jalview

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JAL-2586 Clarification to URL link code

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    /test/jalview/urls/UrlLinkDisplayTest.java
JAL-2586 Checkstyle flagged fix of unintended fall through

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    /src/jalview/urls/UrlLinkDisplay.java
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    /test/jalview/urls/UrlLinkDisplayTest.java
JAL-2571 Missed (alwaysRun=true) for @BeforeMethod

JAL-2228 java 1.7 compliance

JAL-2291 updated docs

JAL-2291 only hide/show columns intersecting with currently selected region.

JAL-2291 get bitset representing hidden columns

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2291 use HiddenColumns.hideMarkedBits and take union of selection and sequence under popup

JAL-2291 method taking a BitSet for hiding columns

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2291 bug fix - BitSet.set is [start,end+1)

JAL-2291 fixed broken asserts for SequenceI.getInsertionsAsBits

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    /test/jalview/datamodel/SequenceTest.java
JAL-2291 ‘Hide Insertions’ now operates on selection or if none available, the sequence that was right-clicked on.

JAL-2291 SequenceI.getInsertionsAsBits for convenient logical operations

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    /src/jalview/datamodel/Sequence.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-2582 comment about IDs being lost if they resembl ensembl IDs but can’t be resolved to a genomic ID.

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    /src/jalview/ext/ensembl/EnsemblGene.java
JAL-2582 recognise ENS…P peptide IDs and make two getParent requests to get gene ID.

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    /src/jalview/ext/ensembl/EnsemblGene.java
Merge branch 'bug/JAL-2578' into develop

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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'bug/JAL-2577' into develop

Merge branch 'features/JAL-2228_featureSetCounts_minRangeTweak' into develop

JAL-2473 revised default minimum dimension for Alignment Frame windows

JAL-2228 always create zero score annotations, since select/hide annotation filter ignores null positions in rows

JAL-2228 always set minimum for count to zero for annotation row

JAL-2577 Don't allow viewport ranges below 0. Unit tests updated.

JAL-2578 Moved hidden columns reveal to before selection adjustment

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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'features/JAL-1648_cache_user_inputs' into develop

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2418 release notes for JAL-2547, JAL-2563, JAL-1256

Merge branch 'JAL-2571' into develop

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2398 - updated groovy script for direct field modification

JAL-2418 JAL-2563 release notes