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jalview.git
2014-05-02 Jim ProcterMerge branch 'Release_2_8_1_Branch' into JAL-1372_refer... commit | commitdiff | tree | snapshot
2014-05-02 Jim ProcterMerge branch 'JAL-1397' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-05-02 Jim ProcterJAL-1397 JAL-1066 JAL-1233 refactored annotation colour... commit | commitdiff | tree | snapshot
2014-05-02 Jim ProcterJAL-1369 JAL-1397 version check to support correct... commit | commitdiff | tree | snapshot
2014-05-02 Jim Procterformatting commit | commitdiff | tree | snapshot
2014-05-02 Jim ProcterJAL-1233 JAL-1066 fix for JAL-1397 test: allow per... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1397 (probably buggy) test for recovery of backgrou... commit | commitdiff | tree | snapshot
2014-05-01 Jim Procterremove todo commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1492 formatting and squash NPEs commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1092 TODO - allow Jalview/JalviewLite to generate... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1492 JAL-1397 make AnnotatedCollectionI context... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1492 JAL-1397 JAL-643 JAL-969 factory method to... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on... commit | commitdiff | tree | snapshot
2014-05-01 Jim Procterjavadoc commit | commitdiff | tree | snapshot
2014-05-01 Jim Procterproperly quit so JUnit marks tests as successful commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-1497 check to see if tree structure is ready for... commit | commitdiff | tree | snapshot
2014-05-01 Jim Procterfix for JAL-1495 - initialise menu entry from current... commit | commitdiff | tree | snapshot
2014-05-01 Jim Procterfix for JAL-1494 tweaked logic to fix NPEs and modify... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-969 remove unnecessary overrides commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-961 configure conservation worker from alignment... commit | commitdiff | tree | snapshot
2014-05-01 Jim ProcterJAL-961 store result of conservation analysis worker... commit | commitdiff | tree | snapshot
2014-05-01 Jim Proctermake sure valid value for non-gapped calculation with... commit | commitdiff | tree | snapshot
2014-04-29 Jim ProcterJAL-643 - abstracted colourscheme components to allow... commit | commitdiff | tree | snapshot
2014-04-29 Jim ProcterMerge branch 'JAL-1340_redundancy' into Release_2_8_1_B... commit | commitdiff | tree | snapshot
2014-04-28 Jim ProcterJAL-1340 mark redundant sequences as soon as redundancy... commit | commitdiff | tree | snapshot
2014-04-28 Jim ProcterJAL-1340 simpler and more efficient interactive highlig... commit | commitdiff | tree | snapshot
2014-04-28 Jim ProcterJAL-1340 ensure slider value wide enough to see three... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterMerge branch 'JAL-1322' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-1322 avoid rounding error causing non functional... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-1322 allow slider to reach maximum value for parameter commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-1322 only update slider when return is pressed commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterMerge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterMerge branch 'JAL-1164_regression' into Release_2_8_1_B... commit | commitdiff | tree | snapshot
2014-04-27 Jim Procterworkaround for JAL-1319 - catch unexpected NPE thrown... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-1164 (regression) reinstate 'apply disorder predict... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-952 JAL-1268 document TCoffee and RNA helices colou... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-952 JAL-1268 document RNA Helices and T-Coffee... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-952 JAL-1268 add RNA Helices and T-Coffee to list... commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-952 resolve colour scheme as 'RNA Helices' commit | commitdiff | tree | snapshot
2014-04-27 Jim ProcterJAL-952 refactor code to select annotation for colourin... commit | commitdiff | tree | snapshot
2014-04-27 Jim Proctertest for JAL-952 commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterMerge branch 'JAL-1177_prop_rnasecstr' into Release_2_8... commit | commitdiff | tree | snapshot
2014-04-25 Jim Procterfix for JAL-1268 commit | commitdiff | tree | snapshot
2014-04-25 Jim Proctertest for JAL-1268 commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterJAL-1177 additional saveState calls to write a dataset... commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterJAL-1177 patches to loader to cope with dataset only... commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterJAL-1177 new flag to write a dataset only jalview XML... commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterJAL-1177 allow jalview alignments to be saved that... commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterJAL-1177 propagate sequence associated annotation to... commit | commitdiff | tree | snapshot
2014-04-25 Jim ProcterJAL-1177 refactored command line test harness commit | commitdiff | tree | snapshot
2014-04-25 Jim Proctertest for JAL-1177 store and recover RNA secondary struc... commit | commitdiff | tree | snapshot
2014-04-24 Jim ProcterJAL-1232 fix - ensure display all columns flag is set... commit | commitdiff | tree | snapshot
2014-04-23 Jim ProcterMerge branch 'JAL-1486_hiddenStartEnd' into Release_2_8... commit | commitdiff | tree | snapshot
2014-04-23 Jim ProcterJAL-1486 todo for 2.8.2 release commit | commitdiff | tree | snapshot
2014-04-23 Jim ProcterMerge branch 'jims_marckhacks' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1458 updated logo for installer commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1383 scrubbed envision GUI and documentation commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1355 keys for colours commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterfix for JAL-1438 commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterMerge branch 'jims_marckhacks' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 define defaults for DNA/Protein PCA calculation commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1485 JAL-1483 show i18n key for different available... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 JAL-1355 i18n for score model submenu commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1485 JAL-1473 use compound i18n messages to constru... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1485 commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1484 always update the dataset sequence if 'trimDat... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1466 don't include empty columns if no upstream... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1355 JAL-1466 i18n for flanking sequence menu entry... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterMerge branch 'jims_marckhacks' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-741 (poss related JAL-971) - fix NPE raised when... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1476 JAL-1016 avoid NPE messiness if structures... commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterdon't unhook existing group associated annotation JAL... commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterfix for JAL-1478 commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1478 test to demonstrate bug commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1477 tooltip commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1476 - don't send broken commands to Jmol when... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1477 first implementation of 'View all representati... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1466 import full length sequence to dataset sequenc... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1466 flag and jalview_properties setting to control... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1466 improved test and patched off by one that... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1466 new calculation menu option to recover the... commit | commitdiff | tree | snapshot
2014-04-21 Jim Proctertidy imports commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterpatch v2 for JAL-1474 add the newly recovered dataset... commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterpatch v1 for JAL-1474 - make sure we actually set the... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1474 note about buggy 'merge sequence' operation... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 tree calcs performed with ScoreModelI instances commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterdon't finness the alignment annotation modification... commit | commitdiff | tree | snapshot
2014-04-21 Jim Procterpatch for JAL-1465 - set min/max thresholds for each... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 menu entries for different score models availa... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 provide Amino acid physicochemical conservatio... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 show available score matrices for use in PCA... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1473 refactor score matrices and tree score calcula... commit | commitdiff | tree | snapshot
2014-04-21 Jim ProcterJAL-1355 missing message commit | commitdiff | tree | snapshot
2014-04-06 Jim Procterfix for JAL-1464 avoid NPE with per-sequence annotation... commit | commitdiff | tree | snapshot
2014-04-05 Jim ProcterMerge branch 'r281_JAL-1211' into Release_2_8_1_Branch commit | commitdiff | tree | snapshot
2014-04-04 Jim ProcterJAL-1211 - set annotation panel height according to... commit | commitdiff | tree | snapshot
2014-04-04 Jim ProcterJAL-1211 - pick up site-defined defined window geometry... commit | commitdiff | tree | snapshot
2014-04-04 Jim Procterfix for JAL-1461 - check that filetype setting in brows... commit | commitdiff | tree | snapshot
2014-04-04 Jim ProcterMerge branch 'Release_2_8_1_Branch_i18n' into Release_2... commit | commitdiff | tree | snapshot
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