jalview

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Merge branch 'bug/JAL-2983negativeSliderMin' into develop

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/gui/FeatureTypeSettings.java

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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/FeatureTypeSettings.java
JAL - 3690 AlignCalc rebuilt - WIP

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/ws/jws2/Jws2ClientFactory.java
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
Merge branch 'releases/Release_2_11_1_Branch' into bug/JAL-3509hideResnum

Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch

JAL-3633 last minute refinement so password box doesn't get focus all the time

JAL-3633 last minute refinement so password box doesn't get focus all the time

JAL-3633 Apply (proxy) button enabled when needed

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    /src/jalview/jbgui/GPreferences.java
JAL-3633 Apply (proxy) button enabled when needed

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    /src/jalview/jbgui/GPreferences.java
JAL-3633 Help documentation updated

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    /help/help/html/features/preferences.html
JAL-3633 Help documentation updated

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    /help/help/html/features/preferences.html
JAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview-JS, Most NPE fixes for tests

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    /src/jalview/io/BackupFiles.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview-JS, Most NPE fixes for tests

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    /src/jalview/io/BackupFiles.java
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    /src/jalview/jbgui/GPreferences.java
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch

JAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel

JAL-3675 mention -open argument in the command line arguments table

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    /help/help/html/features/clarguments.html
JAL-3675 JAL-3570 JAL-3608 JAL-2983 release notes and docs

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    /help/help/html/features/commandline.html
JAL-3275 JAL-3633: JAL-3275 Turned Preferences into a Singleton that checks renews if it's been closed. Removed some debugging for JAL-3633. Added focus/highlight to proxy password box when needed. Forced WS lookup wheb proxy settings changed.

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3275 JAL-3633: JAL-3275 Turned Preferences into a Singleton that checks renews if it's been closed. Removed some debugging for JAL-3633. Added focus/highlight to proxy password box when needed. Forced WS lookup wheb proxy settings changed.

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3675 update release note for JAL-2656

Merge branch 'feature/JAL-3615gzipXfam' into develop

JAL-3615 JAL-2656 missing import after cherrypick

JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header

JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header

JAL-2656 recognise Gzipped file input streams by their content, not their filename

Conflicts:

src/jalview/io/FileParse.java

cherypicked from 2.11.1.1 release patch

JAL-2656 recognise Gzipped file input streams by their content, not their filename

JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java