jalview

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JAL-1933 update threshold on focus lost in text field

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    /src/jalview/gui/AnnotationRowFilter.java
Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2370 fix bug when hiding a range including two or more hidden ranges

JAL-1270 class renamed

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    /test/jalview/analysis/DnaAlignmentGenerator.java
JAL-2380 fix Matrix.postMultiply()

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    /src/jalview/math/Matrix.java
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    /test/jalview/math/MatrixTest.java
JAL-1270 tweaks to AlignmentGenerator / client class

JAL-1270 renamed AlignmentGenerator, and added peptide option

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    /test/jalview/analysis/AlignmentGenerator.java
JAL-2379 null references to PCA model when panel is closed

JAL-2344 now flagging formats as 'identifiable' instead of 'dynamic'

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    /src/jalview/io/FileFormats.java
JAL-2344 separated AlignmentFileI into AlignmentFileReaderI, AlignmentFileWriterI

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    /src/jalview/gui/CutAndPasteTransfer.java
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    /src/jalview/io/AlignmentFileI.java
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    /src/jalview/io/AlignmentFileReaderI.java
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    /src/jalview/io/AlignmentFileWriterI.java
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    /src/jalview/io/AppletFormatAdapter.java
JAL-2344 groovy script that registers a new file format

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    /examples/groovy/fileFormat.groovy
JAL-2344 FileFormats singleton for formats, FileFormatI simplified

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/bin/JalviewLiteURLRetrieve.java
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    /src/jalview/gui/CutAndPasteTransfer.java
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    /src/jalview/io/AppletFormatAdapter.java
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    /src/jalview/io/FileFormat.java
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    /src/jalview/io/FileFormatI.java
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    /src/jalview/io/FileFormats.java
  1. … 10 more files in changeset.
JAL-2344 addSequence() method added to support Groovy parser

JAL-2377 avoid infinite loop formatting 1.0E-310

JAL-2374 unit test for (modified) Alignment.findGroup()

JAL-2374 fix popup out by one and multiple groups bugs

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    /src/jalview/appletgui/SeqPanel.java
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    /src/jalview/datamodel/AlignmentI.java
JAL-2373 set state of Above PID, By Conservation in Popup Menu

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    /src/jalview/appletgui/APopupMenu.java
JAL-2356 enhanced unit test to verify reuse (or not) of file from cache

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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
Merge branch 'patch/JAL-2197_jpredforjnets' into develop merge was missed for 2.10.1 release!

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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/AlignFrame.java
JAL-2105 updated for reviewed REST version 4.8

JAL-1895 suppress RNA interaction colour option

Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2359 add Window menu entry only after all danger of error is passed

JAL-2356 use cached Sifts file if not expired

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2354 handle error response when fetching features

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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-2344 handle null format, simplify JalviewFileChooser constructor

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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/gui/WsParamSetManager.java
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    /src/jalview/io/JalviewFileChooser.java
JAL-1753 JAL-1596 JAL-1933 ensure AWT updates are on AWT thread

Merge branch 'features/JAL-1933_occupancy' into features/JAL-2295setChimeraAttributes

JAL-1933 show occupancy count as a tooltip

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    /src/jalview/analysis/AAFrequency.java
JAL-1933 switch from gap count to occupancy

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    /src/jalview/analysis/AAFrequency.java