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JAL-3303 suppressed for 2.11.1
[jalview.git]
/
src
/
jalview
/
io
/
2019-07-26
gmungoc
Merge branch 'features/JAL-3375vcfValidation' into
tree
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commitdiff
2019-07-26
gmungoc
JAL-1793 only decode specific special characters in...
tree
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commitdiff
2019-07-26
gmungoc
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature...
features/JAL-3375vcfValidation
tree
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commitdiff
2019-07-26
gmungoc
JAL-3375 format validate VCF Integer and Float fields
tree
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commitdiff
2019-07-25
gmungoc
JAL-3375 ignore '.' values for VCF data
tree
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commitdiff
2019-07-10
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-08
gmungoc
JAL-3187 derived peptide variants tweaks and tests
tree
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commitdiff
2019-07-05
gmungoc
JAL-1793 apply URL decoding when saving VCF attribute...
tree
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commitdiff
2019-06-18
gmungoc
JAL-3187 javadoc
tree
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commitdiff
2019-06-18
gmungoc
JAL-3304 option to export linked features also for...
tree
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commitdiff
2019-06-18
gmungoc
JAL-3304 option to export linked features in Jalview...
tree
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commitdiff
2019-06-13
gmungoc
JAL-3143 recognise lnc_RNA as transcript
tree
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-05-29
gmungoc
JAL-2738 error logging if no ##reference found
tree
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commitdiff
2019-05-29
gmungoc
JAL-2738 accept .csi, default to GRCh37:homo_sapiens...
tree
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commitdiff
2019-05-27
Ben Soares
JAL-3141 Added HashMap types for Java 1.8 compatibility
tree
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commitdiff
2019-05-25
Ben Soares
JAL-3141 One more error log fix
tree
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commitdiff
2019-05-25
Ben Soares
JAL-3141 Added tooltips on Schemes dropdown and Customi...
tree
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commitdiff
2019-05-24
Ben Soares
JAL-3141 Fixes recommended from gmc's test
tree
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commitdiff
2019-05-24
Ben Soares
JAL-3141 Reworked a lot of BackupFiles to allow the...
tree
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commitdiff
2019-04-29
gmungoc
JAL-2738 JAL-2743 update unit test to match new VCF...
tree
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commitdiff
2019-04-26
gmungoc
JAL-2738 JAL-2743 properties to map VCF header to speci...
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-19
Ben Soares
JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben...
tree
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commitdiff
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-2791exportFilteredFeature' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'feature/JAL-3093wrappedModeTooltips'...
tree
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commitdiff
2019-02-28
gmungoc
Merge branch 'feature/JAL-3169cancelOverwrite' into...
tree
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commitdiff
2019-02-28
gmungoc
Merge remote-tracking branch 'origin/feature/JAL-3141_b...
tree
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commitdiff
2019-02-28
Jim Procter
Merge branch 'feature/JAL-3141_backupfiles_for211'...
merge/develop_feature/JAL-3141_backupfiles_for211
tree
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commitdiff
2019-02-22
gmungoc
JAL-2738 don't set AF as feature score
tree
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commitdiff
2019-02-22
Ben Soares
JAL-3141 improved message for asking whether to delete...
tree
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commitdiff
2019-02-21
Ben Soares
JAL-3141 Sensible refactoring for confirming deleting...
tree
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commitdiff
2019-02-17
Ben Soares
JAL-3141 User warning when deleting old backup files...
tree
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commitdiff
2019-02-15
Ben Soares
JAL-3141 re-order deletion of old files and check lastM...
tree
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commitdiff
2019-02-14
Ben Soares
JAL-3141 Added warning/confirmation when suffixReverse...
tree
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commitdiff
2019-02-01
Ben Soares
JAL-3141 Slight efficiency gain in detecting backupfile...
tree
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commitdiff
2019-01-30
Ben Soares
JAL-3141 Enabled the 'Include backpup files' checkbox...
tree
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commitdiff
2019-01-29
Ben Soares
JAL-3141 Found a good fix for updating the FileChooser...
tree
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commitdiff
2019-01-29
Ben Soares
JAL-3141 Found a (not ideal) fix for updating the FileC...
tree
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commitdiff
2019-01-28
Ben Soares
JAL-3141 improvement on BackupFilenameParts filename...
tree
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commitdiff
2019-01-25
Ben Soares
JAL-3141. This adds quite a lot of code to allow an...
tree
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commitdiff
2019-01-25
gmungoc
JAL-3187 don't compute variant features on peptide...
tree
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commitdiff
2019-01-24
Ben Soares
JAL-3141 New layout and wording of Backups Preferences...
tree
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commitdiff
2019-01-24
Ben Soares
JAL-3141 Reformatted code in eclipse
tree
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commitdiff
2019-01-23
Ben Soares
JAL-3141 Added Presets options in the Backups Preferenc...
tree
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commitdiff
2019-01-22
Ben Soares
JAL-3141 Fixed what happens when suffix template has...
tree
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commitdiff
2019-01-20
Ben Soares
JAL-3141 removing diagnostic output
tree
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commitdiff
2019-01-20
Ben Soares
JAL-3141 Changed suffix position to after the extension...
tree
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commitdiff
2019-01-18
Jim Procter
Merge branch 'feature/JAL-3063jaxbNoCastor' into featur...
tree
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commitdiff
2019-01-14
Ben Soares
JAL-3141 Made more constants
tree
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commitdiff
2019-01-09
Ben Soares
JAL-3141 removed redundant method to tests
tree
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commitdiff
2019-01-09
Ben Soares
JAL-3141 forgot to add this file after extracting the...
tree
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commitdiff
2019-01-09
Ben Soares
JAL-3141 Made one more suggested change from code review
tree
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commitdiff
2019-01-08
Ben Soares
JAL-3141 Made some more suggested changes from code...
tree
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commitdiff
2019-01-08
Ben Soares
JAL-3141 Made some suggested changes from code review
tree
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commitdiff
2018-12-19
gmungoc
JAL-3178 include non-positional features in their group...
bug/JAL-2791exportFilteredFeature
tree
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commitdiff
2018-12-13
Ben Soares
JAL-3130 Attempting to fix 8 tests that pass on a Mac...
tree
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commitdiff
2018-12-10
gmungoc
JAL-1421 added type to List and Vector
feature/JAL-3169cancelOverwrite
tree
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commitdiff
2018-12-10
gmungoc
JAL-3169 leave file browser open on Cancel in overwrite...
tree
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commitdiff
2018-12-06
Ben Soares
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
tree
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commitdiff
2018-12-03
gmungoc
JAL-3063 Castor removed from codebase
tree
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commitdiff
2018-11-02
Ben Soares
JAL-3141 Tests now available and working, bringing...
tree
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commitdiff
2018-10-31
Ben Soares
JAL-3141 Preferences 'Backups' tab now working. Doesn...
tree
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commitdiff
2018-10-25
Ben Soares
JAL-3141 Ostensibly all backups working for alignment...
tree
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commitdiff
2018-10-24
Ben Soares
JAL-3141 Code checkout. Not compiling.
tree
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commitdiff
2018-10-24
Ben Soares
JAL-3141 Code checkout. Not compiling.
tree
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commitdiff
2018-10-23
Ben Soares
BackupFilter and other unfinished business
tree
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commitdiff
2018-10-22
Ben Soares
JAL-3141 Taken the backing up code out of FileChooser...
tree
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commitdiff
2018-10-22
Ben Soares
JAL-3141 Taken the backing up code out of FileChooser...
tree
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commitdiff
2018-10-22
Ben Soares
JAL-3141 Tidying
tree
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commitdiff
2018-10-19
Ben Soares
JAL-3141 Backup files being created with default suffix...
tree
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commitdiff
2018-10-09
Jim Procter
JAL-3127 TODO - resolve reference to Viewport for group...
tree
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commitdiff
2018-10-04
gmungoc
JAL-3132 set status message when over sequence id or...
tree
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commitdiff
2018-09-27
gmungoc
JAL-2791 refactored Export Features to apply all visibi...
tree
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commitdiff
2018-09-19
gmungoc
JAL-3063 use JAXB for 'Save as Project' and load projec...
tree
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commitdiff
2018-09-11
Jim Procter
Merge branch 'develop' into releases/Release_2_11_Branch
tree
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commitdiff
2018-09-09
Jim Procter
JAL-3106 normalise extension before checking if it...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-2988 if selected file is null (On Java 10/OSX ...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-2988 workaround: overload getSelectedFile() because...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-3106 use .jvp as default
tree
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commitdiff
2018-09-03
Jim Procter
Merge branch 'patch/VAqua_saveload_update_JAL-2988...
tree
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commitdiff
2018-08-22
Jim Procter
JAL-2988 workaround for jalview save as dialogs - clear...
tree
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commitdiff
2018-08-03
Ben Soares
JAL-3061
tree
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commitdiff
2018-08-02
Ben Soares
JAL-3053
tree
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commitdiff
2018-07-30
bsoares
Fixed bug ignoring "alpha" extended braces in RNA SS...
tree
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commitdiff
2018-06-26
Jim Procter
JAL-3042 don't allow user to change default history...
tree
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commitdiff
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-05-24
gmungoc
JAL-2997 additional tests
tree
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commitdiff
2018-05-23
gmungoc
JAL-2997 handle tab-delimited trailing column number...
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 ensure default is ‘parseImmediately=true’
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 isParseImmediately() allows the parse() method...
tree
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
tree
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
tree
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commitdiff
2018-01-30
gmungoc
JAL-2897 generate peptide variants for synonymous codon...
tree
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commitdiff
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