jalview

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JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.

JAL-3490 don't init the combo box's history cache for JS execution

JAL-3490 merged with 2.11.2 develop

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/Finder.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1

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    /help/help/html/features/search.html
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    /help/help/html/features/search.png
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'task/JAL-3597memoryLeakTest' into develop

JAL-3675 JAL-3597 release notes

Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

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    /resources/lang/Messages_es.properties
JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

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    /resources/lang/Messages_es.properties
JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3675 brought forward patch to build.gradle for changed main class variable in build.properties

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.

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    /src/jalview/io/BackupFiles.java
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    /src/jalview/io/BackupFilesPresetEntry.java
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.

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    /src/jalview/io/BackupFiles.java
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    /src/jalview/io/BackupFilesPresetEntry.java
JAL-3675 added JAL-3576 as known defect (colocated features appear in different order when exported/reimported)

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

Merge branch 'task/JAL-3608_property_set_laf_and_tests' into develop

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    /src/jalview/bin/Jalview.java
JAL-3675 fix issue attribution for JAL-3667 release note line

JAL-3675 update release notes for JAL-3673 and tested merge of additional patch for JAL-2983

Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch

JAL-3705 JAL-3251 unused attribute repurposed/renamed to mappedFromId

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    /src/jalview/xml/binding/jalview/Mapping.java
JAL-3705 unit test and "fix" borrowing unused schema attribute

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    /src/jalview/project/Jalview2XML.java
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    /test/jalview/io/CrossRef2xmlTests.java
JAL-3706 handle e.g. mapped exon feature extending beyond mapped range

JAL-3371 more fine-grained slider; set Param slider to initial default

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    /src/jalview/gui/OptsAndParamsPage.java
JAL-3371 more fine-grained slider; set Param slider to initial default

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    /src/jalview/gui/OptsAndParamsPage.java
JAL-3706 handle virtual feature extending to unmapped stop codon

JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

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    /src/jalview/io/JnetAnnotationMaker.java
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    /src/jalview/io/packed/ParsePackedSet.java
JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

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    /src/jalview/io/JnetAnnotationMaker.java
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    /src/jalview/io/packed/ParsePackedSet.java