jalview/src/jalview

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Tuesday 08 Mar
9:30 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3438 spotless for 2.11.2.0

Options
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    • +39
    ./binding/embl/EntrySetType.java
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    • +2225
    ./binding/embl/EntryType.java
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    ./binding/embl/ObjectFactory.java
    • -55
    • +53
    ./binding/embl/ROOT.java
    • -77
    • +78
    ./binding/embl/XrefType.java
    • -255
    • +233
    ./binding/jalview/AlcodonFrame.java
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    ./binding/jalview/Annotation.java
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    • +229
    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
    • -37
    • +37
    ./binding/jalview/FilterBy.java
  16. … 647 more files in changeset.
Wednesday 02 Mar
6:25 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3438 - all src and test run through spotless..

Options
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    ./binding/embl/EntrySetType.java
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    ./binding/embl/EntryType.java
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    ./binding/embl/ObjectFactory.java
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    ./binding/embl/ROOT.java
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    ./binding/embl/XrefType.java
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    ./binding/jalview/AlcodonFrame.java
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    ./binding/jalview/Annotation.java
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
    • -37
    • +37
    ./binding/jalview/FilterBy.java
  16. … 654 more files in changeset.
Monday 07 Feb
5:04 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop regenerated jaxb bindings for updated schemas on develop & feature branch Conflicts: src/jalview/gui/Preferences.java src/jalview/xml/binding/jalview/JalviewModel.java src/jalview/xml/binding/jalview/ObjectFactory.java src/jalview/xml/binding/jalview/package-info.java

Options
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    ./binding/embl/EntrySetType.java
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    ./binding/embl/EntryType.java
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    ./binding/embl/ObjectFactory.java
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    • +17
    ./binding/embl/ROOT.java
    • -16
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    ./binding/embl/XrefType.java
    • -1
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    ./binding/jalview/AlcodonFrame.java
    • -1
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    ./binding/jalview/Annotation.java
    • -1
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
    • -1
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    ./binding/jalview/FilterBy.java
  16. … 57 more files in changeset.
Monday 30 Aug 2021
11:14 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3863 add canonical DBRefEntry flag to Jalview project

Options
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    • +77
    ./binding/jalview/AlcodonFrame.java
    • -93
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    ./binding/jalview/Annotation.java
    • -21
    • +21
    ./binding/jalview/AnnotationColourScheme.java
    • -27
    • +27
    ./binding/jalview/AnnotationElement.java
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    • +26
    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/FilterBy.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/MapListType.java
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    ./binding/jalview/Mapping.java
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    ./binding/jalview/NoValueColour.java
  16. … 12 more files in changeset.
11:14 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3863 add canonical DBRefEntry flag to Jalview project

Options
    • -77
    • +77
    ./binding/jalview/AlcodonFrame.java
    • -93
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    ./binding/jalview/Annotation.java
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
    • -15
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    ./binding/jalview/FilterBy.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/MapListType.java
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    ./binding/jalview/Mapping.java
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    ./binding/jalview/NoValueColour.java
  16. … 12 more files in changeset.
Thursday 10 Dec 2020
3:53 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 save Overview title in project, don't save Overview on New View

Options
    • -75
    • +104
    ./binding/jalview/JalviewModel.java
    • -1
    • +1
    ./binding/jalview/package-info.java
  3. … 2 more files in changeset.
1:02 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 schema and JAXB changes to save Overview in project file

Options
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    ./binding/jalview/JalviewModel.java
    • -1
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    ./binding/jalview/ObjectFactory.java
    • -1
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    ./binding/jalview/package-info.java
  4. … 1 more file in changeset.
Tuesday 11 Aug 2020
2:50 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3705 JAL-3251 unused attribute repurposed/renamed to mappedFromId

Options
    • -10
    • +10
    ./binding/jalview/Mapping.java
  2. … 2 more files in changeset.
Thursday 16 Jan 2020
3:29 pm

Jim Procter

3:26 pm

Jim Procter

Shouldn't these be optional ? 2.11.0 project files will not have these options.

Shouldn't these be optional ? 2.11.0 project files will not have these options.

3:22 pm

Jim Procter

also probably necessary

also probably necessary

3:20 pm

Jim Procter

needs an issue

needs an issue

3:12 pm

Jim Procter

The routine doesn't match the documentation - should really fix it up

The routine doesn't match the documentation - should really fix it up

3:10 pm

Jim Procter

JAL-3081: Let manual annotation ordering take precedence over automatic
JAL-3081: Let manual annotation ordering take precedence over automatic
Friday 08 Nov 2019
9:32 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3081 schema and binding class changes to save annotation sort order

Options
    • -75
    • +131
    ./binding/jalview/JalviewModel.java
  2. … 1 more file in changeset.
Friday 30 Aug 2019
5:19 pm

Ben Soares

JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

Options
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    • +0
    ./binding/jalview/JalviewModelType.java
  2. … 343 more files in changeset.
Tuesday 27 Aug 2019
10:20 pm

Ben Soares

JAL-3210 Barebones gradle/buildship/eclipse. See README

Options
    • -0
    • +5090
    ./binding/jalview/JalviewModelType.java
  2. … 1990 more files in changeset.
Wednesday 10 Jul 2019
1:05 pm

Jim Procter

Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha

Options
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    ./binding/jalview/AlcodonFrame.java
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/FilterBy.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/MapListType.java
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    ./binding/jalview/Mapping.java
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    ./binding/jalview/NoValueColour.java
  16. … 32 more files in changeset.
Friday 07 Jun 2019
2:03 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType

Options
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    ./binding/jalview/AlcodonFrame.java
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    ./binding/jalview/Annotation.java
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/Mapping.java
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    ./binding/jalview/NoValueColour.java
  16. … 11 more files in changeset.
2:03 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType

Conflicts:

src/jalview/xml/binding/jalview/AlcodonFrame.java

src/jalview/xml/binding/jalview/Annotation.java

src/jalview/xml/binding/jalview/AnnotationColourScheme.java

src/jalview/xml/binding/jalview/AnnotationElement.java

src/jalview/xml/binding/jalview/DoubleMatrix.java

src/jalview/xml/binding/jalview/DoubleVector.java

src/jalview/xml/binding/jalview/Feature.java

src/jalview/xml/binding/jalview/FeatureMatcher.java

src/jalview/xml/binding/jalview/FeatureMatcherSet.java

src/jalview/xml/binding/jalview/FilterBy.java

src/jalview/xml/binding/jalview/JalviewModel.java

src/jalview/xml/binding/jalview/JalviewUserColours.java

src/jalview/xml/binding/jalview/MapListType.java

src/jalview/xml/binding/jalview/Mapping.java

src/jalview/xml/binding/jalview/NoValueColour.java

src/jalview/xml/binding/jalview/ObjectFactory.java

src/jalview/xml/binding/jalview/PcaDataType.java

src/jalview/xml/binding/jalview/Pdbentry.java

src/jalview/xml/binding/jalview/Sequence.java

src/jalview/xml/binding/jalview/SequenceSet.java

src/jalview/xml/binding/jalview/SequenceType.java

src/jalview/xml/binding/jalview/ThresholdType.java

src/jalview/xml/binding/jalview/VAMSAS.java

src/jalview/xml/binding/jalview/WebServiceParameterSet.java

src/jalview/xml/binding/jalview/package-info.java

Options
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    ./binding/jalview/AlcodonFrame.java
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    ./binding/jalview/Annotation.java
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/FilterBy.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/MapListType.java
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    ./binding/jalview/Mapping.java
    • -1
    • +1
    ./binding/jalview/NoValueColour.java
  16. … 11 more files in changeset.
1:42 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3187 Viewport schema attributes for showComplementFeatures[OnTop]

Options
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/MapListType.java
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    ./binding/jalview/Mapping.java
    • -1
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    ./binding/jalview/NoValueColour.java
  16. … 11 more files in changeset.
1:42 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3187 Viewport schema attributes for showComplementFeatures[OnTop]

Conflicts:

src/jalview/xml/binding/jalview/AlcodonFrame.java

src/jalview/xml/binding/jalview/Annotation.java

src/jalview/xml/binding/jalview/AnnotationColourScheme.java

src/jalview/xml/binding/jalview/AnnotationElement.java

src/jalview/xml/binding/jalview/DoubleMatrix.java

src/jalview/xml/binding/jalview/DoubleVector.java

src/jalview/xml/binding/jalview/Feature.java

src/jalview/xml/binding/jalview/FeatureMatcher.java

src/jalview/xml/binding/jalview/FeatureMatcherSet.java

src/jalview/xml/binding/jalview/FilterBy.java

src/jalview/xml/binding/jalview/JalviewModel.java

src/jalview/xml/binding/jalview/JalviewUserColours.java

src/jalview/xml/binding/jalview/MapListType.java

src/jalview/xml/binding/jalview/Mapping.java

src/jalview/xml/binding/jalview/NoValueColour.java

src/jalview/xml/binding/jalview/ObjectFactory.java

src/jalview/xml/binding/jalview/PcaDataType.java

src/jalview/xml/binding/jalview/Pdbentry.java

src/jalview/xml/binding/jalview/Sequence.java

src/jalview/xml/binding/jalview/SequenceSet.java

src/jalview/xml/binding/jalview/SequenceType.java

src/jalview/xml/binding/jalview/ThresholdType.java

src/jalview/xml/binding/jalview/VAMSAS.java

src/jalview/xml/binding/jalview/WebServiceParameterSet.java

src/jalview/xml/binding/jalview/package-info.java

Options
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    ./binding/jalview/AlcodonFrame.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/Feature.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/MapListType.java
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    ./binding/jalview/Mapping.java
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    ./binding/jalview/NoValueColour.java
  16. … 11 more files in changeset.
Thursday 06 Jun 2019
5:00 pm

tva <tva@10.205.251.175>

JAL-3285 build Jalview XML file for current version

Options
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    ./binding/jalview/Annotation.java
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    ./binding/jalview/AnnotationColourScheme.java
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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/FilterBy.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
    • -1
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    ./binding/jalview/MapListType.java
    • -1
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    ./binding/jalview/Mapping.java
    • -1
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    ./binding/jalview/NoValueColour.java
  16. … 12 more files in changeset.
Friday 05 Apr 2019
8:08 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3204 update to uniprot schema

Options
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    ./binding/uniprot/CitationType.java
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    ./binding/uniprot/CofactorType.java
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    ./binding/uniprot/CommentType.java
    • -1
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    ./binding/uniprot/ConsortiumType.java
    • -1
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    ./binding/uniprot/DbReferenceType.java
    • -1
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    ./binding/uniprot/Entry.java
    • -1
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    ./binding/uniprot/EventType.java
    • -1
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    ./binding/uniprot/EvidenceType.java
    • -1
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    ./binding/uniprot/EvidencedStringType.java
    • -1
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    ./binding/uniprot/FeatureType.java
    • -1
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    ./binding/uniprot/GeneLocationType.java
    • -1
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    ./binding/uniprot/GeneNameType.java
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    ./binding/uniprot/GeneType.java
    • -1
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    ./binding/uniprot/ImportedFromType.java
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    ./binding/uniprot/InteractantType.java
  16. … 24 more files in changeset.
Wednesday 06 Feb 2019
3:27 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

Options
    • -1
    • +33
    ./binding/jalview/Sequence.java
  2. … 15 more files in changeset.
3:27 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

Options
    • -1
    • +33
    ./binding/jalview/Sequence.java
  2. … 15 more files in changeset.
Wednesday 09 Jan 2019
4:23 pm

Jim Procter

JAL-3063 remove stale JAXB binding POJO

Options
    • -5090
    • +0
    ./binding/jalview/JalviewModelType.java
Thursday 20 Dec 2018
1:36 pm

Jim Procter

JAL-1767 port save/load PCA panel to JAXB - JAL-3063

Options
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    • +76
    ./binding/jalview/DoubleVector.java
    • -1
    • +1
    ./binding/jalview/Feature.java
    • -1
    • +1
    ./binding/jalview/FeatureMatcher.java
    • -1
    • +1
    ./binding/jalview/FeatureMatcherSet.java
    • -1
    • +1
    ./binding/jalview/FilterBy.java
    • -116
    • +1341
    ./binding/jalview/JalviewModel.java
    • -1
    • +1
    ./binding/jalview/JalviewUserColours.java
    • -1
    • +1
    ./binding/jalview/MapListType.java
    • -1
    • +1
    ./binding/jalview/Mapping.java
    • -1
    • +1
    ./binding/jalview/NoValueColour.java
  16. … 15 more files in changeset.
Thursday 06 Dec 2018
4:29 pm

Ben Soares

JAL-3130 incorporating feature/JAL-3063jaxbNoCastor and new script utils/jdeps_jlink_all.sh which works out module dependencies (not as straightforward as it should be) and makes a java 11 JRE

Options
    • -0
    • +76
    ./binding/embl/EntrySetType.java
    • -0
    • +2680
    ./binding/embl/EntryType.java
    • -0
    • +159
    ./binding/embl/ObjectFactory.java
    • -0
    • +96
    ./binding/embl/ROOT.java
    • -0
    • +121
    ./binding/embl/XrefType.java
    • -0
    • +326
    ./binding/jalview/AlcodonFrame.java
    • -0
    • +857
    ./binding/jalview/Annotation.java
    • -0
    • +254
    ./binding/jalview/AnnotationColourScheme.java
    • -0
    • +203
    ./binding/jalview/AnnotationElement.java
    • -0
    • +363
    ./binding/jalview/Feature.java
    • -0
    • +160
    ./binding/jalview/FeatureMatcher.java
    • -0
    • +192
    ./binding/jalview/FeatureMatcherSet.java
    • -0
    • +61
    ./binding/jalview/FilterBy.java
    • -0
    • +5090
    ./binding/jalview/JalviewModel.java
    • -0
    • +5090
    ./binding/jalview/JalviewModelType.java
  16. … 1447 more files in changeset.
Friday 02 Nov 2018
1:39 am

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

JAXB update site + transpiler

- ObjectFactory hack (does not actually use the methods)

- removal of jalviewBH

- new SwingJS-site and transpiler

Options
    • -5241
    • +0
    ./binding/jalviewBH/JalviewModel.java
    • -324
    • +0
    ./binding/jalviewBH/SequenceSet.java
    • -109
    • +0
    ./binding/jalviewBH/VAMSAS.java
  4. … 7 more files in changeset.