jalview

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JAL-3179 exe and app creation -- not complete

JAL-3032 revert change to tooltip StringBuilder length

JAL-3141 improvement on BackupFilenameParts filename matching

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    /src/jalview/io/BackupFilenameParts.java
JAL-3141 fixed test

final timing checks for optimization

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    /optimization/timing-java-bh-2.txt
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    /optimization/timing-js-firefox-bh-2.txt
Platform.timecheck calls removed or commented out.

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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
removing cyclic call

Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/CrossRef.java
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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/datamodel/DBRefSource.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/datamodel/SequenceI.java
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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
  1. … 38 more files in changeset.

changeset discussion

  1. Mungo Carstairs: why are loops in removeAlreadyRetrievedSeqs now backwards?
timestamp just before major refactoring in relation to preliminary contructor/iterator optimization

JAL-3141. This adds quite a lot of code to allow an 'Include backup files' checkbox in the 'Load Project' JalviewFileChooser. However I cannot for the life of me get the file list in the FileChooser to refresh /reliably/ on a mac at least anyway (it does about 1 time in 9git status).

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    /resources/lang/Messages_es.properties
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    /src/jalview/io/BackupFilenameFilter.java
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    /src/jalview/io/BackupFilenameParts.java
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    /src/jalview/io/JalviewFileChooser.java
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    /src/jalview/io/JalviewFileFilter.java
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    /src/jalview/io/JalviewFileView.java
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into Jalview-JS/demo

Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into Jalview-JS/20190123

JAL-3187 return a colour for linked features with transparency

JAL-3187 set initial state of checkbox from viewport

SwingJS update (maybe nothing?)

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    /swingjs/ver/3.2.4/SwingJS-site.zip
timing code

JSON refactoring

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblInfo.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/ensembl/EnsemblSymbol.java
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    /src/jalview/ext/ensembl/EnsemblXref.java
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    /src/jalview/ext/paradise/Annotate3D.java
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    /src/jalview/urls/IdentifiersUrlProvider.java
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    /src/jalview/util/JSONUtils.java
JavaScript browser-based JSON parsing

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    /src/jalview/javascript/json/JSON.java
Timing code

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    /optimization/timing-java-bh.txt
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    /optimization/timing-js-chrome-bh.txt
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    /optimization/timing-js-firefox-bh.txt
JAL-3187 don't compute variant features on peptide, show on demand

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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3141 Added a '.fa' to filename examples

JAL-3141 Change of label (change of '_' character to ' ')

JAL-3141 Change of label

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    /resources/lang/Messages_es.properties
JAL-3141 Removed border around example filenames in Backups Preferences pane

Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into Jalview-JS/20190123

JAL-3141 New layout and wording of Backups Preferences pane after consultation with SD. Seriously rationalised 'backupfiles...SetEnable' to allow for more complex widget enabling/disabling depending on other widget values. Fixed a buglet or two when there's an unusual selection of options (when suffix has no '%n' or is completely empty).

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/jbgui/GPreferences.java
JAL-3141 Eclipse re-formatting of file

JAL-3018 Ensembl version updated to 9.0

adds File..Load Project file for JS

fixes DnD

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip