jalview

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JAL-2515 Id panel in applet updated for NPE on urlProvider

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    /src/jalview/appletgui/IdPanel.java
JAL-2506 allow graduated colour as default in new Sequence Feature dialog

JAL-2510 ensure modified feature type is displayed

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    /src/jalview/gui/FeatureRenderer.java
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-2504 allow feature type to be specified for Create Features dialog

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/gui/FeatureRenderer.java
Merge branch 'bug/JAL-2507_rnasecstrstockholmoutput' into develop

Merge branch 'features/JAL-2503_filteronquantitativeannotation' into develop

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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'features/JAL-2393customMatrices' into develop

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    /resources/lang/Messages_es.properties
JAL-1656 make RNAML->Stockholm round trip test pass by ignoring differences in secondary structure annotation visibility

JAL-2507 JAL-2509 allow differences in visibility of annotation rows to be ignored when comparing round-tripped alignments

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    /test/jalview/io/StockholmFileTest.java
JAL-2507 JAL-2509 new assert to compare secondary structure in two annotation rows

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    /test/jalview/io/StockholmFileTest.java
fix for JAL-2509 - don’t replace all bracket types with ()

fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label or 'isRNA' RNA secondary structure annotation flag

Merge branch 'features/JAL-2473_set-minimium-dimensions' into develop

Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL-2473_set-minimium-dimensions

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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'features/JAL-2503_filteronquantitativeannotation' into develop

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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'features/JAL-2393customMatrices' into develop

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    /resources/lang/Messages_es.properties
JAL-2393 JAL-2416 refresh the score model menu when updating gui enabled/disabled settings

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    /src/jalview/gui/CalculationChooser.java
JAL-2503 show threshold slider for quantitative annotation rows

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    /src/jalview/gui/AnnotationColumnChooser.java
JAL-2503 AlignmentAnnotation.isQuantitative() test

JAL-2246 basic sanity test of fetching example accessions

Merge branch 'features/JAL-2432_annotbypercent' into develop

JAL-1933 JAL-2501 i18n for all auto calculated descriptions

JAL-1933 show occupancy in tooltip for row

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    /src/jalview/analysis/AAFrequency.java
JAL-2246 test a Uniprot fetch

JAL-2432 honour percentage checkbox when entering values in text box

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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationRowFilter.java
JAL-2432 applet: only enable percent checkbox when threshold is active

JAL-2432 percentage checkbox follows threshold value field

JAL-2105 Ensembl REST now at 5.0

JAL-2485 JAL-2246 test Uniprot FTS summary

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    /test/jalview/ws/dbsources/RemoteFormatTest.java