jalview

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JAL-1767 test that changing view association for PCA panel can be restored

JAL-1767 refactor associated view logic to public method and synchronise PCAPanel.av/ap with RotateableCanvac.ap/av

JAL-1767 patch buggy PCA view association test

JAL-1767 failing test to check if the PCA view association is correctly saved and restored

Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767

JAL-3063 remove stale JAXB binding POJO

Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767

JAL-3063 - ant task for regenerating JAXB schema - could be optimised further

JAL-1767 minimise local variable scope

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

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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/gui/RotatableCanvas.java
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/jalview/DoubleMatrix.java
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    /src/jalview/xml/binding/jalview/DoubleVector.java
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JAL-3171 JAL-3063 merge updates from JAL-1767

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

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/gui/PCAPanel.java
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    /test/jalview/io/Jalview2xmlTests.java
JAL-3171 dataset reference tests now in Functional group

JAL-3171 record mapping between unmarshalled sequence’s dataset sequence ID and materialised dataset to allow belt-and-braces discovery of existing dataset - test now passes

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    /src/jalview/project/Jalview2XML.java
JAL-3171 raise warning when a dataset reference exists *and* a different dataset exists for the sequenceSetID

JAL-3171 more complex project test - where sequences were copied from one alignment view into a new alignment and more views created.

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    /examples/testdata/projects/manyViews.jvp
JAL-3171 resolve dataset for imported projects via the alignment’s SequenceSetId

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    /src/jalview/project/Jalview2XML.java
JAL-3171 failing test for legacy projects and fixing multiple dataset references

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    /examples/testdata/projects/twoViews.jvp
JAL-3171 register existing dataset for new view

JAL-3171 failing test checking preservation of dataset

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    /test/jalview/gui/AlignFrameTest.java
JAL-3063 service param files read/saved using JAXB not Castor binding

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    /src/jalview/gui/WsParamSetManager.java
JAL-3063 top level element added to JalviewWsParamSet.xsd

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

JAL-3063 tidy commented out code

JAL-3063 wrappers with check for null getting optional Integer, Float, Boolean XML attributes

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    /src/jalview/project/Jalview2XML.java
JAL-3063 use JAXB for 'Save as Project' and load project from parameter

JAL-3063 unit test for save/load project switched to JAXB

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    /test/jalview/project/Jalview2xmlTests.java
JAL-3063 Save/Load user defined colours using JAXB

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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/schemes/ColourSchemeLoader.java
JAL-3063 Save/Load user colour scheme using JAXB

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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/project/Jalview2XML.java
JAL-3063 top level element added to colours schema, JAXB classes regen'd

  1. … 8 more files in changeset.