jalview

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JAL-1819 commented out debugging message to stderr

JAL-1551 JAL-1819 formatting/imports

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    /src/jalview/datamodel/Annotation.java
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    /src/jalview/io/vamsas/Sequencefeature.java
JAL-1819 use Float.isNaN() to check for NaNs!

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    /src/jalview/datamodel/Annotation.java
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    /src/jalview/io/vamsas/Sequencefeature.java
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    /src/jalview/schemes/GraduatedColor.java
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    /src/jalview/ws/jws2/AADisorderClient.java
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-1598 replaced faulty regex, amended Varna call, to get pseudo-knots

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    /test/jalview/gui/AppVarnaTest.java
JAL-1641 biojson documentation with docson

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    /examples/biojson-doc/.gitignore
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    /examples/biojson-doc/LICENSE
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    /examples/biojson-doc/README.md
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    /examples/biojson-doc/biojsonschema.json
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    /examples/biojson-doc/bower.json
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    /examples/biojson-doc/css/docson.css
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    /examples/biojson-doc/docson-swagger.js
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    /examples/biojson-doc/docson.js
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    /examples/biojson-doc/index.html
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    /examples/biojson-doc/lib/handlebars.js
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    /examples/biojson-doc/lib/highlight.js
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    /examples/biojson-doc/lib/jquery.js
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    /examples/biojson-doc/lib/jsonpointer.js
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    /examples/biojson-doc/lib/marked.js
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    /examples/biojson-doc/lib/require.js
  1. … 39 more files in changeset.
JAL-1769 fixed output to jalview (.jpv) file in headless mode. Initial cause of failure: NPE while trying to save varna viewers (Desktop.destop is null in headless mode)

JAL-1805 test envirionment separation

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    /test/jalview/analysis/AlignSeqTest.java
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    /test/jalview/analysis/AlignmentUtilsTests.java
  1. … 82 more files in changeset.
Merge branch 'features/1769_headless-mode-test' into develop

JAL-1641 added json schema for jalview JSON model, the schema is employed for documentation but can be more usefull for validation in the future

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    /examples/biojsonschema.json
JAL-1769 fixed headless execution mode and created test for all possible outputs

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    /src/jalview/gui/AlignExportSettings.java
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    /test/jalview/bin/CommandLineOperations.java
JAL-1081 unit tests added

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    /test/jalview/analysis/RnaTest.java
JAL-1782 refactored test to ensure it passes in TestNG

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    /test/jalview/analysis/AnnotationSorterTest.java
JAL-1421 generics used for leaner safer code

JAL-1799 tweaked calculation for applet, now showing 2 not 3 seqs

JAL-1799 equivalent logic in applet

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    /src/jalview/appletgui/AlignFrame.java
JAL-892 jnlp, installAnywhere, build, licence references updated to 3.93

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    /utils/InstallAnywhere/Jalview.iap_xml
Merge branch 'develop' into features/JAL-892varnaToProject

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    /src/jalview/gui/AlignFrame.java
JAL-892 1 second delay for correct initial rendering; code tidy up

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    /src/jalview/gui/AppVarnaBinding.java
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    /src/jalview/gui/Jalview2XML.java
Merge branch 'bug/JAL-1443_loading-empty-file' into develop

JAL-1443 data validation for empty content before loading alignment from file or clipboard

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    /src/jalview/gui/CutAndPasteTransfer.java
JAL-1677 check all response lines when parsing REST server port

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-1681 more condensed tooltip where codons share same percentage

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    /src/jalview/analysis/AAFrequency.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

house keeping

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    /src/jalview/jbgui/PDBDocFieldPreferences.java
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    /src/jalview/ws/dbsources/PDBRestClient.java
JAL-1802 explanatory comment added

JAL-1802 handle slide sequences edits in split frame mode

JAL-1799 deduct more space for decorators on Windows

JAL-1619 align the added sequences to match what they are added to