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JAL-2349 JAL-3855 resolve sequence position for contact lookup and catch out bound...
[jalview.git]
/
src
/
jalview
/
2021-02-18
gmungoc
JAL-2422 remove temporary patch (requires ChimeraX...
tree
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commitdiff
2021-02-17
Jim Procter
JAL-3821 patch for 2.11.2 to retrieve RNA ENA records...
patch/for2.11.2/JAL-3821_ena_rna_moltype
tree
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commitdiff
2021-02-17
Jim Procter
Merge branch 'feature/JAL-3692enaEndpoint' into patch...
tree
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commitdiff
2021-02-11
gmungoc
JAL-3818 process Jmol callbacks in AWT thread
bug/JAL-3818_jmolDeadlock
tree
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commitdiff
2021-02-10
Ben Soares
JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClas...
tree
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commitdiff
2021-02-10
Ben Soares
JAL-3521 Change grouped Jalview windows on linux taskba...
tree
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commitdiff
2021-02-05
Jim Procter
JAL-3814 don’t automatically launch the news browser...
tree
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commitdiff
2021-02-05
Jim Procter
JAL-3813 NOIDENTIFIERSSERVICE preference disables jalvi...
tree
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commitdiff
2021-02-05
Jim Procter
JAL-3812 new argument ‘-nohtmltemplates’ and user prefe...
tree
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commitdiff
2021-02-05
Jim Procter
JAL-3811 document SHOW_JWS2_SERVICES user preference...
tree
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commitdiff
2021-02-05
Jim Procter
JAL-3814 NONEWS property
tree
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commitdiff
2021-02-04
gmungoc
JAL-2422 a fix and a fudge for two failing ChimeraX...
tree
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commitdiff
2021-02-04
gmungoc
JAL-3806 fix and test for one-to-many sequence mapping...
bug/JAL-3806_mappingCoversCDS_reprise
tree
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commitdiff
2021-01-28
gmungoc
JAL-3806 more lax allowance (3 positions) for stop...
tree
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commitdiff
2021-01-21
gmungoc
JAL-3038 corrected code that reads editable JComboBox...
tree
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commitdiff
2020-12-14
Ben Soares
JAL-3280 Fixed the version checking URL formulation...
Develop-2_11_2_0-d20201215
tree
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commitdiff
2020-12-14
Ben Soares
JAL-3594 Allow setting of getdownappbase and getdowndis...
tree
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commitdiff
2020-12-14
Ben Soares
JAL-3280 Test for remote release build_properties file...
tree
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commitdiff
2020-12-14
Ben Soares
JAL-3280 fixes after CR-JAL-241. Now only checking...
tree
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commitdiff
2020-12-14
Ben Soares
JAL-3280 Pass appbase and appdir from getdown to jalvew...
tree
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commitdiff
2020-12-11
Ben Soares
JAL-3594 Defintely want SplashScreen to appear in the...
tree
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commitdiff
2020-12-11
Ben Soares
JAL-3594 Adjustments to allow JalviewJS to use ChannelP...
tree
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commitdiff
2020-12-11
Ben Soares
JAL-3775 JAL-3633 Make java.net.Authenticator code...
tree
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commitdiff
2020-12-09
Ben Soares
JAL-3594 Images for splash screen
tree
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commitdiff
2020-12-09
Ben Soares
JAL-3594 JAL-3728 Added taskbar icons to desktop and...
tree
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commitdiff
2020-12-08
Ben Soares
Merge branch 'merge/develop_and_rebase_squashed_merge_J...
tree
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commitdiff
2020-12-08
Ben Soares
JAL-3594 Change main window title
tree
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commitdiff
2020-12-07
Ben Soares
JAL-3594 added BG logo. Changed some named Jalviews...
tree
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commitdiff
2020-12-05
Ben Soares
JAL-3594 Default values for channel properties defined...
tree
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commitdiff
2020-12-04
Ben Soares
JAL-3594 Added rotating logo png
tree
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commitdiff
2020-12-04
Ben Soares
JAL-3594 New jalview.util.ChannelProperties to get...
tree
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commitdiff
2020-12-01
Ben Soares
JAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting
tree
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commitdiff
2020-12-01
Ben Soares
JAL-3609 JAL-3775 Refactoring a bit of jalview.bin...
tree
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commitdiff
2020-12-01
Ben Soares
JAL-3660 Fix for specified output format when using...
tree
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commitdiff
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
2020-10-29
Jim Procter
JAL-3759 exclude hidden columns when processing...
tree
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commitdiff
2020-10-29
Jim Procter
Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11...
tree
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commitdiff
2020-10-29
gmungoc
JAL-3700 mapped sequence group includes short (or all...
patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
tree
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commitdiff
2020-10-28
Jim Procter
JAL-3725 patch EMBL flat file to exclude stop codon...
tree
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commitdiff
2020-10-28
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2020-10-28
gmungoc
JAL-3725 helper methods for computing mapped feature...
tree
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commitdiff
2020-10-28
gmungoc
JAL-3725 exclude stop codon from CDS-to-protein mapping
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
Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides...
tree
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commitdiff
2020-10-28
Jim Procter
fix for JAL-3765
tree
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commitdiff
2020-10-27
Jim Procter
JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
tree
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commitdiff
2020-10-22
gmungoc
JAL-3751 only merge strictly contiguous ranges of mappings
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 failsafe check for null
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 always make a new dataset sequence for CDS...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3700 additions and corrections to unit tests
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
task/JAL-3763_newDatasetForCds
tree
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commitdiff
2020-10-22
gmungoc
JAL-3751 only merge strictly contiguous ranges of mappings
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
tree
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commitdiff
2020-10-20
Jim Procter
fix for JAL-3765
tree
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commitdiff
2020-10-15
gmungoc
JAL-3763 unused method removed
tree
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commitdiff
2020-10-08
gmungoc
JAL-3763 failsafe check for null
tree
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commitdiff
2020-10-08
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
tree
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commitdiff
2020-10-08
gmungoc
JAL-3763 always make a new dataset sequence for CDS...
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
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