jalview

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JAL-2525 lookup transcript features by Ontology

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    /src/jalview/ext/ensembl/EnsemblGene.java
JAL-2738 filter VEP consequence data to that for current transcript

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    /src/jalview/io/vcf/VCFLoader.java
JAL-2674 iterator for visible blocks with absolute positions

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    /src/jalview/datamodel/HiddenColumns.java
Merge branch 'releases/Release_2_10_2b1_Branch' of https://source.jalview.org/git/jalview.git into bug/JAL-2750

Added check for negative start columns

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    /src/jalview/datamodel/SequenceGroup.java
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    /test/jalview/gui/ValidColumnSelectionTest.java
Merge branch 'releases/Release_2_10_2b1_Branch'

Merge branch 'documentation/JAL-2751patch2102b2' into releases/Release_2_10_2b1_Branch

JAL-2751 what's new for 2.10.2b2 patch

JAL-2751 patch release notes

JAL-2751 bump version and new releases entry

Merge branch 'feature/JAL-2745ebiHttps' into develop

Begin separation of GUI and tree calculation logic

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    /src/jalview/gui/CalculationChooser.java
JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher

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    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher

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    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-2745 patch tests for https

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    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-2745 patch tests for https

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    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-2748 formatting

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-2748 formatting

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-2745 JAL-2748 direct download of XML from uniprot.org patch for 2.10.2b1 branch

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-2745 JAL-2748 direct download of XML from uniprot.org

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-2738 one sequence feature per (SNP) VCF allele

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    /src/jalview/io/vcf/VCFLoader.java
JAL-2744 indent CSQ lines to catch the eye

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer

JAL-2674 Tidies

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 finish with iterators for now

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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/gui/VamsasApplication.java
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    /test/jalview/analysis/DnaTest.java
Merge branch 'feature/JAL-2745ebiHttps' into develop

Revert "JAL-2745 update SIFTS FTP URL to HTTPS" EBI ftp confirmed to remain accesible via HTTP This reverts commit c7f663521cb82b94d832015010fa488d3dc7ff58.

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    /src/jalview/ws/sifts/SiftsClient.java
Revert "JAL-2745 update SIFTS FTP URL to HTTPS" EBI ftp confirmed to remain accesible via HTTP This reverts commit c7f663521cb82b94d832015010fa488d3dc7ff58.

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    /src/jalview/ws/sifts/SiftsClient.java
JAL=2674 Removed getHiddenColumnsCopy

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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/datamodel/CigarArray.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 reverted attempt at visible regions iterator

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/datamodel/HiddenColumns.java