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JAL-3829 isCanonical should by default be false - ensure JalviewJS offers 3d-beacons...
[jalview.git]
/
src
/
jalview
/
2020-12-01
Ben Soares
JAL-3530 Added a -nowebservicediscovery command line...
tree
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commitdiff
2020-11-27
Ben Soares
JAL-3660 Fix for specified output format when using...
tree
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commitdiff
2020-11-13
Jim Procter
JAL-3757 JAL-3689 use AppletFormat.checkProtocol to...
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3757 JAL-3689 Fixed checks for URLs by adding check...
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3775 Eclipse re-formatting commit
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3633 last minute refinement so password box doesn...
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3633 Apply (proxy) button enabled when needed
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
2020-11-13
Ben Soares
JAL-3275 JAL-3633: JAL-3275 Turned Preferences into...
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3633 Set proxy preferences before web calls in...
tree
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commitdiff
2020-11-13
Ben Soares
JAL-3633 Memory only proxy auth password storage. Open...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3633 Added Proxy Authentication credentials in...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3633 Added Preferences for Proxy Authentication...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3633 label.proxy_server -> label.proxy_servers
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3633 Remember system set proxy properties. Add...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3633 ensure check both or https:// for urls
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3628 Error when saving alert box has been moved...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3676 More explicit tooltip about resetting log...
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-3676 improvement for visual selection of console...
tree
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commitdiff
2020-11-10
Ben Soares
JAL-3676 code review -- added non-listed Level into...
tree
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commitdiff
2020-11-10
Ben Soares
JAL-3676 Added Log Level ComboBox and Copy to Clipboard...
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
2020-11-06
Ben Soares
JAL-3609 formatting save after cherry-picks
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3609 Report when scale setting used.
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3609 New auto-scale 'formula' for linux HiDPI....
tree
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commitdiff
2020-11-06
soares
JAL-3609 corrected maxdimension to mindimension. Adjust...
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3609 removed debugging prints
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3609 changed property names to something more palat...
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3609 system properties to force a scale, or automat...
tree
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commitdiff
2020-11-06
Ben Soares
JAL-3609 Added a -DforceHiDPISetting=true option mainly...
tree
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commitdiff
2020-11-05
Ben Soares
JAL-3608 cherry pick of 92cb745e7
tree
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commitdiff
2020-10-28
Jim Procter
JAL-3760 refactor nucleotide proportion test to per...
tree
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commitdiff
2020-10-28
Jim Procter
fix for JAL-3765
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 check for !args || args=="" before overwriting
Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 more typo fixing :q
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 syntax error typo
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 check if Info.args already defined before...
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 '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
2020-08-31
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
2020-08-24
gmungoc
JAL-3018 updated reviewed REST version to 12.0
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
2020-08-17
Jim Procter
Merge branch 'task/JAL-3597memoryLeakTest' into develop
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
2020-08-09
Ben Soares
JAL-3691 Changed .toUppoerCase().startsWith(...) to...
tree
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commitdiff
2020-08-05
gmungoc
JAL-3692 parse multiline feature qualifiers and escaped...
tree
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commitdiff
2020-08-04
Ben Soares
JAL-3477 Added -help text for jvmmempc and jvmmemmax...
tree
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commitdiff
2020-08-03
Jim Procter
Merge branch 'bug/JAL-2983negativeSliderMin' into develop
tree
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commitdiff
2020-07-29
Jim Procter
JAL-3371 JAL-2983 don't modify 'extent' of slider ...
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
gmungoc
JAL-3692 set CDS /product as EMBLCDSPROTEIN description
tree
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commitdiff
2020-07-27
gmungoc
JAL-3692 refactor/complete parsing, more unit test...
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
2020-07-24
gmungoc
JAL-3692 parse DE for description, and other refactoring...
tree
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commitdiff
2020-07-22
gmungoc
JAL-3692 unit test (J03321), fixes, dbrefs; todo: prote...
tree
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commitdiff
2020-07-21
gmungoc
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
tree
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commitdiff
2020-07-14
gmungoc
JAL-1421 last change tidied up properly
tree
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commitdiff
2020-07-14
gmungoc
JAL-1421 types added to nameHash and nodeHash maps
tree
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commitdiff
2020-07-14
gmungoc
JAL-3597 additional references nulled, bug in test...
tree
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commitdiff
2020-07-07
Ben Soares
JAL-3608 Changes from code review CR-JAL-236
tree
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commitdiff
2020-07-07
gmungoc
JAL-1424 streamlined message checker, corrected applet...
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
2020-06-29
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2020-06-29
Jim Procter
JAL-3493 clear search highlights when escape/deselect all
tree
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commitdiff
2020-06-29
gmungoc
JAL-3674 more finessed asynchronous structure commands
tree
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commitdiff
2020-06-29
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2020-06-29
gmungoc
JAL-3518 corrected pulled up focusView() command
tree
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commitdiff
2020-06-29
gmungoc
JAL-3518 corrected action on pulled up closeViewer()
tree
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commitdiff
2020-06-28
gmungoc
JAL-3551 PyMOL command constants tidied
tree
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commitdiff
2020-06-28
gmungoc
JAL-3551 fit to window (zoom) command for PyMOL
tree
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commitdiff
2020-06-26
Jim Procter
JAL-3673 make sure font metrics are updated if dealing...
tree
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commitdiff
2020-06-26
Jim Procter
JAL-3518 fix highlighting in Jalview for selections...
tree
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commitdiff
2020-06-26
Jim Procter
JAL-3672 more efficient when debug not enabled
tree
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commitdiff
2020-06-26
Jim Procter
JAL-3671 hardwire log4j.root logger to INFO to supress...
tree
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commitdiff
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