Tochukwu Charles N Ofoegbu

JAL-2136 New Phyre2 branch + attempt to resynced with develop

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/io/AnnotationFile.java
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Merge branch 'features/JAL-2136_phyre2_integration' into spikes/phyre

JAL-2136 Introduced DynamicData model, modified AnnotionFile to store Phyre meta-data in DynamicData object, modified SequenceAnnotationReport to build Phyre html meta-data from DynamicData list

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    /src/jalview/datamodel/DynamicData.java
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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/io/AnnotationUtil.java
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    /test/jalview/io/AnnotationFileIOTest.java
Merge branch 'spikes/phyre' into features/JAL-2136_phyre2_integration

JAL-2473 revised default minimum dimension for Alignment Frame windows

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

JAL-2375 fix unit test to reflect improvement

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    /test/jalview/gui/StructureChooserTest.java
Fixed failing tests

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    /src/jalview/io/AppletFormatAdapter.java
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    /test/jalview/ext/jmol/JmolViewerTest.java
JAL-2533 updated unit test to reflect improvement

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    /test/jalview/ext/jmol/JmolParserTest.java
JAL-1648 improvement on finder searchbox keyboard control - Enter to update search box if popup is displayed otherwise perform find next action

JAL-1648 code fix - enter key should pick selected item on finder searchbox

JAL-2465 Improvement to re-instate storing recently opened URLs for alignments loaded from a structure format via URL

JAL-2465 fix to prevent files loaded from the system's temporary directory from being included in recently opend files store

Merge branch 'features/JAL-1648_cache_user_inputs' of https://source.jalview.org/git/jalview into features/JAL-1648_cache_user_inputs

JAL-1648 fix to transfer focus back to alignment frame when Finder window is close via hitting cancel or the excape key

JAL-2536 Overview window sizing not subject to min size restrictions
JAL-2536 Overview window sizing not subject to min size restrictions
All code changes look ok. Confirmed that overview window size is no longer being set to the default min size.

All code changes look ok. Confirmed that overview window size is no longer being set to the default min size.

Merge branch 'features/JAL-2136_phyre2_integration' into spikes/phyre

JAL-2136 broken build fix attempt

JAL-2520 improvement to use URL leaf name for creating temp file for URL file download

JAL-2533 improvement to prune off file extension when imported seqs are named with the data file

JAL-2520 improvement to download and update structure files loaded via URL to a local file before parsing the file

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    /src/jalview/ws/utils/UrlDownloadClient.java
JAL-2520 unit test for improvement to download structure files from URL before parsing

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    /test/jalview/io/FileLoaderTest.java
JAL-2465 fix to dynamically specify data source type in StructureSelectionManager.setMapping(...) method

Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url

JAL-2484 adjusted default cache settings panel's left border width

JAL-1648 improvements: enter key closes the popup and updates cache immidately, uniform font applied to all popup's component

JAL-1648 resolved CR-JAL-41 review issues

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    /src/jalview/io/cache/AppCache.java
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    /test/jalview/io/cache/AppCacheTest.java
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    /test/jalview/io/cache/JvCacheableInputBoxTest.java
Added more comment. Regarding InitCache, is should only be called by JvCacheableInputBox constructor. Hence, at the point of invocation there shouldn't be any un-persisted in-memory cache item yet....

Added more comment. Regarding InitCache, is should only be called by JvCacheableInputBox constructor. Hence, at the point of invocation there shouldn't be any un-persisted in-memory cache item yet. I've made it private and moved it to JvCachableInputBox class accordingly.