jalview

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Commits this week: 71
Total Committers: 60
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Commits this week: 71

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Today
2 hrs ago

Ben Soares

JAL-3225 Eclipse flagged Java 11 incompatible code (not found in cli compiling)

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    /src/jalview/bin/Jalview.java
2 hrs ago

Ben Soares

JAL-3225 fixed settings for Eclipse

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    • -25
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    /.classpath
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    • +0
    /.project
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    /.settings/org.eclipse.jdt.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
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    /build.gradle
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    /gradle.properties
Thursday 18 Apr
7:15 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

minor code clean up

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    /src/jalview/datamodel/Alignment.java
7:15 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

minor code clean up

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    /src/jalview/datamodel/Sequence.java
6:59 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

// BH 2018.04.18 comment: addNotify() is not appropriate here. We // are not changing ancestors, and keyboard action listeners do // not need to be reset. addNotify() is a very expensive operation, // requiring a full re-layout of all parents and children. // Note in JComponent: // This method is called by the toolkit internally and should // not be called directly by programs. // I note that addNotify() is called in several areas of Jalview.

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    /src/jalview/gui/AlignmentPanel.java
6:55 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

Adds check for gap padding to disallow fast paint upon pasting if alignment has been modified.

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    • -17
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    /src/jalview/gui/SeqCanvas.java
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    /src/jalview/viewmodel/AlignmentViewport.java
6:54 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

removes unnecessary clearFastPaint

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    /src/jalview/appletgui/AlignmentPanel.java
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    /src/jalview/gui/AlignmentPanel.java
6:54 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

Corrects incorrect calls to ViewportRanges.setEndSeq()

This function has the limit of height - 1, not height. Also adds safety

for start < 0 in ViewportRanges.setEndSeq();

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/viewmodel/ViewportRanges.java
4:51 pm

Ben Soares

JAL-3225 moved getdown eclipse project files so not picked up when importing Jalview

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    /getdown/src/getdown/.project
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    /getdown/src/getdown/.project-MOVED
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    /getdown/src/getdown/ant/.project
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    /getdown/src/getdown/ant/.project-MOVED
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    /getdown/src/getdown/core/.project
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    /getdown/src/getdown/core/.project-MOVED
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    /getdown/src/getdown/launcher/.project
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    /getdown/src/getdown/launcher/.project-MOVED
4:29 pm

Ben Soares

JAL-3225 Formatting when save

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    /.settings/org.eclipse.jdt.core.prefs
    • -4
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    /build.gradle
4:03 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

pushing again, just comments

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    /src/jalview/gui/SeqCanvas.java
3:32 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

hack for fastpaint Java bug upshifting one line after a sequence selection paste. Covered in Java by a full paint by ConsensusThread.

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    /src/jalview/appletgui/AlignmentPanel.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/SeqCanvas.java
3:32 pm

Mungo Carstairs

JAL-1793 basic help text for VCF option

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    /help/html/menus/alwfile.html
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    /help/html/releases.html
3:17 pm

Mungo Carstairs

JAL-3111 additional release notes

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    /help/html/releases.html
3:08 pm

Ben Soares

JAL-3225 Edited .project and .classpath, and adjusted build.gradle for running within eclipse [note, pwd is different -- use 'file' and not 'new File'\!]

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    /.classpath
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    /.gitignore
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    /.project
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    /.settings/org.eclipse.jdt.core.prefs
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    /build-j11.xml
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    /build.gradle
1:24 pm

Mungo Carstairs

JAL-3111 small simplification of table tags, valign top

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    /help/html/releases.html
1:08 pm

Mungo Carstairs

JAL-3111 release notes first pass complete

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    /help/html/releases.html
1:02 pm

Ben Soares

JAL-3130 moved jar needed for getdown to libs (not a module)

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    • binary
    /j11mod/commons-compress-1.18.jar
    • binary
    /lib/commons-compress-1.18.jar
12:53 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

reverting seqPanel.seqCanvas.clearFastPaint();

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    /src/jalview/appletgui/AlignmentPanel.java
12:37 pm

Ben Soares

JAL-3224 Removed JREs (these now need to be in ~/buildtools/jre/openjdk-java_vm/...). Moved install4j config to utils. Made install4j template file (gradle will edit this correctly). Fixed symbolic link in bundled MacOS JRE problem. Added getdown launcher with .tgz unbundling support [currently broken].

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    /.gitignore
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    /build.gradle
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    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
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    /getdown/lib/getdown-launcher.jar
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    /gradle.properties
    • binary
    /j11lib/JGoogleAnalytics_0.3.jar
    • binary
    /j11lib/Jmol-14.6.4_2016.10.26.jar
    • binary
    /j11lib/VARNAv3-93.jar
    • binary
    /j11lib/VAqua5-patch.jar
    • binary
    /j11lib/apache-mime4j-0.6.jar
    • binary
    /j11lib/axis.jar
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    /j11lib/biojava-core-4.1.0.jar
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    /j11lib/biojava-ontology-4.1.0.jar
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    /j11lib/commons-codec-1.3.jar
    • binary
    /j11lib/commons-compress-1.18.jar
  16. … 452 more files in changeset.
12:36 pm

Mungo Carstairs

JAL-2620 updated help page to mention alternative genetic code tables

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    /help/html/menus/alwcalculate.html
9:36 am

Mungo Carstairs

Merge branch 'develop' into Jalview-JS/develop

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9:36 am

Mungo Carstairs

JAL-3193 dbSource always "ENSEMBL"

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    /src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
9:31 am

Mungo Carstairs

Merge branch 'develop' into Jalview-JS/develop

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4:54 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

explicit Hashtable objects

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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/StructureFrequency.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/io/FileLoader.java
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    /src/jalview/jbgui/GAlignmentPanel.java
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    /src/jalview/renderer/AnnotationRenderer.java
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    /src/jalview/viewmodel/AlignmentViewport.java
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    /src/jalview/workers/ComplementConsensusThread.java
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    /src/jalview/workers/ConsensusThread.java
4:53 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

adds an explicit clearing of the SeqCanvas fastPaint flag upon viewport adjustment

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    /src/jalview/appletgui/AlignmentPanel.java
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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/SeqCanvas.java
Wednesday 17 Apr
4:34 pm

Mungo Carstairs

JAL-3026 fix bug loading Jalview Project (in Java)

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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/io/FileLoader.java
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    /src/jalview/project/Jalview2XML.java
3:34 pm

Jim Procter

JAL-3111 fix 2.11 html anchor in docs

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    /help/html/releases.html
3:32 pm

Jim Procter

Merge branch 'documentation/JAL-3111_release_211' into develop

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3:32 pm

Jim Procter

JAL-3111 Jalview 2.11 what’s New and estimated release date

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    /help/html/releases.html
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    /help/html/whatsNew.html