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JAL-2517 release notes

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:

src/jalview/appletgui/SeqPanel.java

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/SeqPanel.java
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    /src/jalview/gui/AlignmentPanel.java
JAL-2526 Sequence.findPositions to get residue positions for column range

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /test/jalview/datamodel/SequenceTest.java
Merge branch 'bug/JAL-2517cancelAppletColour' into develop

release notes JAL-2550 known defect JAL-2535 stockholm->PP annotation

JAL-2418 updated JABAWS server in what’s new

Merge branch 'bug/JAL-2491' into develop

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    /src/jalview/appletgui/SeqPanel.java
Merge branch 'bug/JAL-2547tooltipOnGap' into develop

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    /src/jalview/appletgui/SeqPanel.java
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop

JAL-2563 failing test to verify SetStatus returns position and message includes the position for ambiguous peptide ‘B’.

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    /test/jalview/gui/SeqPanelTest.java
JAL-2563 test to verify SetStatus returns -1 so mouseOver events are raised via StructureSelectionManager (JAL-2491, expected fixed by JAL-2547)

Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop

JAL-2547 JAL-2562 rejig SetStatusMessage return value test for legibility and maximum assert coverage before JAL-2526 causes failure

Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop

JAL-2526 test and documentation for SeqPanel.setStatus behaviour needed to fix bug noted on JAL-2491 where mouseover at gap highlights position for sequence to right of gap in complementary view.

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    /test/jalview/gui/SeqPanelTest.java
JAL-2562 javadoc TODO

JAL-2491 Missed port to applet from JAL-1691

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2418 updated JPred documentation and screenshot for JPred4

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    /help/html/webServices/jnet.html
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    /help/html/webServices/jnetprediction.gif
JAL-2418 JAL-2549 JABAWS 2.2 release notes

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    /help/html/webServices/msaclient.html
Merge branch 'features/JAL-2549_updateJABAWSto220' into develop

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-2290 no update if no change of residue JAL-2547 no features on tooltip over gap

JAL-2480 move ContiguousI and Range to jalview.datamodel

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    /src/jalview/datamodel/ContiguousI.java
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    /src/jalview/datamodel/Range.java
JAL-2557 removal of Sequence.sequenceFeatures

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    /src/jalview/analysis/CrossRef.java
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    /src/jalview/analysis/SeqsetUtils.java
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    /src/jalview/commands/EditCommand.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/io/vamsas/Datasetsequence.java
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    /test/jalview/analysis/AlignmentUtilsTests.java
  1. … 9 more files in changeset.
Merge branch 'develop' into features/JAL-1648_cache_user_inputs bugfixes in finder for feature creation and minimum window size merged to topic

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    /resources/lang/Messages.properties
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    /src/jalview/gui/AnnotationColumnChooser.java