jalview

schemas

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Monday 30 Aug 2021
11:14 am

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

JAL-3863 add canonical DBRefEntry flag to Jalview project

Options
    • -0
    • +7
    ./vamsas.xsd
  2. … 26 more files in changeset.
11:14 am

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

JAL-3863 add canonical DBRefEntry flag to Jalview project

Options
    • -0
    • +7
    ./vamsas.xsd
  2. … 26 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
    • -0
    • +1
    ./jalview.xsd
  2. … 3 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
    • -0
    • +9
    ./jalview.xsd
  2. … 3 more files 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
    • -4
    • +1
    ./vamsas.xsd
  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
    • -1
    • +3
    ./jalview.xsd
  2. … 1 more file in changeset.
Friday 01 Nov 2019
3:21 pm

Ben Soares

JAL-3474 removed all .cvsignore files stored in the repo

Options
    • -1
    • +0
    ./.cvsignore
  2. … 22 more files in changeset.
Tuesday 27 Aug 2019
10:20 pm

Ben Soares

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

Options
    • -1
    • +0
    ./.cvsignore
    • -140
    • +0
    ./JalviewUserColours.xsd
    • -81
    • +0
    ./JalviewWsParamSet.xsd
    • -309
    • +0
    ./embl.xsd
    • -15
    • +0
    ./embl_bindings.xml
    • -31
    • +0
    ./jalview.nodesc.properties
    • -31
    • +0
    ./jalview.properties
    • -727
    • +0
    ./jalview.xsd
    • -163
    • +0
    ./jalviewJvV1.xsd
    • -155
    • +0
    ./sifts/alignment.xsd
    • -154
    • +0
    ./sifts/dataTypes.xsd
    • -154
    • +0
    ./sifts/eFamily.xsd
    • -1117
    • +0
    ./uniprot.xsd
    • -285
    • +0
    ./vamsas.xsd
    • -92
    • +0
    ./vamsasJvV1.xsd
  16. … 1976 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
    • -0
    • +5
    ./jalview.xsd
  2. … 46 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
    • -0
    • +12
    ./vamsas.xsd
  2. … 25 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
    • -0
    • +12
    ./vamsas.xsd
  2. … 25 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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    • +2
    ./jalview.xsd
  2. … 25 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
    • -0
    • +2
    ./jalview.xsd
  2. … 25 more files in changeset.
Tuesday 04 Jun 2019
6:22 pm

Jim Procter

Merge branch 'develop' into developtomchmmer JAL-3285 merged 2.11 develop into the features/mchmmer branch - need to fix code for migration from Castor to JAXB - need to check Stockholm file IO and tests Good luck !

Options
    • -1
    • +93
    ./jalview.xsd
  2. … 58 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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    • +48
    ./uniprot.xsd
  2. … 38 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
    • -0
    • +7
    ./vamsas.xsd
  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
    • -0
    • +7
    ./vamsas.xsd
  2. … 15 more files in changeset.
Wednesday 16 Jan 2019
11:47 am

Jim Procter

JAL-3063 removed all core castor dependent code from Jalview

Options
    • -315
    • +0
    ./castor-mapping.xsd
  2. … 166 more files in changeset.
Wednesday 19 Dec 2018
4:53 pm

Jim Procter

Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_across_views

Options
    • -1
    • +87
    ./jalview.xsd
  2. … 7 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
    • -19
    • +33
    ./JalviewUserColours.xsd
    • -1
    • +7
    ./JalviewWsParamSet.xsd
    • -315
    • +0
    ./castor-mapping.xsd
    • -0
    • +309
    ./embl.xsd
    • -0
    • +15
    ./embl_bindings.xml
    • -0
    • +6
    ./jalview.xsd
    • -0
    • +1077
    ./uniprot.xsd
    • -0
    • +5
    ./vamsas.xsd
  9. … 1454 more files in changeset.
Monday 03 Dec 2018
3:03 pm

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

JAL-3063 Castor removed from codebase

Options
    • -315
    • +0
    ./castor-mapping.xsd
  2. … 166 more files in changeset.
Friday 28 Sep 2018
12:29 pm

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

JAL-3063 top level element added to JalviewWsParamSet.xsd

Options
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    • +7
    ./JalviewWsParamSet.xsd
  2. … 22 more files in changeset.
12:28 pm

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

JAL-3063 comments re use of xjc to generate Java binding classes

Options
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    • +5
    ./JalviewUserColours.xsd
    • -0
    • +5
    ./jalview.xsd
    • -0
    • +5
    ./vamsas.xsd
Tuesday 18 Sep 2018
4:57 pm

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

JAL-3063 top level element added to colours schema, JAXB classes regen'd

Options
    • -0
    • +1
    ./JalviewUserColours.xsd
  2. … 22 more files in changeset.