jalview

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JAL-2576 Proposed fix

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    /src/jalview/util/LinkedIdentityHashSet.java
Merge branch 'bug/JAL-2034contextchange' into develop

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

JAL-2520 properly documented as a fixed bug in release notes

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

JAL-2465,JAL-2520,JAL-2533 release notes

Merge branch 'features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url' into develop

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-2533 update javadoc

JAL-2465 fixed groups for JmolViewerTest.testStructureLoadingViaURL

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    /test/jalview/ext/jmol/JmolViewerTest.java
Merge branch 'bug/JAL-2536' into develop

JAL-2536 tweak javadoc wording

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

JAL-2517 release notes

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