vamsas.xsd

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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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JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

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

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JAL-2089 patch broken merge to master for Release 2.10.0b1

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JAL-1925 update source version in license

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JAL-1894 update year/version in copyright

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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

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JAL-1620 version bump and release notes

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JAL-1578 JAL-674 store/restore alignment annotation properties in Jalview 2.8.2 project (allows the Annotated PDB file import/export to project/import test to pass)

  1. … 6 more files in changeset.
JAL-1517 update copyright to version 2.8.2

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JAL-1503 update version in GPL header

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JAL-1432 updated copyright notices

  1. … 855 more files in changeset.
Jalview 2.8 Source Header

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updated schema to store and recover belowAlignment and calcId for JAL-1109 and JAL-1110

  1. … 4 more files in changeset.
update author list in license for (JAL-826)

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apply version 2.7 copyright

  1. … 755 more files in changeset.
added graphHeight attribute to schema (JAL-784)

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Jalview 2.6 source licence

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jalview 2.5 release banner

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extend XML model for graduated feature colours, group associated manual/auto annotation, consensus profile/histograms, annotation label formatting, viewport highlight follow/select message receive settings

  1. … 10 more files in changeset.
apply gpl development license

  1. … 451 more files in changeset.
jalview XML schema update for 2.4.1 (or 2.5?) introducing IDs for views and treepanels and proper reconstruction of dataset/Alignment relationships

  1. … 110 more files in changeset.
added aligned codon frames, and dataset reference ids for sequenceSet and sequences to project xml

  1. … 23 more files in changeset.
visible

Seqset properties saved

total annotation score is a double for maximum precision.

  1. … 4 more files in changeset.
AlignmentAnnotation: added annotation score attribute and allowed for annotation[] array to be null

  1. … 11 more files in changeset.
aligned not used