jalview

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JAL-3763 Javadoc, check for null, additional tests

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java
JAL-3763 unused method removed

JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
JAL-3763 failsafe check for null

JAL-3763 refactored getCoveringMapping for virtual feature discovery

JAL-3763 always make a new dataset sequence for CDS sequence

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3751 only merge strictly contiguous ranges of mappings

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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3700 additions and corrections to unit tests

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    /test/jalview/util/MappingUtilsTest.java
JAL-3700 fix for propagation of sort commands

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    /src/jalview/util/MappingUtils.java
JAL-3700 check for 'covering' mapping when matching CDS to peptides

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    /src/jalview/util/MappingUtils.java
Merge branch 'feature/JAL-3615gzipXfam' into develop

JAL-3615 JAL-2656 missing import after cherrypick

JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header

JAL-2656 recognise Gzipped file input streams by their content, not their filename

Conflicts:

src/jalview/io/FileParse.java

cherypicked from 2.11.1.1 release patch

JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-3697 show total number of features not shown

JAL-3696 log the error message from the exception to the console

JAL-3695 htsjdk 2.12 -> 2.23 (library change only, no code change. needs gradle refresh in eclipse)

    • binary
    /j11lib/htsjdk-2.23.0.jar
    • binary
    /j8lib/htsjdk-2.23.0.jar
JAL-1424 streamlined message checker, corrected applet lookup keys

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AppletJmol.java
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    /utils/MessageBundleChecker.java
JAL-1424 slight tidying of reporting

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    /utils/MessageBundleChecker.java
JAL-3311 JAL-3141 JAL-3144 tidying obsolete message bundle entries

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/fts/core/FTSRestClient.java
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    /src/jalview/gui/VamsasApplication.java
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    /src/jalview/io/VamsasAppDatastore.java
JAL-3518 Spanish text for 'write features'

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    /resources/lang/Messages_es.properties
JAL-3570 JAL-3187 spanish translations for tabbed feature settings

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    /resources/lang/Messages_es.properties
JAL-3570 updated external help links

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    /help/help/html/webServices/AACon.html
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    /help/help/html/webServices/msaclient.html
JAL-2656 JAL-3615 check response headers to test for gzipped url reply

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    /test/jalview/io/FileParseTest.java
JAL-3615 used gzip endpoints for Pfam and Rfam

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    /src/jalview/ws/dbsources/PfamFull.java
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    /src/jalview/ws/dbsources/PfamSeed.java
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    /src/jalview/ws/dbsources/RfamFull.java
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    /src/jalview/ws/dbsources/RfamSeed.java
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    /test/jalview/io/FileParseTest.java
Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

JAL-3675 2.11.1.1 release notes

JAL-3493 clear search highlights when escape/deselect all