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JAL-4020 Added the +2 arg for PyMOLWin.exe allowing older versions of PyMOL
[jalview.git] / src /
2020-12-11 Ben SoaresJAL-3775 JAL-3633 Make java.net.Authenticator code... tree | commitdiff
2020-12-09 Ben SoaresJAL-3594 Images for splash screen tree | commitdiff
2020-12-09 Ben SoaresJAL-3594 JAL-3728 Added taskbar icons to desktop and... tree | commitdiff
2020-12-08 Ben SoaresMerge branch 'merge/develop_and_rebase_squashed_merge_J... tree | commitdiff
2020-12-08 Ben SoaresJAL-3594 Change main window title tree | commitdiff
2020-12-07 Ben SoaresJAL-3594 added BG logo. Changed some named Jalviews... tree | commitdiff
2020-12-05 Ben SoaresJAL-3594 Default values for channel properties defined... tree | commitdiff
2020-12-04 Ben SoaresJAL-3594 Added rotating logo png tree | commitdiff
2020-12-04 Ben SoaresJAL-3594 New jalview.util.ChannelProperties to get... tree | commitdiff
2020-12-01 Ben SoaresJAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting tree | commitdiff
2020-12-01 Ben SoaresJAL-3609 JAL-3775 Refactoring a bit of jalview.bin... tree | commitdiff
2020-12-01 Ben SoaresJAL-3660 Fix for specified output format when using... tree | commitdiff
2020-12-01 Ben SoaresJAL-3530 Added a -nowebservicediscovery command line... tree | commitdiff
2020-11-27 Ben SoaresJAL-3660 Fix for specified output format when using... tree | commitdiff
2020-11-13 Jim ProcterJAL-3757 JAL-3689 use AppletFormat.checkProtocol to... tree | commitdiff
2020-11-13 Ben SoaresJAL-3757 JAL-3689 Fixed checks for URLs by adding check... tree | commitdiff
2020-11-13 Ben SoaresJAL-3775 Eclipse re-formatting commit tree | commitdiff
2020-11-13 Ben SoaresJAL-3633 last minute refinement so password box doesn... tree | commitdiff
2020-11-13 Ben SoaresJAL-3633 Apply (proxy) button enabled when needed tree | commitdiff
2020-11-13 Ben SoaresJAL-3633 Small changes to allow future fitting with... tree | commitdiff
2020-11-13 Ben SoaresJAL-3275 JAL-3633: JAL-3275 Turned Preferences into... tree | commitdiff
2020-11-13 Ben SoaresJAL-3633 Set proxy preferences before web calls in... tree | commitdiff
2020-11-13 Ben SoaresJAL-3633 Memory only proxy auth password storage. Open... tree | commitdiff
2020-11-12 Ben SoaresJAL-3633 Added Proxy Authentication credentials in... tree | commitdiff
2020-11-12 Ben SoaresJAL-3633 Added Preferences for Proxy Authentication... tree | commitdiff
2020-11-12 Ben SoaresJAL-3633 label.proxy_server -> label.proxy_servers tree | commitdiff
2020-11-12 Ben SoaresJAL-3633 Remember system set proxy properties. Add... tree | commitdiff
2020-11-12 Ben SoaresJAL-3633 ensure check both or https:// for urls tree | commitdiff
2020-11-12 Ben SoaresJAL-3628 Error when saving alert box has been moved... tree | commitdiff
2020-11-12 Ben SoaresJAL-3676 More explicit tooltip about resetting log... tree | commitdiff
2020-11-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error... tree | commitdiff
2020-11-10 Ben SoaresJAL-3676 improvement for visual selection of console... tree | commitdiff
2020-11-10 Ben SoaresJAL-3676 code review -- added non-listed Level into... tree | commitdiff
2020-11-10 Ben SoaresJAL-3676 Added Log Level ComboBox and Copy to Clipboard... tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 Fix for slightly incorrect boolean usage to... tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 Even more Cache.log.debug statements tree | commitdiff
2020-11-10 Ben SoaresJAL-3628 More Cache.log.debug statements tree | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... tree | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed all file1.renameTo(file2) calls to... tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 formatting save after cherry-picks tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 Report when scale setting used. tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 New auto-scale 'formula' for linux HiDPI.... tree | commitdiff
2020-11-06 soaresJAL-3609 corrected maxdimension to mindimension. Adjust... tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 removed debugging prints tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 changed property names to something more palat... tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 system properties to force a scale, or automat... tree | commitdiff
2020-11-06 Ben SoaresJAL-3609 Added a -DforceHiDPISetting=true option mainly... tree | commitdiff
2020-11-05 Ben SoaresJAL-3608 cherry pick of 92cb745e7 tree | commitdiff
2020-10-29 Jim Procter JAL-3759 exclude hidden columns when processing... tree | commitdiff
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11... tree | commitdiff
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3 tree | commitdiff
2020-10-28 Jim ProcterJAL-3725 patch EMBL flat file to exclude stop codon... tree | commitdiff
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2020-10-28 Jim ProcterJAL-3760 refactor nucleotide proportion test to per... tree | commitdiff
2020-10-28 Jim ProcterMerge branch 'bug/JAL-3760_protsTreatedAsNucleotides... tree | commitdiff
2020-10-28 Jim Procterfix for JAL-3765 tree | commitdiff
2020-10-27 Jim ProcterJAL-3700 JAL-3748 JAL-3763 don’t add stop codon via... tree | commitdiff
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests tree | commitdiff
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... tree | commitdiff
2020-10-22 gmungocJAL-3763 failsafe check for null tree | commitdiff
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual... tree | commitdiff
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS... tree | commitdiff
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests tree | commitdiff
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests task/JAL-3763_newDatasetForCds tree | commitdiff
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... tree | commitdiff
2020-10-20 Jim Procterfix for JAL-3765 tree | commitdiff
2020-10-15 gmungocJAL-3763 unused method removed tree | commitdiff
2020-10-08 gmungocJAL-3763 failsafe check for null tree | commitdiff
2020-10-08 gmungocJAL-3763 refactored getCoveringMapping for virtual... tree | commitdiff
2020-10-08 gmungocJAL-3763 always make a new dataset sequence for CDS... tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 check for !args || args=="" before overwriting Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 more typo fixing :q tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 syntax error typo tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 check if Info.args already defined before... tree | commitdiff
2020-09-29 Jim ProcterJAL-3760 refactor nucleotide proportion test to per... tree | commitdiff
2020-09-24 Jim ProcterJAL-3757 JAL-3689 use AppletFormat.checkProtocol to... tree | commitdiff
2020-09-23 Ben SoaresJAL-3757 JAL-3689 Fixed checks for URLs by adding check... tree | commitdiff
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2 tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 fix compilation error tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally... tree | commitdiff
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct... tree | commitdiff
2020-09-21 Jim ProcterMerge branch 'merge_review/JAL-3490_2_11_2_develop... tree | commitdiff
2020-09-17 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... tree | commitdiff
2020-09-17 Jim ProcterJAL-3750 parse protocol before checking if argument... tree | commitdiff
2020-09-17 gmungocJAL-3700 additions and corrections to unit tests bug/JAL-3700_mapSequenceSelection tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 preserve sequence IDs from original alignment... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 recover complement alignment from complement... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... tree | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq... tree | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true... tree | commitdiff
2020-09-16 Jim ProcterMerge branch 'failingTest/JAL-3748_reconstructCDSafterP... tree | commitdiff
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands tree | commitdiff
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching... tree | commitdiff
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