jalview/test

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Friday 24 Jun
5:25 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-2349 TODO for tests

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    ./datamodel/AlignmentTest.java
5:24 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-2349 JAL-3855 formatting

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    ./datamodel/AlignmentTest.java
  2. … 2 more files in changeset.
Friday 10 Jun
12:13 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

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    ./gui/SeqPanelTest.java
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    ./ws/seqfetcher/DbRefFetcherTest.java
  3. … 10 more files in changeset.
Thursday 09 Jun
12:16 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 increase timeouts for command line ops

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    ./bin/CommandLineOperations.java
10:38 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.

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    ./gui/AlignViewportTest.java
10:38 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.

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    ./gui/AlignViewportTest.java
Wednesday 08 Jun
11:20 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 more pointless sleeps

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    ./gui/SeqPanelTest.java
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    ./gui/SeqPanelTest_isolate.java
  3. … 2 more files in changeset.
10:49 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 isolate the failing test in its own class

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    ./gui/SeqPanelTest.java
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    ./gui/SeqPanelTest_isolate.java
6:01 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 make jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence sequential

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    ./gui/SeqPanelTest.java
Monday 06 Jun
5:00 pm

Ben Soares

JAL-4020 updated tests

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    ./ext/pymol/PymolManagerTest.java
Friday 03 Jun
2:37 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-1953 fix test and expected for canonical name for PFAM!

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    ./util/DBRefUtilsTest.java
2:22 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-1953 update canonical db test for PFAM canonical name - also note could do the same for JAL-4022

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    ./util/DBRefUtilsTest.java
2:13 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4021 todo & fix FileFormat tests

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    ./io/FileFormatsTest.java
  2. … 2 more files in changeset.
11:37 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-1953 2.11.2 with Archeopteryx! Minimal patches and Merge branch 'kjvdh/features/PhylogenyViewer' into merge/2_11_2/PhylogenyViewer also restored last kjvdh build of forester to j8 and j11lib directories Conflicts: .classpath j8lib/forester.jar resources/lang/Messages.properties src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/project/Jalview2XML.java src/jalview/schemabinding/version2/JalviewModelSequence.java src/jalview/util/DBRefUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/jalviewjs/buildxml/build.xml

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    ./gui/FreeUpMemoryTest.java
  2. … 38 more files in changeset.
Thursday 02 Jun
4:05 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh/features/PhylogenyViewer_tabbedsupport Update from Release 2.11.2 develop branch JAL-1953 Conflicts: .classpath .project resources/lang/Messages.properties src/jalview/bin/Jalview.java src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/CalculationChooser.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/gui/TreePanel.java src/jalview/gui/WebserviceInfo.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/io/NewickFile.java src/jalview/math/Matrix.java src/jalview/math/MatrixI.java src/jalview/util/MappingUtils.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/eclipse/org.eclipse.jdt.core.jalview.prefs utils/eclipse/org.eclipse.jdt.ui.prefs

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    ./gui/FreeUpMemoryTest.java
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    ./io/NewickFileTests.java
  3. … 37 more files in changeset.
Monday 18 Apr
3:02 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3365 the correct Pfam ID

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    ./io/StockholmFileTest.java
  2. … 2 more files in changeset.
Saturday 16 Apr
1:38 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3365 per-sequence secondary structure symbol ‘X’ is not properly exported and reimported

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    ./io/StockholmFileTest.java
  2. … 2 more files in changeset.
1:36 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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    ./io/StockholmFileTest.java
  2. … 2 more files in changeset.
Tuesday 05 Apr
6:37 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3981 patch tests and remove errant imports

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    ./io/SequenceAnnotationReportTest.java
  2. … 1 more file in changeset.
6:14 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3990 gradle spotlessApply

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    ./fts/service/pdb/PDBFTSRestClientTest.java
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    ./gui/structurechooser/StructureChooserQuerySourceTest.java
  3. … 2 more files in changeset.
Thursday 31 Mar
3:17 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3085 update tests and mock responses, new P0dtd1 testcase

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    ./fts/service/pdb/PDBFTSRestClientTest.java
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    ./fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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    ./fts/threedbeacons/p01308_pdbfts_query.txt
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    ./fts/threedbeacons/p01308_tdb_fts_query_resp.txt
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    ./fts/threedbeacons/p01308_tdb_resp.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1_resp.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2_resp.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3_resp.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4.txt
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    ./fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4_resp.txt
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    ./fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt
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    ./fts/threedbeacons/p38398_tdb_fts_query_resp.txt
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    ./gui/structurechooser/StructureChooserQuerySourceTest.java
Wednesday 30 Mar
5:32 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3976 fix mock PDBFTS query & responses

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    ./fts/threedbeacons/p01308_pdbfts_query.txt
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    ./fts/threedbeacons/p01308_pdbfts_resp.txt
Wednesday 23 Mar
12:22 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3976 update tests

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    ./fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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    ./fts/threedbeacons/p01308_pdbfts_resp.txt
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    ./fts/threedbeacons/p01308_tdb_resp.txt
Thursday 10 Mar
5:40 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'master' into releases/Release_2_11_2_Branch

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    ./gui/SplitFrameTest.java
  2. … 6 more files in changeset.
Tuesday 08 Mar
9:58 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 apply copyright to tests

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    ./analysis/AlignmentSorterTest.java
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    ./analysis/GeneticCodesTest.java
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    ./analysis/scoremodels/PIDModelTest.java
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    ./analysis/scoremodels/ScoreMatrixTest.java
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    ./analysis/scoremodels/ScoreModelsTest.java
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    ./bin/HiDPISettingTest1.java
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    ./datamodel/ConcurrentModificationTest.java
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    ./datamodel/MappedFeaturesTest.java
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    ./datamodel/SequenceGroupTest.java
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    ./datamodel/features/FeatureAttributesTest.java
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    ./datamodel/features/FeatureMatcherSetTest.java
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    ./datamodel/features/FeatureMatcherTest.java
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    ./datamodel/features/FeatureStoreTest.java
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    ./datamodel/features/SequenceFeaturesTest.java
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    ./ext/android/SparseDoubleArrayTest.java
  16. … 59 more files in changeset.
9:30 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3438 spotless for 2.11.2.0

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    ./analysis/AAFrequencyTest.java
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    ./analysis/AlignSeqTest.java
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    ./analysis/AlignmentAnnotationUtilsTest.java
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    ./analysis/AlignmentGenerator.java
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    ./analysis/AlignmentSorterTest.java
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    ./analysis/AlignmentUtilsTests.java
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    ./analysis/AnnotationSorterTest.java
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    ./analysis/CodingUtilsTest.java
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    ./analysis/ConservationTest.java
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    ./analysis/CrossRefTest.java
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    ./analysis/DnaTest.java
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    ./analysis/FinderTest.java
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    ./analysis/GroupingTest.java
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    ./analysis/RnaTest.java
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    ./analysis/SeqsetUtilsTest.java
  16. … 647 more files in changeset.
6:53 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3108 updated Ensembl client and model species names

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    ./ext/ensembl/EnsemblGeneTest.java
  2. … 3 more files in changeset.
Wednesday 02 Mar
6:25 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3438 - all src and test run through spotless..

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    ./analysis/AAFrequencyTest.java
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    ./analysis/AlignmentGenerator.java
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    ./analysis/AlignmentSorterTest.java
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    ./analysis/AlignmentUtilsTests.java
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    ./analysis/AnnotationSorterTest.java
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    ./analysis/CodingUtilsTest.java
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    ./analysis/ConservationTest.java
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    ./analysis/CrossRefTest.java
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    ./analysis/DnaTest.java
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    ./analysis/FinderTest.java
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    ./analysis/RnaTest.java
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    ./analysis/SeqsetUtilsTest.java
  16. … 654 more files in changeset.
Thursday 17 Feb
5:15 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 patch superpose test for additional undo dis/enable commands

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    ./ext/pymol/PymolCommandsTest.java
Wednesday 16 Feb
1:27 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855 combined new logic for 2.11.2 3d-beacons with original hack to resolve PAE and CIF Conflicts: src/jalview/ws/dbsources/EBIAlfaFold.java

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    ./ws/seqfetcher/DbRefFetcherTest.java
  2. … 5 more files in changeset.