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JAL-3863 add canonical DBRefEntry flag to Jalview project

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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/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.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/NoValueColour.java
  1. … 12 more files in changeset.
JAL-3863 add canonical DBRefEntry flag to Jalview project

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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/FeatureMatcher.java
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    ./binding/jalview/FeatureMatcherSet.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/NoValueColour.java
  1. … 12 more files in changeset.
JAL-1713 save Overview title in project, don't save Overview on New View

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    ./binding/jalview/JalviewModel.java
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JAL-1713 schema and JAXB changes to save Overview in project file

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    ./binding/jalview/JalviewModel.java
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JAL-3705 JAL-3251 unused attribute repurposed/renamed to mappedFromId

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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.

also probably necessary

also probably necessary

needs an issue

needs an issue

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

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

JAL-3081: Let manual annotation ordering take precedence over automatic
JAL-3081: Let manual annotation ordering take precedence over automatic
JAL-3081 schema and binding class changes to save annotation sort order

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

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    ./binding/jalview/JalviewModelType.java
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JAL-3210 Barebones gradle/buildship/eclipse. See README

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    ./binding/jalview/JalviewModelType.java
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Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha

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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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JAL-3251 added optional attributes Sequence.biotype, Mapping.mappingType

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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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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

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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/JalviewUserColours.java
  1. … 11 more files in changeset.
JAL-3187 Viewport schema attributes for showComplementFeatures[OnTop]

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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
  1. … 11 more files in changeset.
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

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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/FeatureMatcherSet.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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JAL-3285 build Jalview XML file for current version

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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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JAL-3204 update to uniprot schema

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    ./binding/uniprot/DbReferenceType.java
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    ./binding/uniprot/EvidencedStringType.java
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    ./binding/uniprot/GeneLocationType.java
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    ./binding/uniprot/ImportedFromType.java
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    ./binding/uniprot/InteractantType.java
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JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

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JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

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JAL-3063 remove stale JAXB binding POJO

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    ./binding/jalview/JalviewModelType.java
JAL-1767 port save/load PCA panel to JAXB - JAL-3063

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    ./binding/jalview/DoubleMatrix.java
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    ./binding/jalview/DoubleVector.java
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    ./binding/jalview/JalviewModel.java
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    ./binding/jalview/JalviewUserColours.java
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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

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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/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/JalviewModelType.java
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JAXB update site + transpiler

- ObjectFactory hack (does not actually use the methods)

- removal of jalviewBH

- new SwingJS-site and transpiler

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    ./binding/jalviewBH/JalviewModel.java
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    ./binding/jalviewBH/SequenceSet.java
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nonfunctional testing directory - just so I can see how it compiles.

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    ./binding/jalviewBH/JalviewModel.java
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    ./binding/jalviewBH/SequenceSet.java
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    ./binding/jalviewBH/VAMSAS.java
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JAL-3063 top level element added to JalviewWsParamSet.xsd

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    ./binding/jalview/ObjectFactory.java
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JAL-3063 top level element added to colours schema, JAXB classes regen'd

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    ./binding/jalview/AnnotationElement.java
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    ./binding/jalview/JalviewUserColours.java
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    ./binding/jalview/ObjectFactory.java
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