jalview

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Commits this week: 10
Total Committers: 73
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Commits this week: 10

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Tuesday 25 Feb 2014
4:43 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1454 increase max for tqli iterations and throw exception rather than call System.exit()

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    • -10
    • +14
    /src/jalview/math/Matrix.java
1:27 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

kind of pointless addition

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    • -1
    • +1
    /forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
    • -1
    • +2
    /forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
Monday 24 Feb 2014
9:14 pm

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

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    • -0
    • +3
    /forester/java/src/org/forester/archaeopteryx/MainFrame.java
    • -0
    • +8
    /forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
    • -55
    • +65
    /forester/java/src/org/forester/archaeopteryx/Options.java
    • -80
    • +114
    /forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
    • -1
    • +1
    /forester/java/src/org/forester/phylogeny/PhylogenyNode.java
Saturday 22 Feb 2014
1:29 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

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    • -7
    • +3
    /forester/java/src/org/forester/application/msa_compactor.java
    • -11
    • +28
    /forester/java/src/org/forester/msa/MsaCompactor.java
Friday 21 Feb 2014
4:28 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JAL-1364_patch' into develop

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4:28 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JAL-1364_patch' into Release_2_8_1_Branch

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4:27 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

patch for JAL-1449 - continuance of JAL-1364 - check bounds of gapMap - not the VIENNA results

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    • -2
    • +6
    /src/jalview/ws/jws2/RNAalifoldClient.java
3:08 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n

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3:07 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'pathc_JAL-1354' into develop

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    • -1
    • +1
    /src/jalview/jbgui/GAlignFrame.java
3:07 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'pathc_JAL-1354' into Release_2_8_1_Branch

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3:06 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1448 reinstate non-locale sensitive code for reading/writing last read date from RSS and Jalview preferences

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    • -2
    • +3
    /src/jalview/bin/Cache.java
    • -1
    • +1
    /src/jalview/gui/BlogReader.java
2:44 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1354 typo

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    • -1
    • +1
    /src/jalview/jbgui/GAlignFrame.java
2:44 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1354 use real var-args method signature to avoid ambiguity

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    • -2
    • +2
    /src/jalview/gui/AlignFrame.java
    • -2
    • +2
    /src/jalview/util/MessageManager.java
2:43 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1354 quoted format strings are not substituted

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    • -2
    • +2
    /resources/lang/Messages.properties
2:58 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • -0
    • +5
    /forester/java/build.xml
2:57 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • binary
    /forester/java/archaeopteryx_applets.jar
2:57 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • -2
    • +2
    /forester/java/src/org/forester/archaeopteryx/Constants.java
Thursday 20 Feb 2014
3:27 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JAL-1447' into develop

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    • -2
    • +5
    /src/jalview/io/IdentifyFile.java
3:27 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JAL-1447' into Release_2_8_1_Branch

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3:18 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1447 patch to correctly recognise FASTA files containing '*'

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    • -2
    • +5
    /src/jalview/io/IdentifyFile.java
3:17 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

test and data for JAL-1447

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    • -0
    • +16
    /test/jalview/io/FileIOTester.java
    • -0
    • +8
    /test/jalview/io/test_fasta_stars.fa
    • -0
    • +4
    /test/jalview/io/test_fasta_stars2.fa
3:15 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JAL-1447 - more flexible testing for file format Identity detection

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    • -6
    • +8
    /test/jalview/io/FileIOTester.java
Wednesday 19 Feb 2014
2:44 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • binary
    /forester/java/archaeopteryx_applets.jar
2:41 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • -1
    • +1
    /forester/java/src/org/forester/archaeopteryx/Constants.java
    • -2
    • +2
    /forester/java/src/org/forester/util/ForesterConstants.java
2:20 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

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    • -11
    • +10
    /forester/java/src/org/forester/archaeopteryx/AptxUtil.java
    • -0
    • +9
    /forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
    • -2
    • +2
    /forester/java/src/org/forester/archaeopteryx/Constants.java
    • -0
    • +25
    /forester/java/src/org/forester/test/Test.java
12:10 am

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • -14
    • +34
    /forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
    • -1624
    • +1669
    /forester/java/src/org/forester/test/Test.java
Tuesday 18 Feb 2014
10:59 pm

cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>

inprogress

Options
    • -11
    • +13
    /forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
    • -20
    • +71
    /forester/java/src/org/forester/test/Test.java
5:12 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JAL-1445' into develop Carried over source formatting from 2.8.0b1 release

Conflicts:

src/jalview/analysis/StructureFrequency.java

src/jalview/ext/varna/VarnaCommands.java

src/jalview/gui/AppVarna.java

src/jalview/gui/PopupMenu.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GDesktop.java

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    • +4
    /THIRDPARTYLIBS
    • -114
    • +196
    /build.xml
    • -29
    • +30
    /src/MCview/PDBViewer.java
    • -2
    • +3
    /src/MCview/PDBfile.java
    • -2
    • +3
    /src/jalview/analysis/AlignSeq.java
    • -2
    • +3
    /src/jalview/analysis/Rna.java
    • -2
    • +3
    /src/jalview/analysis/StructureFrequency.java
    • -4
    • +11
    /src/jalview/appletgui/AlignFrame.java
    • -2
    • +3
    /src/jalview/bin/Jalview.java
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    /src/jalview/datamodel/AlignmentAnnotation.java
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    /src/jalview/datamodel/Annotation.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    • +22
    /src/jalview/ext/varna/VarnaCommands.java
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    • +8
    /src/jalview/gui/AppVarna.java
  16. … 23 more files in changeset.
4:32 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

Merge branch 'JAL-1445' into Release_2_8_1_Branch

Options
4:30 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

clear out 2.8.0b1 what's new and add JAL-1445 to list of new features

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    • +1
    /help/helpTOC.xml
    • -38
    • +3
    /help/html/whatsNew.html