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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
2017-05-22
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-22
gmungoc
JAL-2544 check feature overlaps selection region
tree
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commitdiff
2017-05-22
gmungoc
JAL-2543 identify as JSON before HTML
tree
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commitdiff
2017-05-22
gmungoc
JAL-2546 JAL-2490 efficient lookup of features, correct...
tree
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commitdiff
2017-05-22
gmungoc
JAL-2480 always include all non-positional features...
tree
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commitdiff
2017-05-22
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2256'...
tree
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commitdiff
2017-05-22
Jim Procter
JAL-2418 patch build - broken htsjdk import
tree
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commitdiff
2017-05-19
gmungoc
JAL-2526 removed redundant call to Sequence.findPosition()
tree
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commitdiff
2017-05-19
gmungoc
JAL-2490 refactored test for 'hasFeatures'
tree
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commitdiff
2017-05-19
gmungoc
JAL-2544 only include features in selected columns...
tree
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commitdiff
2017-05-19
gmungoc
JAL-2490 performant lookup of features for sorting
tree
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commitdiff
2017-05-19
gmungoc
JAL-2490 only count sequences where feature overlap...
tree
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commitdiff
2017-05-19
gmungoc
JAL-2505 unit test for sort by feature density, Javadoc
tree
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commitdiff
2017-05-18
gmungoc
JAL-2490 initial unit tests prior to refactoring
tree
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commitdiff
2017-05-18
Jim Procter
JAL-2388 return empty hidden columns for fully visible...
tree
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commitdiff
2017-05-18
gmungoc
JAL-2490 lookup sequence features for "labelClass"
tree
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commitdiff
2017-05-18
gmungoc
JAL-2490 lookup features at each column position
tree
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commitdiff
2017-05-18
gmungoc
JAL-2543 html-encode quote characters in feature descri...
tree
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commitdiff
2017-05-18
gmungoc
JAL-2490 retrieve visible features only
tree
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commitdiff
2017-05-18
kiramt
JAL-2256 Corrected AllCols/Rows iterator behaviour...
bug/JAL-2256
tree
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commitdiff
2017-05-17
Jim Procter
Merge branch 'bug/JAL-2510amendFeatures' into develop
tree
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commitdiff
2017-05-17
Jim Procter
Merge branch 'features/JAL-2447experimentalFlag' into...
tree
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commitdiff
2017-05-17
gmungoc
JAL-2504 use (and update) defaults for new feature...
tree
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commitdiff
2017-05-17
gmungoc
Merge branch 'develop' into bug/JAL-2510amendFeatures
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 unreachable code (for many years) removed
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 refactored method removed
tree
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commitdiff
2017-05-16
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 set helix number as feature group in SequenceF...
tree
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commitdiff
2017-05-16
gmungoc
JAL-2403 simplify instantiation / configuration of...
tree
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commitdiff
2017-05-16
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-16
kiramt
JAL-2522 Missed fix to applet
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 refactor to set type and group in SequenceFeat...
tree
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commitdiff
2017-05-16
gmungoc
JAL-2525 put in missing "transcript" feature type
tree
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commitdiff
2017-05-16
kiramt
JAL-2388 Rationalised hashCode method in HiddenColumns
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 set SequenceFeature group in constructor
tree
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commitdiff
2017-05-15
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2507 capitalisation for annotation lines generated...
tree
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commitdiff
2017-05-15
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2507 case insensitive recognition of annotation...
tree
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commitdiff
2017-05-15
gmungoc
JAL-2532 new feature types and colour changes from...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2535 quick hack to implement posterior probabilitie...
tree
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commitdiff
2017-05-15
kiramt
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-05-15
kiramt
JAL-2388 Add missed optimisation
tree
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commitdiff
2017-05-15
Jim Procter
Merge branch 'features/JAL-2376_add-horizontal-bar...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2371 create a default ResidueShader when constructi...
tree
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commitdiff
2017-05-15
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-15
gmungoc
JAL-2490 use findFeatures() for efficient feature overl...
tree
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commitdiff
2017-05-15
gmungoc
JAL-2480 redundant code (from merge?) removed
tree
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commitdiff
2017-05-15
gmungoc
JAL-2480 redundant code removed
tree
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commitdiff
2017-05-12
gmungoc
JAL-2490 performant findFeaturesAtRes
tree
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commitdiff
2017-05-12
gmungoc
JAL-2483 efficient lookup of feature types and groups...
tree
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commitdiff
2017-05-12
gmungoc
JAL-2525 get sequence features for Ontology term(s...
tree
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commitdiff
2017-05-12
gmungoc
JAL-2480 more efficient contains check on add; tidied...
tree
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commitdiff
2017-05-12
gmungoc
JAL-2480 java.util.RangeComparator renamed IntRangeComp...
tree
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commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2435splitScreenFont' into...
tree
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commitdiff
2017-05-12
Jim Procter
JAL-2435 mirror antiAlias setting between cDNA and...
tree
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commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2388OverviewWindow' into...
tree
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commitdiff
2017-05-12
Jim Procter
JAL-2388 checkbox in overview popup for applet
tree
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commitdiff
2017-05-12
gmungoc
JAL-2480 efficient test for features present on sequence
tree
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commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2228_efficient_featurecounts...
tree
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commitdiff
2017-05-12
gmungoc
JAL-2480 renamed java.util.RangeComparator to IntRangeC...
tree
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commitdiff
2017-05-11
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2509 JAL-2507 allow whitespace in GS annotation...
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2507 test if an annotation is ‘whitespace’
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitesp...
tree
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commitdiff
2017-05-10
kiramt
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-05-10
kiramt
JAL-2522 Fix to cursor scrolling
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2509 extend set of brackets recognised by stockholm...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2507 output secondary structure regardless of prese...
tree
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commitdiff
2017-05-09
gmungoc
JAL-1632 correct i18n and NPE
tree
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commitdiff
2017-05-09
gmungoc
JAL-2480 include sequenceFeatureStore in createDatasetS...
tree
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commitdiff
2017-05-09
gmungoc
JAL-2483 JAL-2481 fixed findAllFeatures to handle null...
tree
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commitdiff
2017-05-09
kiramt
JAL-2388 Added checkbox to toggle hidden columns menu...
tree
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commitdiff
2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
tree
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commitdiff
2017-05-08
gmungoc
JAL-2505 set type,desc,begin,end,group,score in Sequenc...
tree
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commitdiff
2017-05-08
gmungoc
JAL-2505 refactored SequenceFeature construction so...
tree
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commitdiff
2017-05-08
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-08
gmungoc
JAL-1632 i18n for warning messages
tree
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commitdiff
2017-05-08
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-2515'...
tree
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commitdiff
2017-05-08
kiramt
JAL-2515 Id panel in applet updated for NPE on urlProvider
bug/JAL-2515
tree
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commitdiff
2017-05-08
kiramt
JAL-2512 And applet
tree
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commitdiff
2017-05-08
kiramt
JAL-2512 Fix to show non-gap positions in None colour...
tree
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commitdiff
2017-05-05
gmungoc
Merge branch 'develop' into features/JAL-2435splitScree...
tree
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commitdiff
2017-05-05
gmungoc
JAL-964 JAL-2510 update Feature Settings from Amend...
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2017-05-04
gmungoc
JAL-2506 allow graduated colour as default in new Seque...
tree
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commitdiff
2017-05-04
gmungoc
JAL-2510 ensure modified feature type is displayed
tree
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commitdiff
2017-05-04
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-05-04
gmungoc
JAL-2504 allow feature type to be specified for Create...
tree
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commitdiff
2017-05-04
Jim Procter
Merge branch 'develop' into features/JAL-2228_efficient...
tree
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commitdiff
2017-05-04
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholmoutput...
tree
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commitdiff
2017-05-04
Jim Procter
Merge branch 'features/JAL-2503_filteronquantitativeann...
tree
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commitdiff
2017-05-04
Jim Procter
Merge branch 'features/JAL-2393customMatrices' into...
tree
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commitdiff
2017-05-04
Jim Procter
fix for JAL-2509 - don’t replace all bracket types...
tree
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commitdiff
2017-05-04
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-04
gmungoc
JAL-2505 delete and readd amended sequence feature
tree
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commitdiff
2017-05-04
gmungoc
JAL-2480 JAL-2505 guard against duplicating links
tree
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commitdiff
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