwselect.html b/help/help/html/menus/alwselect.html similarity index 100% rename from help/html/menus/alwselect.html rename to help/help/html/menus/alwselect.html diff --git a/help/html/menus/alwview.html b/help/help/html/menus/alwview.html similarity index 100% rename from help/html/menus/alwview.html rename to help/help/html/menus/alwview.html diff --git a/help/html/menus/desktopMenu.html b/help/help/html/menus/desktopMenu.html similarity index 100% rename from help/html/menus/desktopMenu.html rename to help/help/html/menus/desktopMenu.html diff --git a/help/html/menus/index.html b/help/help/html/menus/index.html similarity index 100% rename from help/html/menus/index.html rename to help/help/html/menus/index.html diff --git a/help/html/menus/popupMenu.html b/help/help/html/menus/popupMenu.html similarity index 100% rename from help/html/menus/popupMenu.html rename to help/help/html/menus/popupMenu.html diff --git a/help/html/menus/wsmenu.html b/help/help/html/menus/wsmenu.html similarity index 100% rename from help/html/menus/wsmenu.html rename to help/help/html/menus/wsmenu.html diff --git a/help/html/misc/.cvsignore b/help/help/html/misc/.cvsignore similarity index 100% rename from help/html/misc/.cvsignore rename to help/help/html/misc/.cvsignore diff --git a/help/html/misc/aaproperties.html b/help/help/html/misc/aaproperties.html similarity index 100% rename from help/html/misc/aaproperties.html rename to help/help/html/misc/aaproperties.html diff --git a/help/html/misc/ala.jpg b/help/help/html/misc/ala.jpg similarity index 100% rename from help/html/misc/ala.jpg rename to help/help/html/misc/ala.jpg diff --git a/help/html/misc/aminoAcids.html b/help/help/html/misc/aminoAcids.html similarity index 100% rename from help/html/misc/aminoAcids.html rename to help/help/html/misc/aminoAcids.html diff --git a/help/html/misc/arg.jpg b/help/help/html/misc/arg.jpg similarity index 100% rename from help/html/misc/arg.jpg rename to help/help/html/misc/arg.jpg diff --git a/help/html/misc/asparagine.jpg b/help/help/html/misc/asparagine.jpg similarity index 100% rename from help/html/misc/asparagine.jpg rename to help/help/html/misc/asparagine.jpg diff --git a/help/html/misc/aspartate.jpg b/help/help/html/misc/aspartate.jpg similarity index 100% rename from help/html/misc/aspartate.jpg rename to help/help/html/misc/aspartate.jpg diff --git a/help/html/misc/cys.jpg b/help/help/html/misc/cys.jpg similarity index 100% rename from help/html/misc/cys.jpg rename to help/help/html/misc/cys.jpg diff --git a/help/html/misc/geneticCode.html b/help/help/html/misc/geneticCode.html similarity index 100% rename from help/html/misc/geneticCode.html rename to help/help/html/misc/geneticCode.html diff --git a/help/html/misc/glutamate.jpg b/help/help/html/misc/glutamate.jpg similarity index 100% rename from help/html/misc/glutamate.jpg rename to help/help/html/misc/glutamate.jpg diff --git a/help/html/misc/glutamine.jpg b/help/help/html/misc/glutamine.jpg similarity index 100% rename from help/html/misc/glutamine.jpg rename to help/help/html/misc/glutamine.jpg diff --git a/help/html/misc/gly.jpg b/help/help/html/misc/gly.jpg similarity index 100% rename from help/html/misc/gly.jpg rename to help/help/html/misc/gly.jpg diff --git a/help/html/misc/his.jpg b/help/help/html/misc/his.jpg similarity index 100% rename from help/html/misc/his.jpg rename to help/help/html/misc/his.jpg diff --git a/help/html/misc/iso.jpg b/help/help/html/misc/iso.jpg similarity index 100% rename from help/html/misc/iso.jpg rename to help/help/html/misc/iso.jpg diff --git a/help/html/misc/leu.jpg b/help/help/html/misc/leu.jpg similarity index 100% rename from help/html/misc/leu.jpg rename to help/help/html/misc/leu.jpg diff --git a/help/html/misc/lys.jpg b/help/help/html/misc/lys.jpg similarity index 100% rename from help/html/misc/lys.jpg rename to help/help/html/misc/lys.jpg diff --git a/help/html/misc/met.jpg b/help/help/html/misc/met.jpg similarity index 100% rename from help/html/misc/met.jpg rename to help/help/html/misc/met.jpg diff --git a/help/html/misc/phe.jpg b/help/help/html/misc/phe.jpg similarity index 100% rename from help/html/misc/phe.jpg rename to help/help/html/misc/phe.jpg diff --git a/help/html/misc/pro.jpg b/help/help/html/misc/pro.jpg similarity index 100% rename from help/html/misc/pro.jpg rename to help/help/html/misc/pro.jpg diff --git a/help/html/misc/properties.gif b/help/help/html/misc/properties.gif similarity index 100% rename from help/html/misc/properties.gif rename to help/help/html/misc/properties.gif diff --git a/help/html/misc/ser.jpg b/help/help/html/misc/ser.jpg similarity index 100% rename from help/html/misc/ser.jpg rename to help/help/html/misc/ser.jpg diff --git a/help/html/misc/thr.jpg b/help/help/html/misc/thr.jpg similarity index 100% rename from help/html/misc/thr.jpg rename to help/help/html/misc/thr.jpg diff --git a/help/html/misc/tryp.jpg b/help/help/html/misc/tryp.jpg similarity index 100% rename from help/html/misc/tryp.jpg rename to help/help/html/misc/tryp.jpg diff --git a/help/html/misc/tyr.jpg b/help/help/html/misc/tyr.jpg similarity index 100% rename from help/html/misc/tyr.jpg rename to help/help/html/misc/tyr.jpg diff --git a/help/html/misc/val.jpg b/help/help/html/misc/val.jpg similarity index 100% rename from help/html/misc/val.jpg rename to help/help/html/misc/val.jpg diff --git a/help/html/na/index.html b/help/help/html/na/index.html similarity index 100% rename from help/html/na/index.html rename to help/help/html/na/index.html diff --git a/help/html/privacy.html b/help/help/html/privacy.html similarity index 100% rename from help/html/privacy.html rename to help/help/html/privacy.html diff --git a/help/html/releases.html b/help/help/html/releases.html similarity index 100% rename from help/html/releases.html rename to help/help/html/releases.html diff --git a/help/html/vamsas/index.html b/help/help/html/vamsas/index.html similarity index 100% rename from help/html/vamsas/index.html rename to help/help/html/vamsas/index.html diff --git a/help/html/webServices/.cvsignore b/help/help/html/webServices/.cvsignore similarity index 100% rename from help/html/webServices/.cvsignore rename to help/help/html/webServices/.cvsignore diff --git a/help/html/webServices/AACon.html b/help/help/html/webServices/AACon.html similarity index 100% rename from help/html/webServices/AACon.html rename to help/help/html/webServices/AACon.html diff --git a/help/html/webServices/JABAWS.html b/help/help/html/webServices/JABAWS.html similarity index 100% rename from help/html/webServices/JABAWS.html rename to help/help/html/webServices/JABAWS.html diff --git a/help/html/webServices/RNAalifold.html b/help/help/html/webServices/RNAalifold.html similarity index 100% rename from help/html/webServices/RNAalifold.html rename to help/help/html/webServices/RNAalifold.html diff --git a/help/html/webServices/RNAalifoldAnnotationRows.png b/help/help/html/webServices/RNAalifoldAnnotationRows.png similarity index 100% rename from help/html/webServices/RNAalifoldAnnotationRows.png rename to help/help/html/webServices/RNAalifoldAnnotationRows.png diff --git a/help/html/webServices/clwqueued.gif b/help/help/html/webServices/clwqueued.gif similarity index 100% rename from help/html/webServices/clwqueued.gif rename to help/help/html/webServices/clwqueued.gif diff --git a/help/html/webServices/dbreffetcher.html b/help/help/html/webServices/dbreffetcher.html similarity index 100% rename from help/html/webServices/dbreffetcher.html rename to help/help/html/webServices/dbreffetcher.html diff --git a/help/html/webServices/index.html b/help/help/html/webServices/index.html similarity index 100% rename from help/html/webServices/index.html rename to help/help/html/webServices/index.html diff --git a/help/html/webServices/invalidurldialog.gif b/help/help/html/webServices/invalidurldialog.gif similarity index 100% rename from help/html/webServices/invalidurldialog.gif rename to help/help/html/webServices/invalidurldialog.gif diff --git a/help/html/webServices/jalviewrssreader.gif b/help/help/html/webServices/jalviewrssreader.gif similarity index 100% rename from help/html/webServices/jalviewrssreader.gif rename to help/help/html/webServices/jalviewrssreader.gif diff --git a/help/html/webServices/jnet.html b/help/help/html/webServices/jnet.html similarity index 100% rename from help/html/webServices/jnet.html rename to help/help/html/webServices/jnet.html diff --git a/help/html/webServices/jnetprediction.gif b/help/help/html/webServices/jnetprediction.gif similarity index 100% rename from help/html/webServices/jnetprediction.gif rename to help/help/html/webServices/jnetprediction.gif diff --git a/help/html/webServices/msaclient.html b/help/help/html/webServices/msaclient.html similarity index 100% rename from help/html/webServices/msaclient.html rename to help/help/html/webServices/msaclient.html diff --git a/help/html/webServices/multimafftjbs.gif b/help/help/html/webServices/multimafftjbs.gif similarity index 100% rename from help/html/webServices/multimafftjbs.gif rename to help/help/html/webServices/multimafftjbs.gif diff --git a/help/html/webServices/newsreader.html b/help/help/html/webServices/newsreader.html similarity index 100% rename from help/html/webServices/newsreader.html rename to help/help/html/webServices/newsreader.html diff --git a/help/html/webServices/proteinDisorder.html b/help/help/html/webServices/proteinDisorder.html similarity index 100% rename from help/html/webServices/proteinDisorder.html rename to help/help/html/webServices/proteinDisorder.html diff --git a/help/html/webServices/shmr.html b/help/help/html/webServices/shmr.html similarity index 100% rename from help/html/webServices/shmr.html rename to help/help/html/webServices/shmr.html diff --git a/help/html/webServices/urllinks.html b/help/help/html/webServices/urllinks.html similarity index 100% rename from help/html/webServices/urllinks.html rename to help/help/html/webServices/urllinks.html diff --git a/help/html/webServices/webServicesParams.html b/help/help/html/webServices/webServicesParams.html similarity index 100% rename from help/html/webServices/webServicesParams.html rename to help/help/html/webServices/webServicesParams.html diff --git a/help/html/webServices/webServicesPrefs.html b/help/help/html/webServices/webServicesPrefs.html similarity index 100% rename from help/html/webServices/webServicesPrefs.html rename to help/help/html/webServices/webServicesPrefs.html diff --git a/help/html/webServices/wsparams.gif b/help/help/html/webServices/wsparams.gif similarity index 100% rename from help/html/webServices/wsparams.gif rename to help/help/html/webServices/wsparams.gif diff --git a/help/html/webServices/wsprefs.gif b/help/help/html/webServices/wsprefs.gif similarity index 100% rename from help/html/webServices/wsprefs.gif rename to help/help/html/webServices/wsprefs.gif diff --git a/help/html/whatsNew.html b/help/help/html/whatsNew.html similarity index 100% rename from help/html/whatsNew.html rename to help/help/html/whatsNew.html diff --git a/help/icons/Home.png b/help/help/icons/Home.png similarity index 100% rename from help/icons/Home.png rename to help/help/icons/Home.png diff --git a/help/icons/back.png b/help/help/icons/back.png similarity index 100% rename from help/icons/back.png rename to help/help/icons/back.png diff --git a/help/icons/forward.png b/help/help/icons/forward.png similarity index 100% rename from help/icons/forward.png rename to help/help/icons/forward.png diff --git a/help/icons/print.png b/help/help/icons/print.png similarity index 100% rename from help/icons/print.png rename to help/help/icons/print.png diff --git a/help/icons/setup.png b/help/help/icons/setup.png similarity index 100% rename from help/icons/setup.png rename to help/help/icons/setup.png -- 1.7.10.2