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jim procter <jprocter@dundee.ac.uk> in jalview

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581 commits
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  • First commit: 04 April 2014
  • Last commit: 17 March 2015
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Monday 19 Oct 2020
11:59 am

Jim Procter

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

Friday 22 May 2020
11:37 am

Jim Procter

relevant issue is JAL-3626

relevant issue is JAL-3626

Thursday 09 Apr 2020
2:34 pm

Ben Soares

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

12:07 pm

Jim Procter

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Wednesday 05 Feb 2020
11:50 am

Jim Procter

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

Friday 01 Feb 2019
2:23 pm

Mungo Carstairs

why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

Tuesday 17 Mar 2015
3:59 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1617 hack to add a fake xref if the uniprot xref isn't present on the embl entry

Options
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    /src/jalview/datamodel/xdb/embl/EmblEntry.java
    • -1
    • +22
    /test/jalview/ws/seqfetcher/DbRefFetcherTest.java
3:56 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1617 formatting and generics

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    • +16
    /src/jalview/util/DBRefUtils.java
3:56 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1617 fake xref database for when Uniprot xrefs aren't added

Options
    • -5
    • +8
    /src/jalview/datamodel/DBRefSource.java
3:56 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1617 toString for DBRefEntry

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    • -0
    • +11
    /src/jalview/datamodel/DBRefEntry.java
Monday 09 Mar 2015
12:54 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'features/JAL-1565_jpred4' into develop

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    • +5
    /src/jalview/gui/AlignFrame.java
12:52 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'features/JAL-1565_jpred4' into Release_2_8_3_Branch

Options
12:51 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1565 loading a concise file causes insertions to be automatically hidden in desktop

Options
    • -0
    • +5
    /src/jalview/gui/AlignFrame.java
Friday 06 Mar 2015
3:43 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop

Options
3:40 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop JAL-1645 bring JAL-845 feature branch up to date ready for develop merge

Conflicts:

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

test/jalview/analysis/DnaTranslation.java

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    /help/html/features/multipleViews.html
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    /schemas/jalview.xsd
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    /src/MCview/AppletPDBCanvas.java
    • -2
    • +2
    /src/MCview/Atom.java
    • -2
    • +2
    /src/MCview/PDBCanvas.java
    • -2
    • +2
    /src/jalview/analysis/AAFrequency.java
    • -2
    • +2
    /src/jalview/analysis/AlignSeq.java
    • -2
    • +2
    /src/jalview/analysis/AlignmentSorter.java
    • -2
    • +2
    /src/jalview/analysis/AlignmentUtils.java
    • -2
    • +2
    /src/jalview/analysis/CrossRef.java
    • -2
    • +2
    /src/jalview/analysis/Dna.java
    • -2
    • +2
    /src/jalview/api/AlignViewportI.java
    • -2
    • +2
    /src/jalview/api/AlignmentViewPanel.java
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    • +2
    /src/jalview/appletgui/APopupMenu.java
    • -3
    • +8
    /src/jalview/appletgui/AlignFrame.java
  16. … 111 more files in changeset.
3:29 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1683 bump version for r2.8.3 branch

Options
    • -2
    • +2
    /RELEASE
3:26 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1683 replace year/version strings with tokens in source

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    /build.xml
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    /doc/AddingGroovySupport.html
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    /doc/JalviewRNASupport.html
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    /doc/building.html
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    /doc/developing.html
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    /doc/index.html
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    /doc/newdmobj.html
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    /examples-jbake/assets/css/ie6.css
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    /examples-jbake/assets/css/ie7.css
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    /examples-jbake/assets/css/reset.css
    • -2
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    /examples-jbake/assets/css/style.css
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    /examples-jbake/assets/exampleFeatures.txt
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    /examples-jbake/assets/javascript/jalview.js
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    /examples-jbake/templates/header.ftl
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    • +2
    /examples/appletParameters.html
  16. … 820 more files in changeset.
3:13 pm

Jim Procter <jprocter@dundee.ac.uk>

reassign features already created/documented for 2.9 to 2.8.3 JAL-1682

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    /help/html/features/annotationsFormat.html
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    /help/html/menus/alwselect.html
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    /help/html/releases.html
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    • +7
    /help/html/webServices/jnet.html
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    • +2
    /src/jalview/io/AnnotationFile.java
2:45 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'Release_2_8_2b1_Branch'

Options
2:44 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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    /build.xml
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    /examples/applets.html
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    /examples/embedded.html
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    /examples/embeddedWJmol.html
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    /examples/formComplete.html
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    /examples/javascriptLaunch.html
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    /examples/linkedapplets_ng.html
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    /help/help.jhm
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    /help/helpTOC.xml
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    /help/html/features/annotationsFormat.html
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    /help/html/menus/alwselect.html
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    /help/html/releases.html
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    /src/MCview/AppletPDBCanvas.java
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    /src/MCview/PDBCanvas.java
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    • +1
    /src/jalview/analysis/AlignSeq.java
  16. … 116 more files in changeset.
2:42 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge commit '6797d65989b01c8fa5bdeaf6a66e35279b66a7f7' into develop

Options
Thursday 05 Mar 2015
3:48 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1678 fix replace token for launchApp in a buildwq

Options
    • -5
    • +14
    /build.xml
3:05 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1678 fix replace token for launchApp in a buildwq

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    • +1
    /build.xml
2:36 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1213 JAL-1395 add Jmol to JalviewLite classpath - need to find a way around this in the future

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    /examples-jbake/templates/jvl_embedded.ftl
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    /examples-jbake/templates/jvl_examples.ftl
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    /examples-jbake/templates/jvl_formComplete.ftl
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    /examples-jbake/templates/jvl_javascriptLaunch.ftl
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    /examples-jbake/templates/jvl_linkedapplets_ng.ftl
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    /examples/applets.html
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    /examples/embedded.html
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    /examples/embeddedWJmol.html
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    /examples/formComplete.html
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    /examples/javascriptLaunch.html
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    /examples/linkedapplets_ng.html
2:26 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1678 add version parameter to example files in publish phase

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    • +1
    /build.xml
2:22 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1678 add version parameter to example files in publish phase

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    • +5
    /build.xml
1:28 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'bug/JAL-1643_File-chooser-improvement' into develop

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1:28 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1643 add quaqua libs as OSX specific resources

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    /build.xml
Friday 27 Feb 2015
5:01 pm

Jim Procter <jprocter@dundee.ac.uk>

Merge branch 'bug/addcustomlaunchdesktopparams' into develop

Options
5:01 pm

Jim Procter <jprocter@dundee.ac.uk>

JAL-1678 - patch to make sure we only compare positions of the last / or ?

Options
    • -1
    • +2
    /src/jalview/appletgui/AlignFrame.java