jalview

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JAL-3518 removed unneeded override in ChimeraCommands

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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

src/jalview/jbgui/GStructureViewer.java

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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3518 corrected pulled up focusView() command

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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3518 corrected action on pulled up closeViewer()

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    /src/jalview/gui/StructureViewerBase.java
JAL-3400 prevent duplications in View Chain menu

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    /src/jalview/gui/StructureViewerBase.java
JAL-3390 respect 'hidden chains' on redisplay after superposition

JAL-3390 improved 'hide chain' commands

Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/pymol/PymolCommands.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/ChimeraXCommands.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/structure/StructureCommandsBase.java

src/jalview/structure/StructureCommandsI.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/pymol/PymolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/gui/ChimeraViewFrame.java
JAL-3551 PyMOL command constants tidied

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3551 fit to window (zoom) command for PyMOL

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3518 tidy up asynchronous structure command execution

JAL-2010 unused prototype method removed

JAL-3518 pull up [get|list]ResidueAttributes to StructureCommandsI

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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/gui/ChimeraViewFrame.java
JAL-3518 separation of ChimeraXManager, pull up of closeViewer etc

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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/structure/AtomSpec.java
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    /test/jalview/structure/AtomSpecTest.java
JAL-3518 pull up closeViewer() and external viewer process monitor

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/gui/PymolBindingModel.java
JAL-3390 unit tests and command and menu refinements

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/gui/StructureViewerBase.java
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    /test/jalview/ext/jmol/JalviewJmolBindingTest.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
  1. … 3 more files in changeset.
JAL-3390 obsolete classes/methods removed

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/rbvi/chimera/AtomSpecModel.java
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    /src/jalview/util/StructureCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

gradle.properties

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/structures/JalviewStructureDisplayI.java

src/jalview/appletgui/AppletJmol.java

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/rbvi/chimera/AtomSpecModel.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AppJmol.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/gui/StructureViewerBase.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/jmol/JmolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/structures/models/AAStructureBindingModelTest.java

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/AppJmol.java
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    /src/jalview/gui/ChimeraViewFrame.java
  1. … 9 more files in changeset.
JAL-3446 new Jmol 15.1.3 jar added to j11lib, old j11lib Jmol-14.29.17-no_netscape.jar removed

    • binary
    /j11lib/Jmol-14.29.17-no_netscape.jar
    • binary
    /j11lib/Jmol-15.1.3.jar
JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

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    /doc/releaseprocess.html
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.

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    /utils/doc/github.css
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.

JAL-3225 some fixes to build.gradle for working in Eclipse and not always changing doc/building.html

JAL-3225 small fixes for building within Eclipse

JAL-3518 test result corrected

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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3518 add alwaysRun = true [sigh]

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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3518 more test coverage for structure commands

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    /test/jalview/ext/jmol/JmolCommandsTest.java
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    /test/jalview/structure/StructureCommandTest.java
JAL-2422 test updated

Merge branch 'feature/JAL-3551Pymol' into develop

JAL-3551 null pointer defence while structure files loading; comments

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/project/Jalview2XML.java