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JAL-1988 Hack to ensure Quit dialog box is moved to front
[jalview.git]
/
src
/
jalview
/
2020-09-24
Jim Procter
JAL-3757 JAL-3689 use AppletFormat.checkProtocol to...
tree
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commitdiff
2020-09-23
Ben Soares
JAL-3757 JAL-3689 Fixed checks for URLs by adding check...
tree
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commitdiff
2020-09-23
Ben Soares
JAL-3633 ensure check both or https:// for urls
tree
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commitdiff
2020-09-23
Jim Procter
JAL-3748 not testing for sequence’s containment in...
bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
tree
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commitdiff
2020-09-23
Jim Procter
JAL-3748 fix compilation error
tree
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commitdiff
2020-09-23
Jim Procter
JAL-3748 allow AlignedCodonFrame.covers to optionally...
tree
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commitdiff
2020-09-22
Jim Procter
JAL-3748 don’t trash start/end on SequenceI reconstruct...
tree
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commitdiff
2020-09-21
Jim Procter
Merge branch 'merge_review/JAL-3490_2_11_2_develop...
tree
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commitdiff
2020-09-17
Jim Procter
JAL-3741 http to https (and jar to jvp for exampleFile...
tree
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commitdiff
2020-09-17
Jim Procter
JAL-3750 parse protocol before checking if argument...
tree
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commitdiff
2020-09-17
gmungoc
JAL-3700 additions and corrections to unit tests
bug/JAL-3700_mapSequenceSelection
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 preserve sequence IDs from original alignment...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 recover complement alignment from complement...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 make findAlignedSequence require mapped from...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 pass a list to findAlignedSequence to return...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
tree
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commitdiff
2020-09-16
Jim Procter
Merge branch 'failingTest/JAL-3748_reconstructCDSafterP...
tree
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commitdiff
2020-09-16
gmungoc
JAL-3700 fix for propagation of sort commands
tree
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commitdiff
2020-09-16
gmungoc
JAL-3700 check for 'covering' mapping when matching...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 store an AlignmentView for the complement...
tree
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commitdiff
2020-09-14
Ben Soares
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2020-09-14
Ben Soares
Merge branch 'feature/JAL-3615gzipXfam' into develop
tree
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commitdiff
2020-09-14
Ben Soares
JAL-3609 HiDPI scale setting done via system prop in...
tree
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commitdiff
2020-09-10
gmungoc
JAL-3518 removed unneeded override in ChimeraCommands
tree
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commitdiff
2020-09-10
gmungoc
JAL-2422 comments updated re ALTLOC handling
tree
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commitdiff
2020-09-03
gmungoc
JAL-3648 resize annotation panel after dragging to...
tree
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commitdiff
2020-09-03
Ben Soares
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2020-09-03
gmungoc
JAL-3648 resize annotation panel after dragging to...
tree
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commitdiff
2020-09-02
Ben Soares
JAL-3280 Test for remote release build_properties file...
tree
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commitdiff
2020-09-01
Ben Soares
JAL-3280 fixes after CR-JAL-241. Now only checking...
tree
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commitdiff
2020-08-31
Ben Soares
JAL-3280 Pass appbase and appdir from getdown to jalvew...
tree
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commitdiff
2020-08-31
Jim Procter
JAL-3732 - sequences can be moved up/down in cursor...
tree
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commitdiff
2020-08-31
Jim Procter
JAL-3732 - sequences can be moved up/down in cursor...
tree
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commitdiff
2020-08-31
gmungoc
JAL-3018 Ensembl reviewed REST version updated to 13.0
tree
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commitdiff
2020-08-31
gmungoc
JAL-1191 use Cache.log for logging
tree
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commitdiff
2020-08-31
gmungoc
JAL-1191 reduce logging level for warnings
tree
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commitdiff
2020-08-27
Ben Soares
Merge branch 'releases/Release_2_11_1_Branch' into...
merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
tree
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commitdiff
2020-08-25
Jim Procter
JAL-3671 hardwire log4j.root logger to INFO to supress...
tree
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commitdiff
2020-08-24
gmungoc
JAL-3018 updated reviewed REST version to 12.0
tree
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commitdiff
2020-08-21
Jim Procter
JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615...
tree
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commitdiff
2020-08-21
Jim Procter
JAL-3615 code tidy, improve unit test
tree
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commitdiff
2020-08-20
Ben Soares
JAL-2656 better read of (potential) gzip magic bytes
tree
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commitdiff
2020-08-18
gmungoc
JAL-2656 Java 8 compatible test for gzipped, refactored...
tree
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commitdiff
2020-08-18
gmungoc
JAL-3692 parse multiline CDS location correctly
tree
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commitdiff
2020-08-17
Jim Procter
Merge branch 'patch/JAL-3691_No_score_models_available...
tree
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commitdiff
2020-08-17
Jim Procter
Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_...
tree
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commitdiff
2020-08-17
Jim Procter
JAL-3490 don't init the combo box's history cache for...
tree
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commitdiff
2020-08-17
Jim Procter
JAL-3490 merged with 2.11.2 develop
tree
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commitdiff
2020-08-17
Jim Procter
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL...
tree
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commitdiff
2020-08-17
Jim Procter
Merge branch 'task/JAL-3597memoryLeakTest' into develop
tree
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commitdiff
2020-08-17
Jim Procter
Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch...
tree
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commitdiff
2020-08-14
Ben Soares
JAL-3676 More explicit tooltip about resetting log...
tree
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commitdiff
2020-08-13
gmungoc
JAL-3597 additional references nulled, bug in test...
tree
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commitdiff
2020-08-12
Ben Soares
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for...
tree
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commitdiff
2020-08-12
Ben Soares
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2020-08-12
Jim Procter
Merge branch 'task/JAL-3608_property_set_laf_and_tests...
tree
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commitdiff
2020-08-12
Ben Soares
JAL-3608 Changes from code review CR-JAL-236
tree
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commitdiff
2020-08-11
Jim Procter
JAL-3673 make sure font metrics are updated if dealing...
tree
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commitdiff
2020-08-11
Jim Procter
Merge branch 'bug/JAL-2983negativeSliderMin' into relea...
tree
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commitdiff
2020-08-11
gmungoc
JAL-3371 more fine-grained slider; set Param slider...
tree
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commitdiff
2020-08-10
gmungoc
JAL-3490 match count independent of contiguous matches...
patch/Release_2_11_1_Branch_patch_JAL-3490
tree
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commitdiff
2020-08-10
Jim Procter
JAL-3691 toUpperCase(Locale.ROOT) for all standard...
tree
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commitdiff
2020-08-10
Jim Procter
Merge branch 'releases/Release_2_11_1_Branch' into...
tree
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commitdiff
2020-08-10
Jim Procter
JAL-3628 JAL-3708 call Cache.initLogger() before using...
tree
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commitdiff
2020-08-09
Ben Soares
JAL-3691 Changed .toUppoerCase().startsWith(...) to...
tree
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commitdiff
2020-08-05
Ben Soares
JAL-3691 Changed .toUppoerCase().startsWith(...) to...
tree
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commitdiff
2020-08-05
Jim Procter
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into...
tree
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commitdiff
2020-08-05
gmungoc
JAL-3692 parse multiline feature qualifiers and escaped...
tree
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commitdiff
2020-08-05
gmungoc
JAL-3692 parse multiline feature qualifiers and escaped...
tree
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commitdiff
2020-08-05
Jim Procter
Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL...
tree
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commitdiff
2020-08-05
gmungoc
JAL-3700 fix for propagation of sort commands
tree
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commitdiff
2020-08-04
Ben Soares
JAL-3477 Added -help text for jvmmempc and jvmmemmax...
tree
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commitdiff
2020-08-04
Ben Soares
JAL-3477 Added -help text for jvmmempc and jvmmemmax...
tree
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commitdiff
2020-08-03
gmungoc
JAL-3700 check for 'covering' mapping when matching...
tree
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commitdiff
2020-08-03
gmungoc
JAL-3692 set CDS /product as EMBLCDSPROTEIN description
tree
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commitdiff
2020-08-03
gmungoc
JAL-3692 refactor/complete parsing, more unit test...
tree
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commitdiff
2020-08-03
gmungoc
JAL-3692 parse DE for description, and other refactoring...
tree
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commitdiff
2020-08-03
gmungoc
JAL-3692 unit test (J03321), fixes, dbrefs; todo: prote...
tree
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commitdiff
2020-08-03
gmungoc
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
tree
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commitdiff
2020-08-03
Jim Procter
Merge branch 'bug/JAL-2983negativeSliderMin' into develop
tree
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commitdiff
2020-07-31
Ben Soares
Merge branch 'releases/Release_2_11_1_Branch' into...
tree
|
commitdiff
2020-07-29
Jim Procter
Merge branch 'bug/JAL-2983negativeSliderMin' into relea...
tree
|
commitdiff
2020-07-29
Jim Procter
JAL-3371 JAL-2983 don't modify 'extent' of slider ...
tree
|
commitdiff
2020-07-28
Jim Procter
Merge branch 'feature/JAL-3615gzipXfam' into develop
tree
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commitdiff
2020-07-28
Jim Procter
JAL-3615 JAL-2656 missing import after cherrypick
tree
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commitdiff
2020-07-28
Jim Procter
JAL-2656 recognise non-HTTP URI input streams as gzippe...
tree
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commitdiff
2020-07-28
Jim Procter
JAL-2656 recognise Gzipped file input streams by their...
tree
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commitdiff
2020-07-28
Jim Procter
JAL-2656 recognise non-HTTP URI input streams as gzippe...
tree
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commitdiff
2020-07-28
Jim Procter
JAL-2656 recognise Gzipped file input streams by their...
tree
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commitdiff
2020-07-27
gmungoc
JAL-2656 JAL-3615 check response headers to test for...
tree
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commitdiff
2020-07-27
gmungoc
JAL-3615 used gzip endpoints for Pfam and Rfam
tree
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commitdiff
2020-07-27
Jim Procter
Merge branch 'bug/JAL-2983negativeSliderMin' into relea...
tree
|
commitdiff
2020-07-27
gmungoc
JAL-3692 set CDS /product as EMBLCDSPROTEIN description
tree
|
commitdiff
2020-07-27
gmungoc
JAL-3692 refactor/complete parsing, more unit test...
tree
|
commitdiff
2020-07-27
gmungoc
JAL-3621 corrected sequence feature sort and test
tree
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commitdiff
2020-07-27
gmungoc
JAL-3621 update to intervalstore v1.1
tree
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commitdiff
2020-07-27
Jim Procter
JAL-3697 show total number of features not shown
tree
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commitdiff
2020-07-27
Jim Procter
JAL-3696 log the error message from the exception to...
tree
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commitdiff
2020-07-27
Jim Procter
JAL-3697 show total number of features not shown
tree
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commitdiff
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