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JAL-3851 remove old interface
[jalview.git]
/
src
/
jalview
/
io
/
2020-11-13
Ben Soares
JAL-3775 Eclipse re-formatting commit
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3633 Small changes to allow future fitting with...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for...
tree
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commitdiff
2020-11-10
Ben Soares
JAL-3628 Fixed oddly worded and non-formatted error...
tree
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commitdiff
2020-11-10
Ben Soares
JAL-3628 Fix for slightly incorrect boolean usage to...
tree
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commitdiff
2020-11-10
Ben Soares
JAL-3628 Even more Cache.log.debug statements
tree
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commitdiff
2020-11-10
Ben Soares
JAL-3628 More Cache.log.debug statements
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3628 Changed other calls to renameTo to use BackupF...
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3628 Changed all file1.renameTo(file2) calls to...
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
2020-09-14
Ben Soares
Merge branch 'feature/JAL-3615gzipXfam' into develop
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
2020-08-17
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
2020-08-09
Ben Soares
JAL-3691 Changed .toUppoerCase().startsWith(...) to...
tree
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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
2020-07-27
Jim Procter
JAL-3696 log the error message from the exception to...
tree
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commitdiff
2020-07-06
gmungoc
JAL-3311 JAL-3141 JAL-3144 tidying obsolete message...
tree
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commitdiff
2020-07-02
gmungoc
JAL-2656 JAL-3615 check response headers to test for...
tree
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commitdiff
2020-07-02
gmungoc
JAL-3615 used gzip endpoints for Pfam and Rfam
tree
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
tree
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
tree
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commitdiff
2020-04-21
Jim Procter
Merge branch 'bug/JAL-3567virtualFeatureCoordinates...
tree
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commitdiff
2020-04-21
gmungoc
JAL-3603 load annotation file from RELATIVE_URL in...
tree
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commitdiff
2020-04-17
gmungoc
JAL-3567 unit tests for linked feature tooltips
tree
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commitdiff
2020-04-16
gmungoc
JAL-3567 report mapped location for virtual features...
tree
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commitdiff
2020-04-14
Jim Procter
Merge branch 'bug/JAL-3529_uniprotidsinstockholm' into...
tree
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commitdiff
2020-04-14
gmungoc
JAL-3583 remove debug logging, Javadoc added
tree
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commitdiff
2020-03-31
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2020-03-30
Jim Procter
JAL-3407 JAL-3130 back out java 9+ syntax that breaks...
tree
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2020-03-06
gmungoc
Merge branch 'feature/JAL-3468featureDescriptionEllipsi...
tree
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commitdiff
2020-03-04
Ben Soares
JAL-3468 small tidy
tree
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commitdiff
2020-03-04
Ben Soares
JAL-3468 improvement to feature description truncation...
tree
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commitdiff
2020-03-04
Ben Soares
JAL-3468 Obsessively fixed self-closing <br/> tags
tree
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commitdiff
2020-03-03
soares
JAL-3468 Adapted methods to report how many features...
tree
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commitdiff
2020-02-18
Jim Procter
JAL-3529 attempt to guess database for a sequence’s...
tree
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commitdiff
2020-02-14
Jim Procter
JAL-3532 TODO comment
tree
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commitdiff
2020-02-14
Jim Procter
JAL-3529 preferentially output source dbrefs or princip...
tree
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commitdiff
2020-01-28
gmungoc
Merge branch 'feature/JAL-3121gffAttributeMap' into...
tree
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commitdiff
2020-01-24
gmungoc
JAL=3121 more data format validation/tests, help text...
feature/JAL-3121gffAttributeMap
tree
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commitdiff
2020-01-23
gmungoc
JAL-3121 'attributes map' in GFF3 without special ...
tree
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commitdiff
2019-11-01
Ben Soares
JAL-3474 removed all .cvsignore files stored in the...
improvement/JAL-3474_lots_of_.cvsignore_files
tree
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commitdiff
2019-10-31
gmungoc
JAL-3468 truncate feature description to 40 chars in...
tree
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-08-22
gmungoc
JAL-3121 slightly cleaner parsing of, and unit test...
tree
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commitdiff
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
tree
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commitdiff
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
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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
2019-04-18
hansonr
explicit Hashtable objects
tree
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commitdiff
2019-04-17
gmungoc
JAL-3026 fix bug loading Jalview Project (in Java)
tree
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commitdiff
2019-04-04
gmungoc
JAL-3220 j2sIgnore on 3 more main methods
tree
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commitdiff
2019-04-04
gmungoc
JAL-3220 j2sIgnore on main methods on test / utility...
tree
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commitdiff
2019-04-03
hansonr
replacing @j2sNative with @j2sIgnore where appropriate...
tree
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commitdiff
2019-04-03
hansonr
j2sNative clean-up. Fixes problem with second try of...
tree
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commitdiff
2019-03-27
hansonr
consolidation of Platform isJS calls
tree
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commitdiff
2019-03-27
hansonr
isJS cleanup
tree
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commitdiff
2019-03-27
hansonr
clean-up of isJS business for (temporarily) noneditable...
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
2019-03-14
gmungoc
JAL-3210 JAL-3141 JAL-3056 disable backups in JalviewJS
tree
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commitdiff
2019-03-13
gmungoc
JAL-3210 merge conflict tidying
tree
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commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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
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