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Jalview Git

Ben Soares 08 Jun 2020 8939be9b96e7e3f7e836037b972ddce75fa4a17e

JAL-3446 new Jmol 15.1.3 jar added to j11lib, old j11lib Jmol-14.29.17-no_netscape.jar removed
- j11lib/Jmol-14.29.17-no_netscape.jar (version 8939be9b96e7e3f7e836037b972ddce75fa4a17e) (diffs)
- j11lib/Jmol-15.1.3.jar (version 8939be9b96e7e3f7e836037b972ddce75fa4a17e) (diffs)
Ben Soares 04 Jun 2020 91cf2210f6440d85c8a488c1bd18b0d3feb93f19

JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers
- doc/building.html (version 91cf2210f6440d85c8a488c1bd18b0d3feb93f19) (diffs)
- doc/building.md (version 91cf2210f6440d85c8a488c1bd18b0d3feb93f19) (diffs)
- doc/releaseprocess.html (version 91cf2210f6440d85c8a488c1bd18b0d3feb93f19) (diffs)
Ben Soares 04 Jun 2020 316d7fc8af1d26b1c7e7e99341648bc01699ac1e

JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.
- build.gradle (version 316d7fc8af1d26b1c7e7e99341648bc01699ac1e) (diffs)
- doc/github.css (version 316d7fc8af1d26b1c7e7e99341648bc01699ac1e) (diffs)
- gradle.properties (version 316d7fc8af1d26b1c7e7e99341648bc01699ac1e) (diffs)
- utils/doc/github.css (version 316d7fc8af1d26b1c7e7e99341648bc01699ac1e) (diffs)
Ben Soares <b.soares@dundee.ac.uk> 02 Jun 2020 d59675fab74acfcb19063b7f0081cb22ef3e4d5e

JAL-3225 Using Gradle Git-Version plugin to set gitHash and gitBranch
Using Gradle Git-Version instead of exec to run git directly allows
buildship to successfully import the project into eclipse without a
command line git installed. Essential for development within Eclipse in
Windows without having to install either gradle or git as command line
tools.
- build.gradle (version d59675fab74acfcb19063b7f0081cb22ef3e4d5e) (diffs)
Ben Soares 02 Jun 2020 1475d0d9f790dca1dbd9314defd464ac948f92b5

JAL-3225 small fixes for building within Eclipse
- build.gradle (version 1475d0d9f790dca1dbd9314defd464ac948f92b5) (diffs)
- gradle.properties (version 1475d0d9f790dca1dbd9314defd464ac948f92b5) (diffs)
Ben Soares 02 Jun 2020 a41ec37ec3b4c09409391fb02524db1f07b82030

JAL-3225 some fixes to build.gradle for working in Eclipse and not always changing doc/building.html
- build.gradle (version a41ec37ec3b4c09409391fb02524db1f07b82030) (diffs)
Mungo Carstairs 01 Jun 2020 02f3c2cbb832cf4d15b88231007563cc243b04c3

JAL-3518 test result corrected
- test/jalview/ext/jmol/JmolCommandsTest.java (version 02f3c2cbb832cf4d15b88231007563cc243b04c3) (diffs)
Mungo Carstairs 01 Jun 2020 a69ff693f6d3bc0969874e12812316a9c0bbc6fd

JAL-3518 add alwaysRun = true [sigh]
- test/jalview/ext/jmol/JmolCommandsTest.java (version a69ff693f6d3bc0969874e12812316a9c0bbc6fd) (diffs)
- test/jalview/ext/pymol/PymolCommandsTest.java (version a69ff693f6d3bc0969874e12812316a9c0bbc6fd) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java (version a69ff693f6d3bc0969874e12812316a9c0bbc6fd) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java (version a69ff693f6d3bc0969874e12812316a9c0bbc6fd) (diffs)
Mungo Carstairs 01 Jun 2020 600851b134c738f1453881fa60a7b699377b8e52

JAL-3518 more test coverage for structure commands
- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
- src/jalview/structure/StructureCommand.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
- test/jalview/ext/jmol/JmolCommandsTest.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
- test/jalview/ext/pymol/PymolCommandsTest.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
- test/jalview/structure/StructureCommandTest.java (version 600851b134c738f1453881fa60a7b699377b8e52) (diffs)
Mungo Carstairs 29 May 2020 bee310c7b5755403cedfb7f717f65769bb4b59d5

JAL-2422 test updated
- src/jalview/gui/Desktop.java (version bee310c7b5755403cedfb7f717f65769bb4b59d5) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java (version bee310c7b5755403cedfb7f717f65769bb4b59d5) (diffs)
Mungo Carstairs 29 May 2020 c38d37887ae51d63942ac4321f6769308188ed6b

Merge branch 'feature/JAL-3551Pymol' into develop
Mungo Carstairs 29 May 2020 ca4ed63aacf92872319f2bf64225c2742c338184

JAL-3551 null pointer defence while structure files loading; comments
- src/jalview/ext/jmol/JalviewJmolBinding.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/ext/pymol/PymolCommands.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraCommands.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/gui/AppJmolBinding.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/gui/StructureViewerBase.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/project/Jalview2XML.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version ca4ed63aacf92872319f2bf64225c2742c338184) (diffs)
Mungo Carstairs 28 May 2020 2dea2608f1b4acefbedaaa88f931080ed882fc71

JAL-3551 corrected Pymol open session command
- src/jalview/ext/pymol/PymolCommands.java (version 2dea2608f1b4acefbedaaa88f931080ed882fc71) (diffs)
Mungo Carstairs 28 May 2020 639070f3bd8d2e1502952c54d58ab3ff95538431

JAL-2422 correct ChimeraX save/open session commands; check for null
- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java (version 639070f3bd8d2e1502952c54d58ab3ff95538431) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version 639070f3bd8d2e1502952c54d58ab3ff95538431) (diffs)
Ben Soares 27 May 2020 b04cbef0dac19e60f693e64fdb5855ebdc675f80

JAL-3541 ensure deletion of cloverReportDir
- build.gradle (version b04cbef0dac19e60f693e64fdb5855ebdc675f80) (diffs)
Ben Soares 27 May 2020 a02114f9eb9665810b4c1d89c9806dabcb2b4fd7

JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity
- build.gradle (version a02114f9eb9665810b4c1d89c9806dabcb2b4fd7) (diffs)
- gradle.properties (version a02114f9eb9665810b4c1d89c9806dabcb2b4fd7) (diffs)
Mungo Carstairs 26 May 2020 f80d893b05dab20f45ec5598e49cac8818b642cb

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Mungo Carstairs 26 May 2020 2309d617e715b513fa750569a8ef49b81cd40e34

JAL-1889 disable test failing on build server
- test/jalview/gui/SeqCanvasTest.java (version 2309d617e715b513fa750569a8ef49b81cd40e34) (diffs)
Ben Soares 26 May 2020 e34c136813102a83b827b6ee0be888857246c9ca

Merge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop
Ben Soares 26 May 2020 fc59e4fa8e496692052905f4427fe03cc118dbf2

JAL-3541 added a property/variable style comment to build.gradle
- build.gradle (version fc59e4fa8e496692052905f4427fe03cc118dbf2) (diffs)
Mungo Carstairs 26 May 2020 fce1dd217a498f97f794c622b3651a33b8210932

JAL-3624 log when SIFTS mapping fails
- src/jalview/structure/StructureSelectionManager.java (version fce1dd217a498f97f794c622b3651a33b8210932) (diffs)
Mungo Carstairs 26 May 2020 b449c203e4a60965c8ee141183b25a8161c3dfea

Merge branch 'feature/JAL-3624siftsInJS' into develop
Mungo Carstairs 26 May 2020 7720585dc8cc56cdad2486b330ed37ddd0133531

JAL-1761 pattern for structure viewer construction from project file
- src/jalview/ext/jmol/JalviewJmolBinding.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/ext/jmol/JmolCommands.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/ext/pymol/PymolCommands.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraCommands.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/gui/AppJmol.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/gui/ChimeraViewFrame.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/gui/ChimeraXViewFrame.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/gui/PymolBindingModel.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/gui/PymolViewer.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/gui/StructureViewer.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/jbgui/GStructureViewer.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/project/Jalview2XML.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/structure/StructureCommandsI.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/structure/StructureSelectionManager.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version 7720585dc8cc56cdad2486b330ed37ddd0133531) (diffs)
Ben Soares 26 May 2020 ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8

JAL-3541 selectively merged build.gradle and gradle.properties
James Procter 25 May 2020 6650b1dc05cddec8301d52017db0dca93b7a6c95

JAL-3626 rescue automatic configuration of JALVIEW_VERSION from the RELEASE properties file, and exclusion of ‘examples’ from the windows installer. 
- build.gradle (version 6650b1dc05cddec8301d52017db0dca93b7a6c95) (diffs)
James Procter 24 May 2020 81566f0db459762fb716dcd54e1c04086f7ed72b

JAL-3407 redact Java 8 incompatible '<>' with anonymous inner classes
- src/jalview/gui/Preferences.java (version 81566f0db459762fb716dcd54e1c04086f7ed72b) (diffs)
Mungo Carstairs 21 May 2020 2107a91322a1988a8a6b724c74f9d244795341e3

JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)
- resources/lang/Messages.properties (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- resources/lang/Messages_es.properties (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/ext/jmol/JalviewJmolBinding.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/ext/jmol/JmolCommands.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/ext/pymol/PymolCommands.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraCommands.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/gui/AppJmol.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/gui/ChimeraViewFrame.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/gui/ChimeraXViewFrame.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/gui/PymolBindingModel.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/gui/PymolViewer.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/gui/StructureViewerBase.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/structure/StructureCommandsBase.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/structure/StructureCommandsI.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- test/jalview/ext/pymol/PymolCommandsTest.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
- test/jalview/structures/models/AAStructureBindingModelTest.java (version 2107a91322a1988a8a6b724c74f9d244795341e3) (diffs)
Mungo Carstairs 21 May 2020 cc4e7c2176bfc8c9c50ef2d8dde62f7bd80517db

JAL-2422 highlight ChimeraX selection (ChimeraX-1.0-rc-2020.05.21 +)
- src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java (version cc4e7c2176bfc8c9c50ef2d8dde62f7bd80517db) (diffs)
Mungo Carstairs 20 May 2020 4a67afac64ed574a5b79c7d33c97e58e26f60f30

JAL-3626 use Viewer.scriptWait() to send Jmol commands (Bob Hanson)
- src/jalview/ext/jmol/JalviewJmolBinding.java (version 4a67afac64ed574a5b79c7d33c97e58e26f60f30) (diffs)
- src/jalview/gui/AppJmol.java (version 4a67afac64ed574a5b79c7d33c97e58e26f60f30) (diffs)
Mungo Carstairs 19 May 2020 7dc7404ce7a339c600130e9828e3efc05b1e3270

JAL-3621 corrected sequence feature sort and test
- test/jalview/datamodel/features/SequenceFeaturesTest.java (version 7dc7404ce7a339c600130e9828e3efc05b1e3270) (diffs)
Mungo Carstairs 19 May 2020 2181580d96944496f2da0b3648c674c202083a65

JAL-3621 corrected sequence feature sort and test
- src/jalview/datamodel/features/SequenceFeatures.java (version 2181580d96944496f2da0b3648c674c202083a65) (diffs)
- test/jalview/datamodel/features/SequenceFeaturesTest.java (version 2181580d96944496f2da0b3648c674c202083a65) (diffs)
Mungo Carstairs 19 May 2020 4f30214e8098748469c6a4269ac2ed6c5750e4b0

Merge branch 'develop' into feature/JAL-3551Pymol
Conflicts:
        src/jalview/ext/jmol/JalviewJmolBinding.java
        src/jalview/ext/jmol/JmolCommands.java
        src/jalview/gui/AppJmol.java
        src/jalview/gui/AppJmolBinding.java
        src/jalview/gui/ChimeraViewFrame.java
        src/jalview/gui/StructureViewerBase.java
        src/jalview/jbgui/GPreferences.java
        src/jalview/jbgui/GStructureViewer.java
        src/jalview/project/Jalview2XML.java
Mungo Carstairs 19 May 2020 3acad896ec7aabf1df54556a2959c00bf50eff0f

JAL-3624 use temp file for SIFT download in JS, correct unmarshalling
- src/jalview/ws/sifts/SiftsClient.java (version 3acad896ec7aabf1df54556a2959c00bf50eff0f) (diffs)
Mungo Carstairs 18 May 2020 0bc9297afd18a3e2b412364bf1af426570555b9a

JAL-3463 avoid Thread.sleep() as not supported in SwingJS
- src/jalview/ws/DBRefFetcher.java (version 0bc9297afd18a3e2b412364bf1af426570555b9a) (diffs)
Mungo Carstairs 18 May 2020 d7e106a685363a77d7548051014deab532911ac3

JAL-3621 update to intervalstore v1.1
- j11lib/intervalstore-v1.0.jar (version d7e106a685363a77d7548051014deab532911ac3) (diffs)
- j11lib/intervalstore-v1.1.jar (version d7e106a685363a77d7548051014deab532911ac3) (diffs)
- j8lib/intervalstore-v1.0.jar (version d7e106a685363a77d7548051014deab532911ac3) (diffs)
- j8lib/intervalstore-v1.1.jar (version d7e106a685363a77d7548051014deab532911ac3) (diffs)
- src/jalview/datamodel/features/FeatureStore.java (version d7e106a685363a77d7548051014deab532911ac3) (diffs)
- src/jalview/datamodel/features/SequenceFeatures.java (version d7e106a685363a77d7548051014deab532911ac3) (diffs)
Mungo Carstairs 18 May 2020 e1dbbc5edc07f65706eeb1dda9f4c9bcdee9d3a5

JAL-3529 test updated for revised signature of getDBRefs()
- test/jalview/io/StockholmFileTest.java (version e1dbbc5edc07f65706eeb1dda9f4c9bcdee9d3a5) (diffs)
Mungo Carstairs 18 May 2020 65740880573a48adc758bec3939ece9d9ae104dd

Merge branch 'Jalview-JS/develop' into develop
Conflicts:
        build.gradle
        src/jalview/gui/PopupMenu.java
        src/jalview/io/SequenceAnnotationReport.java
        src/jalview/io/StockholmFile.java
        src/jalview/util/DBRefUtils.java
        src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Mungo Carstairs 18 May 2020 71aa78b8a7d54e5aeb6b278310dfd735efb77477

JAL-3613 remove debug code committed in error
- src/jalview/util/BrowserLauncher.java (version 71aa78b8a7d54e5aeb6b278310dfd735efb77477) (diffs)
Mungo Carstairs 15 May 2020 9dabc02511e3a334a5749a504f57f69d6c9017bd

JAL-2422 JAL-3551 unit tests updated for code changes
- test/jalview/ext/jmol/JmolCommandsTest.java (version 9dabc02511e3a334a5749a504f57f69d6c9017bd) (diffs)
- test/jalview/ext/pymol/PymolCommandsTest.java (version 9dabc02511e3a334a5749a504f57f69d6c9017bd) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java (version 9dabc02511e3a334a5749a504f57f69d6c9017bd) (diffs)
- test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java (version 9dabc02511e3a334a5749a504f57f69d6c9017bd) (diffs)
- test/jalview/structures/models/AAStructureBindingModelTest.java (version 9dabc02511e3a334a5749a504f57f69d6c9017bd) (diffs)
Mungo Carstairs 15 May 2020 7ec3bb005b1dd1621d386b05087ebab33fc47d0f

JAL-3619 default silently to Jmol if viewerType absent (Jalview < 2.9)
- src/jalview/project/Jalview2XML.java (version 7ec3bb005b1dd1621d386b05087ebab33fc47d0f) (diffs)
Mungo Carstairs 15 May 2020 d85a2741994c169e1b81db8f9166f5214ff1f561

JAL-3551 pull up Close Viewer dialog to base class
- resources/lang/Messages.properties (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- resources/lang/Messages_es.properties (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/appletgui/AppletJmol.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/ext/jmol/JalviewJmolBinding.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/gui/AppJmol.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/gui/ChimeraViewFrame.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/gui/PymolBindingModel.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/gui/PymolViewer.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/gui/StructureViewerBase.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
- test/jalview/ext/rbvi/chimera/JalviewChimeraView.java (version d85a2741994c169e1b81db8f9166f5214ff1f561) (diffs)
Mungo Carstairs 15 May 2020 74e963518532e173a8b026bf0de00993ab678ad0

Merge branch 'feature/JAL-3551Pymol' into feature/JAL-2422ChimeraX
Mungo Carstairs 15 May 2020 b145d2b4a617f452801953c1b49dae6b65521f14

JAL-3551 raise label on ('highlight') structure residue (wip)
- src/jalview/gui/PymolBindingModel.java (version b145d2b4a617f452801953c1b49dae6b65521f14) (diffs)
Ben Soares 15 May 2020 056dad85a910551cc95e44d451a61f6b8c4dd35d

JAL-3541 Fixed report path for build artifacts
- build.gradle (version 056dad85a910551cc95e44d451a61f6b8c4dd35d) (diffs)
Ben Soares 14 May 2020 1b7f570e89db9e6f0b0604a49cf0f04f90a60629

JAL-3541 Added mem setting and jvmArgs for cloverReporting
- build.gradle (version 1b7f570e89db9e6f0b0604a49cf0f04f90a60629) (diffs)
- gradle.properties (version 1b7f570e89db9e6f0b0604a49cf0f04f90a60629) (diffs)
Ben Soares 14 May 2020 1b2665812e6967ebe7fb887c62b1ab3848cf3ce8

JAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.
- build.gradle (version 1b2665812e6967ebe7fb887c62b1ab3848cf3ce8) (diffs)
Ben Soares 12 May 2020 b64c4e784adf02548947ea7cef7aff5062cae7ac

JAL-3541 Helpers for running tests, and other commands headlessly
- utils/cmd-nox.sh (version b64c4e784adf02548947ea7cef7aff5062cae7ac) (diffs)
- utils/gradle-nox.sh (version b64c4e784adf02548947ea7cef7aff5062cae7ac) (diffs)
Ben Soares 12 May 2020 0c54460ece7ad1ded16fd0d29c01d84cc4fd0ebb

JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.
- build.gradle (version 0c54460ece7ad1ded16fd0d29c01d84cc4fd0ebb) (diffs)
- gradle.properties (version 0c54460ece7ad1ded16fd0d29c01d84cc4fd0ebb) (diffs)
- utils/clover/lib/clover-ant-4.4.1.jar (version 0c54460ece7ad1ded16fd0d29c01d84cc4fd0ebb) (diffs)
Mungo Carstairs 12 May 2020 dadeab44d8d46ef588e326efb69599baa86a083b

JAL-3518 tidy method, remove obsolete comment
- src/jalview/ext/jmol/JalviewJmolBinding.java (version dadeab44d8d46ef588e326efb69599baa86a083b) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version dadeab44d8d46ef588e326efb69599baa86a083b) (diffs)
Mungo Carstairs 12 May 2020 f236e4e9e66583ca15dce3c3ef0cc43b02bf092e

JAL-3518 failsafe check for null Jmol filename while loading files
- src/jalview/ext/jmol/JalviewJmolBinding.java (version f236e4e9e66583ca15dce3c3ef0cc43b02bf092e) (diffs)
Mungo Carstairs 11 May 2020 27f24d1f14b8e8704d72797286f7a6e5f60b2119

JAL-3551 concatenate colour by sequence commands for all except PyMOL
- src/jalview/ext/jmol/JmolCommands.java (version 27f24d1f14b8e8704d72797286f7a6e5f60b2119) (diffs)
- src/jalview/ext/pymol/PymolCommands.java (version 27f24d1f14b8e8704d72797286f7a6e5f60b2119) (diffs)
- src/jalview/ext/rbvi/chimera/ChimeraCommands.java (version 27f24d1f14b8e8704d72797286f7a6e5f60b2119) (diffs)
- src/jalview/structure/StructureCommandsBase.java (version 27f24d1f14b8e8704d72797286f7a6e5f60b2119) (diffs)
Mungo Carstairs 11 May 2020 aa643d0f2f5f506df2771e216af1618549d32050

JAL-2422 JAL-3551 viewer text/variables generalised, Pymol paths added
- resources/lang/Messages.properties (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- resources/lang/Messages_es.properties (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- src/jalview/ext/pymol/PymolManager.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- src/jalview/gui/AppJmol.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- src/jalview/gui/ChimeraViewFrame.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- src/jalview/gui/Preferences.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- src/jalview/gui/StructureViewerBase.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- src/jalview/jbgui/GPreferences.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
- test/jalview/ext/pymol/PymolManagerTest.java (version aa643d0f2f5f506df2771e216af1618549d32050) (diffs)
Mungo Carstairs 11 May 2020 26eac0ada672f0b0377054cef2899c1161931655

JAL-2422 ChimeraX paths (versions up to 1.0) added for Windows
- src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version 26eac0ada672f0b0377054cef2899c1161931655) (diffs)
Mungo Carstairs 11 May 2020 970515ee49290a4b8fbb63b9f69e48ccba23a7b9

JAL-1333 additional Chimera versions for Windows installation paths
- src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version 970515ee49290a4b8fbb63b9f69e48ccba23a7b9) (diffs)
Mungo Carstairs 11 May 2020 0fef78440888c7cf6980fe1349661512e3f1b62d

JAL-2422 restore saved ChimeraX session from project
- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java (version 0fef78440888c7cf6980fe1349661512e3f1b62d) (diffs)
- src/jalview/gui/ChimeraXViewFrame.java (version 0fef78440888c7cf6980fe1349661512e3f1b62d) (diffs)
- src/jalview/gui/JalviewChimeraXBindingModel.java (version 0fef78440888c7cf6980fe1349661512e3f1b62d) (diffs)
- src/jalview/project/Jalview2XML.java (version 0fef78440888c7cf6980fe1349661512e3f1b62d) (diffs)
Mungo Carstairs 01 May 2020 c1e22e204c48fe7fc30dbb95be46e5a04808898a

JAL-3613 check sequence overlap when matching search results
- src/jalview/datamodel/SearchResults.java (version c1e22e204c48fe7fc30dbb95be46e5a04808898a) (diffs)
- src/jalview/gui/SeqPanel.java (version c1e22e204c48fe7fc30dbb95be46e5a04808898a) (diffs)
- src/jalview/util/BrowserLauncher.java (version c1e22e204c48fe7fc30dbb95be46e5a04808898a) (diffs)
- test/jalview/datamodel/SearchResultsTest.java (version c1e22e204c48fe7fc30dbb95be46e5a04808898a) (diffs)
Mungo Carstairs 30 Apr 2020 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b

JAL-3551 save structure viewer session refactorings, PyMol added
- src/jalview/ext/jmol/JalviewJmolBinding.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/ext/jmol/JmolCommands.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/ext/pymol/PymolCommands.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/AppJmol.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/AppJmolBinding.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/ChimeraViewFrame.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/JalviewChimeraXBindingModel.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/PymolBindingModel.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/PymolViewer.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/gui/StructureViewerBase.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/project/Jalview2XML.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
- src/jalview/structures/models/AAStructureBindingModel.java (version 1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b) (diffs)
Mungo Carstairs 30 Apr 2020 6e0685c38078ddcf959db75d001f8c92b114c8ae

JAL-3551 tidied error handling for HTTP request
- src/jalview/ext/pymol/PymolManager.java (version 6e0685c38078ddcf959db75d001f8c92b114c8ae) (diffs)
Mungo Carstairs 25 Apr 2020 26bb6eb4cbe7da79d8e1c43b23f68071e40a3380

Merge branch 'develop' into feature/JAL-3551Pymol
Ben Soares 22 Apr 2020 26f79fac447ccf6235bbf52992455f0a2bc6cbcd

JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used
- utils/eclipse/org.eclipse.jdt.ui.prefs (version 26f79fac447ccf6235bbf52992455f0a2bc6cbcd) (diffs)
James Procter 22 Apr 2020 eda1adb8ef48c7c0da70635db7253a7489335603

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
James Procter 22 Apr 2020 c7827c8c0d28158fcea4ebc132c7b457d60f557d

JAL-3407 add GPL license to Jalview source files
- src/jalview/analysis/GeneticCodeI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/analysis/GeneticCodes.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/api/FinderI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/bin/GetMemory.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/bin/JalviewTaskbar.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/bin/Launcher.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/bin/MemorySetting.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/GeneLociI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/GeneLocus.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/MappedFeatures.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/Point.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureAttributeType.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureAttributes.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureMatcher.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureMatcherI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureMatcherSet.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureMatcherSetI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureSource.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureSourceI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/datamodel/features/FeatureSources.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/android/ContainerHelpers.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/android/SparseDoubleArray.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/android/SparseIntArray.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/android/SparseShortArray.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/ensembl/EnsemblInfo.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/ensembl/EnsemblMap.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/ext/htsjdk/VCFReader.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/gui/APQHandlers.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/gui/JalviewBooleanRadioButtons.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/io/BackupFilenameFilter.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/io/BackupFilenameParts.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/io/BackupFiles.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/io/BackupFilesPresetEntry.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/io/IntKeyStringValueEntry.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/io/vcf/VCFLoader.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/JSONUtils.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/MathUtils.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/ShortcutKeyMaskExWrapper.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/ShortcutKeyMaskExWrapper11.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/ShortcutKeyMaskExWrapper8.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/ShortcutKeyMaskExWrapperI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/matcher/Condition.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/matcher/Matcher.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
- src/jalview/util/matcher/MatcherI.java (version c7827c8c0d28158fcea4ebc132c7b457d60f557d) (diffs)
James Procter 22 Apr 2020 68e1026a95c29b90a9ef4d65984c0c0ba191c0e9

JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera
- help/help/html/releases.html (version 68e1026a95c29b90a9ef4d65984c0c0ba191c0e9) (diffs)
James Procter 21 Apr 2020 39845a5bd6ca82da33a9c800ec7282de4e2a96f1

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
James Procter 21 Apr 2020 85283704c950febdca739d7dd857a1068cd73bbb

JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0
- help/help/html/releases.html (version 85283704c950febdca739d7dd857a1068cd73bbb) (diffs)
James Procter 21 Apr 2020 17bd1863c6cbe218dcf4604b44c5d940a9832248

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
James Procter 21 Apr 2020 0b6d277e8fc98b1bc61d040932dba670340db344

JAL-3574 JAL-3407 release notes
- help/help/html/releases.html (version 0b6d277e8fc98b1bc61d040932dba670340db344) (diffs)
James Procter 21 Apr 2020 68b236e066089eaa850813edb5294a23d19798bb

Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release
James Procter 21 Apr 2020 a0c4d49a6d4a4c37a61b4ac8b533235bb60d503b

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
James Procter 21 Apr 2020 cfcd397b19f70fb39d6d21437db8eb6ffcac3914

JAL-3407 add and document ComputePeptideVariants.groovy
- examples/groovy/ComputePeptideVariants.groovy (version cfcd397b19f70fb39d6d21437db8eb6ffcac3914) (diffs)
- help/help/html/features/importvcf.html (version cfcd397b19f70fb39d6d21437db8eb6ffcac3914) (diffs)
- help/help/html/releases.html (version cfcd397b19f70fb39d6d21437db8eb6ffcac3914) (diffs)
- help/help/html/whatsNew.html (version cfcd397b19f70fb39d6d21437db8eb6ffcac3914) (diffs)
Ben Soares 21 Apr 2020 1072cecb0ae3fbeadfc9065cb4475efa845b7308

JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time
- build.gradle (version 1072cecb0ae3fbeadfc9065cb4475efa845b7308) (diffs)
James Procter 21 Apr 2020 aeabb519838924aee2a3a90bbc789f593620d5c1

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop
James Procter 21 Apr 2020 2720003e4d3537f99f6c1643561cbdb3d0120d2d

JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April
- help/help/help.jhm (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
- help/help/helpTOC.xml (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
- help/help/html/features/seqfeaturereport.html (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
- help/help/html/features/seqfeaturesrep.png (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
- help/help/html/features/splitView.html (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
- help/help/html/menus/popupMenu.html (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
- help/help/html/releases.html (version 2720003e4d3537f99f6c1643561cbdb3d0120d2d) (diffs)
Mungo Carstairs 21 Apr 2020 421a5c8265f5d65c7dca1827e8f5af0b66ab3fe9

JAL-3210 try adding setup method to unit test failing on server...
- test/jalview/gui/SeqCanvasTest.java (version 421a5c8265f5d65c7dca1827e8f5af0b66ab3fe9) (diffs)
Mungo Carstairs 21 Apr 2020 0c9de94f49ef0e4eba3f4f5d6d7b61abae2d6cc6

JAL-1889 corrected wait for consensus to be calculated
- test/jalview/gui/AlignFrameTest.java (version 0c9de94f49ef0e4eba3f4f5d6d7b61abae2d6cc6) (diffs)
- test/jalview/gui/AlignViewportTest.java (version 0c9de94f49ef0e4eba3f4f5d6d7b61abae2d6cc6) (diffs)
- test/jalview/gui/AlignmentPanelTest.java (version 0c9de94f49ef0e4eba3f4f5d6d7b61abae2d6cc6) (diffs)
- test/jalview/schemes/PIDColourSchemeTest.java (version 0c9de94f49ef0e4eba3f4f5d6d7b61abae2d6cc6) (diffs)
Ben Soares 21 Apr 2020 ab2d7f57cf2a9540f99d26ac7268becab4c30539

JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list
- utils/install4j/install4j8_template.install4j (version ab2d7f57cf2a9540f99d26ac7268becab4c30539) (diffs)
James Procter 21 Apr 2020 f6dbc1f173fe70d90949cfb887d8cf35bb514e91

Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop
James Procter 21 Apr 2020 56e3fef5ed30e5a12c5ab5618622118ac863bb58

JAL-367 code tidy
- src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java (version 56e3fef5ed30e5a12c5ab5618622118ac863bb58) (diffs)
James Procter 21 Apr 2020 8886aa756d24c0f1a06f54474298c4c93b0cbccf

JAL-3567 translated rather than imputed peptide
- src/jalview/datamodel/SequenceFeature.java (version 8886aa756d24c0f1a06f54474298c4c93b0cbccf) (diffs)
- test/jalview/datamodel/SequenceFeatureTest.java (version 8886aa756d24c0f1a06f54474298c4c93b0cbccf) (diffs)
Mungo Carstairs 21 Apr 2020 c424c88d659c131acbcc917fc34d89bff46f7b15

JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies
- src/jalview/gui/AlignFrame.java (version c424c88d659c131acbcc917fc34d89bff46f7b15) (diffs)
- src/jalview/io/AnnotationFile.java (version c424c88d659c131acbcc917fc34d89bff46f7b15) (diffs)
- src/jalview/io/FileLoader.java (version c424c88d659c131acbcc917fc34d89bff46f7b15) (diffs)
- src/jalview/io/FileParse.java (version c424c88d659c131acbcc917fc34d89bff46f7b15) (diffs)
Ben Soares 21 Apr 2020 439d89cfdb49de11de73e31b2604672edcc5a45d

JAL-3602 Added configuration for enforced use of UTF-8 for creating the core js files and also in the closure-compiler.
- build.gradle (version 439d89cfdb49de11de73e31b2604672edcc5a45d) (diffs)
- gradle.properties (version 439d89cfdb49de11de73e31b2604672edcc5a45d) (diffs)
Mungo Carstairs 17 Apr 2020 69e8792b5f1ed2c02cff0a1ee328793ab5c0f423

JAL-3567 unit tests for linked feature tooltips
- src/jalview/datamodel/MappedFeatures.java (version 69e8792b5f1ed2c02cff0a1ee328793ab5c0f423) (diffs)
- src/jalview/io/SequenceAnnotationReport.java (version 69e8792b5f1ed2c02cff0a1ee328793ab5c0f423) (diffs)
- test/jalview/datamodel/SequenceFeatureTest.java (version 69e8792b5f1ed2c02cff0a1ee328793ab5c0f423) (diffs)
- test/jalview/io/SequenceAnnotationReportTest.java (version 69e8792b5f1ed2c02cff0a1ee328793ab5c0f423) (diffs)
Bob Hanson 17 Apr 2020 0b824fead908ef95c957138ec017e5b5f8bfb051

added .gitignore paths
I need these until I fully grasp the ways that gradle works.
- .gitignore (version 0b824fead908ef95c957138ec017e5b5f8bfb051) (diffs)
Bob Hanson 16 Apr 2020 2e10281fc7181b019c7885a516cc743574403a43

JAL-3587 Load Project bug
Fixed 2019.01.24 in Applet branch.

commit db8caac49ea663fbc2b8b78f7eb2e6ae893f40da

didn't have a JAL number. My mistake.
- src/jalview/gui/Desktop.java (version 2e10281fc7181b019c7885a516cc743574403a43) (diffs)
Mungo Carstairs 16 Apr 2020 de96de2488774840f2f6298d757369f9e43acaee

JAL-3567 adjust layout of linked feature report, unit test
- src/jalview/datamodel/MappedFeatures.java (version de96de2488774840f2f6298d757369f9e43acaee) (diffs)
- src/jalview/datamodel/SequenceFeature.java (version de96de2488774840f2f6298d757369f9e43acaee) (diffs)
- test/jalview/datamodel/SequenceFeatureTest.java (version de96de2488774840f2f6298d757369f9e43acaee) (diffs)
Mungo Carstairs 16 Apr 2020 ceeba9a56384d551389260f71366fe414be37e34

JAL-3567 added 'imputed by Jalview' to protein consequence in report
- src/jalview/datamodel/SequenceFeature.java (version ceeba9a56384d551389260f71366fe414be37e34) (diffs)
Mungo Carstairs 16 Apr 2020 5a631296dd1dcc1df7b50487a647c27333696c74

JAL-3567 report mapped location for virtual features in tooltip etc
- src/jalview/appletgui/APopupMenu.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/datamodel/MappedFeatures.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/datamodel/SequenceFeature.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/gui/IdPanel.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/gui/PopupMenu.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/gui/SeqPanel.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/io/FeaturesFile.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/io/SequenceAnnotationReport.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- test/jalview/datamodel/SequenceFeatureTest.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
- test/jalview/io/SequenceAnnotationReportTest.java (version 5a631296dd1dcc1df7b50487a647c27333696c74) (diffs)
James Procter 14 Apr 2020 23a6193c05af862c01bbb11d84c88234af8348bc

JAL-3407 JAL-3529 release notes
- help/help/html/releases.html (version 23a6193c05af862c01bbb11d84c88234af8348bc) (diffs)
James Procter 14 Apr 2020 f60b33ad2547914dfcb536db65dd793a7f82e9de

Merge branch 'bug/JAL-3529_uniprotidsinstockholm' into develop
James Procter 14 Apr 2020 e0c07d892616e9c206b36f4d23c2b050b1ca8c9d m

JAL-3529 revert ordering of DBRef addition so it reflects situation after Pfam import </picky>
- test/jalview/io/StockholmFileTest.java (version e0c07d892616e9c206b36f4d23c2b050b1ca8c9d) (diffs)
James Procter 14 Apr 2020 69f67d45544fc63d5fd60ae71cd21f7138a3e9e4

JAL-3597 improved Memory test suite by detecting base memory usage rather than assuming it is constant for each release.
- test/jalview/gui/FreeUpMemoryTest.java (version 69f67d45544fc63d5fd60ae71cd21f7138a3e9e4) (diffs)
James Procter 14 Apr 2020 bb20eae9b226c6c4237fac2c8933a3e213513068

JAL-3407 release date set to 16th April, known issue report for JAL-3574
- help/help/html/releases.html (version bb20eae9b226c6c4237fac2c8933a3e213513068) (diffs)
James Procter 14 Apr 2020 c8694dc0f354eea1f8fb74428d3cf20270eb73c2

Merge branch 'testing/JAL-3577_jalviewversion_autoset_fixed' into develop
Mungo Carstairs 14 Apr 2020 2b21aa74fdc06b43a1c6d80653e7bd51574b78bf

JAL-3583 remove debug logging, Javadoc added
- src/jalview/gui/SeqPanel.java (version 2b21aa74fdc06b43a1c6d80653e7bd51574b78bf) (diffs)
- src/jalview/io/SequenceAnnotationReport.java (version 2b21aa74fdc06b43a1c6d80653e7bd51574b78bf) (diffs)
Mungo Carstairs 13 Apr 2020 d7f669694da3aefe896e649e2ba52f68ae5b790b

JAL-3574 test coverage corners
- test/jalview/util/matcher/MatcherTest.java (version d7f669694da3aefe896e649e2ba52f68ae5b790b) (diffs)
Mungo Carstairs 13 Apr 2020 06ab16e2f61b0d30302e645be386ce02c26086b4

JAL-3574 Matcher with integer/long value pattern (e.g. VCF POS locus)
- src/jalview/util/matcher/Matcher.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
- src/jalview/util/matcher/MatcherI.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
- test/jalview/datamodel/features/FeatureMatcherTest.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
- test/jalview/gui/FeatureSettingsTest.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
- test/jalview/io/FeaturesFileTest.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
- test/jalview/project/Jalview2xmlTests.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
- test/jalview/util/matcher/MatcherTest.java (version 06ab16e2f61b0d30302e645be386ce02c26086b4) (diffs)
Mungo Carstairs 12 Apr 2020 e9a1285c3e0df3505d85121d84c2d33d899820f2

JAL-3596 change redacted
- src/jalview/renderer/seqfeatures/FeatureRenderer.java (version e9a1285c3e0df3505d85121d84c2d33d899820f2) (diffs)
Mungo Carstairs 12 Apr 2020 0eca06f81d58886f044eb37f8a1a702f497434cf

JAL-3596 don't draw text over features if Show Text is unselected
- src/jalview/renderer/seqfeatures/FeatureRenderer.java (version 0eca06f81d58886f044eb37f8a1a702f497434cf) (diffs)
Mungo Carstairs 12 Apr 2020 d281dbb95856e0796188c810b819519878235e36

JAL-3583 consistent last[Formatted]Tooltip, show once only per residue
- src/jalview/gui/AnnotationPanel.java (version d281dbb95856e0796188c810b819519878235e36) (diffs)
- src/jalview/gui/SeqPanel.java (version d281dbb95856e0796188c810b819519878235e36) (diffs)
Bob Hanson 09 Apr 2020 a43bec27a288700b58f4db8ce599b19c6c22c66a

JAL-3587 save and reload project file fix
- swingjs/net.sf.j2s.core-j11.jar (version a43bec27a288700b58f4db8ce599b19c6c22c66a) (diffs)
- swingjs/timestamp (version a43bec27a288700b58f4db8ce599b19c6c22c66a) (diffs)
- swingjs/ver/3.2.9/net.sf.j2s.core-j11.jar (version a43bec27a288700b58f4db8ce599b19c6c22c66a) (diffs)
- swingjs/ver/3.2.9/timestamp (version a43bec27a288700b58f4db8ce599b19c6c22c66a) (diffs)

Build: #24 did not complete Manual run by Ben Soares

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Ben Soares 08 Jun 2020 8939be9b96e7e3f7e836037b972ddce75fa4a17e

Ben Soares 04 Jun 2020 91cf2210f6440d85c8a488c1bd18b0d3feb93f19

Ben Soares 04 Jun 2020 316d7fc8af1d26b1c7e7e99341648bc01699ac1e

Ben Soares <b.soares@dundee.ac.uk> 02 Jun 2020 d59675fab74acfcb19063b7f0081cb22ef3e4d5e

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