jalview

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

JAL-3225 fixed settings for Eclipse

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    /.settings/org.eclipse.jdt.core.prefs
minor code clean up

minor code clean up

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    /src/jalview/datamodel/Sequence.java
// 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.

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

removes unnecessary clearFastPaint

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

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    /getdown/src/getdown/.project-MOVED
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    /getdown/src/getdown/ant/.project-MOVED
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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
JAL-3225 Formatting when save

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    /.settings/org.eclipse.jdt.core.prefs
pushing again, just comments

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

JAL-1793 basic help text for VCF option

JAL-3111 additional release notes

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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    /.settings/org.eclipse.jdt.core.prefs
JAL-3111 small simplification of table tags, valign top

JAL-3111 release notes first pass complete

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

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    /lib/commons-compress-1.18.jar
reverting seqPanel.seqCanvas.clearFastPaint();

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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    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
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    /j11lib/JGoogleAnalytics_0.3.jar
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    /j11lib/Jmol-14.6.4_2016.10.26.jar
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    /j11lib/VARNAv3-93.jar
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    /j11lib/VAqua5-patch.jar
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    /j11lib/apache-mime4j-0.6.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
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    /j11lib/commons-compress-1.18.jar
  1. … 452 more files in changeset.
JAL-2620 updated help page to mention alternative genetic code tables

Merge branch 'develop' into Jalview-JS/develop

JAL-3193 dbSource always "ENSEMBL"

Merge branch 'develop' into Jalview-JS/develop

explicit Hashtable objects

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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/jbgui/GAlignmentPanel.java
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    /src/jalview/workers/ConsensusThread.java
adds an explicit clearing of the SeqCanvas fastPaint flag upon viewport adjustment

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    /src/jalview/appletgui/SeqCanvas.java
JAL-3026 fix bug loading Jalview Project (in Java)

JAL-3111 fix 2.11 html anchor in docs

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

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