JAL-2754 Sequence.findFeatures(fromCol, toCol)

JAL-2563 JAL-2547 amended unit tests for amended setStatusMessage

JAL-2483 JAL-2575 don't sort newly discovered features

JAL-2574 preparation for Sequence.findFeatures(col1, col2)

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

JAL-2547 handle contact features 'around' a gap correctly

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

Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/SeqPanel.java

JAL-2547 tooltip/AmendFeatures on gap straddled by feature, not for
adjacent feature

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

Conflicts:
src/jalview/appletgui/SeqPanel.java

JAL-2570 don't zap group colour scheme when mapping over split frame

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

JAL-2533 update javadoc

JAL-2465 fixed groups for JmolViewerTest.testStructureLoadingViaURL

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

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 'develop' into features/JAL-2446NCList

Conflicts:
src/jalview/appletgui/SeqPanel.java

JAL-2526 Sequence.findPositions to get residue positions for column
range

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

JAL-2491 JAL-2526 JAL-2566 JAL-2563 JAL-2547 release notes

Merge branch 'bug/JAL-2491' into develop

Merge branch 'bug/JAL-2547tooltipOnGap' into develop

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’.

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.

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

JAL-2418 JAL-2549 JABAWS 2.2 release notes

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

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

JAL-2557 removal of Sequence.sequenceFeatures

JAl-2034 Ported to applet

JAL-2034 don't update overview after click without drag on group

JAL-2050 make SequenceFeature.score final, adjust constructor calls

JAL-2505 simplifying number of SequenceFeature constructors JAL-2060
constant for NO_SCORE defined in SequenceFeature

JAL-2505 removed SequenceFeature constructor JAL-1641 include
description, otherDetails in feature roundtrip verification

JAL-2490 test coverage of empty and null feature group in Jalview format
export

Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange

JAL-2505 make SequenceFeature type, begin, end, featureGroup final

JAL-2506 relocate Uniprot binding classes, bind to UniprotFeature not
SequenceFeature

JAL-2505 remove setters for SequenceFeature.begin,end,type,featureGroup

JAL-2529 add object_type=cdna to EnsemblCdna parameters

Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

JAL-2505 JAL-2542 SequenceFeatures.shift() to shift all positional
features

JAL-2551 Fix to group colouring when group extent is reduced

JAL-2542 correct adjustment of sequence features for flanking sequence

JAL-2034 Added isDefined flag to SequenceGroup

JAL-2505 delete and readd modified feature after Cut or Paste

JAL-2549 RNAAliFold result to annotation file roundtrip test fails test due to JAL-2550 - Upper/lower case alphabet recognised as WUSS RNA annotation

JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get supported services list

JAL-2549 replace JABAWS 2.1 with 2.2 client and remove JPredWS client and tests

JAL-2490 find features for export as GFF, JAL-2548 respect group
visibility

JAL-2490 test coverage for printGffFormat before refactoring

JAL-2490 unit tests for getFeaturesForGroup

JAL-2547 don't show features in tooltip over a gap

JAL-2490 tidy code and tests for feature export in Jalview format

JAL-2490 improved lookup of features for Export Features (Jalview
format)

JAL-2480 methods to get features for group

JAL-2505 use setter not direct access to sf.description

JAL-2505 updates after conflicting merge of JAL-2504

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

Conflicts:
src/jalview/gui/FeatureRenderer.java

JAL-2504 update the right feature colour when creating a new feature

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

Conflicts:
src/jalview/analysis/AlignmentSorter.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/analysis/AlignmentSorterTest.java

JAL-2544 unit tests for sort by feature score

JAL-2544 check feature overlaps selection region

JAL-2543 identify as JSON before HTML

JAL-2546 JAL-2490 efficient lookup of features, correct handling of
non-positional features

JAL-2490 add non-positional feature case to test prior to refactoring

JAL-2480 always include all non-positional features in getAllFeatures()

Merge remote-tracking branch 'origin/bug/JAL-2256' into develop

JAL-2418 patch build - broken htsjdk import

JAL-2526 removed redundant call to Sequence.findPosition()

JAL-2490 refactored test for 'hasFeatures'

JAL-2544 only include features in selected columns for sort

JAL-2490 performant lookup of features for sorting

JAL-2490 only count sequences where feature overlap is confirmed

JAL-2505 unit test for sort by feature density, Javadoc

JAL-2490 initial unit tests prior to refactoring

Merge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop

JAL-2388 return empty hidden columns for fully visible alignment view

JAL-2490 lookup sequence features for "labelClass"

JAL-2490 lookup features at each column position