jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3225 Edited .project and .classpath, and adjusted build.gradle for running within eclipse [note, pwd is different -- use 'file' and not 'new File'\!]

    • -288
    • +4
    /.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)

    • binary
    /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].

    • binary
    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
    • 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/biojava-core-4.1.0.jar
    • binary
    /j11lib/biojava-ontology-4.1.0.jar
    • binary
    /j11lib/commons-codec-1.3.jar
    • binary
    /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

    • -5
    • +7
    /src/jalview/analysis/AAFrequency.java
    • -1
    • +2
    /src/jalview/jbgui/GAlignmentPanel.java
    • -1
    • +1
    /src/jalview/workers/ConsensusThread.java
adds an explicit clearing of the SeqCanvas fastPaint flag upon viewport adjustment

    • -0
    • +16
    /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

JAL-3111 tweak PCA documentation

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

Merge branch 'develop' into Jalview-JS/develop

    • -13
    • +22
    /src/jalview/gui/ScalePanel.java
JAL-3224 Add commons-compress-1.18.jar

    • binary
    /getdown/lib/commons-compress-1.18.jar
    • binary
    /utils/install4j/commons-compress-1.18.jar
JAL-3224 Bundling appropriate Mac OS/Windows JRE as java_vm in install4j

  1. … 375 more files in changeset.
JAL-3224 New version of getdown which will cope with unpacking .tgz resources, specifically for the java_vm and symbolic links within

    • binary
    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
  1. … 46 more files in changeset.
JAL-3130 moved resources/install4j to utils/install4j

    • binary
    /utils/install4j/DS_Store
    • binary
    /utils/install4j/jalview_dmg_background.png
    • binary
    /utils/install4j/jalview_dmg_background1.png
    • binary
    /utils/install4j/jalview_dmg_background1.xcf
    • binary
    /utils/install4j/jalview_dmg_background2.png
    • binary
    /utils/install4j/jalview_dmg_background3.png
    • -0
    • +1711
    /utils/install4j/jalview_getdown.install4j
better resource loading/file caching

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
caching of DnD files dropped

jmol-app updated for SwingJS ZipTools upgrade

localizes Thread colourby so that it does not cause ThreadStateException in Java

    • -19
    • +24
    /src/jalview/ext/jmol/JalviewJmolBinding.java
comments only

JAL-3130 tidy up system.output

    • -1
    • +0
    /test/jalview/bin/CommandLineOperations.java
JAL-3130 call Jalview via the Test JVM’s JAVA_HOME/bin/java

    • -1
    • +7
    /test/jalview/bin/CommandLineOperations.java