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2024-01-23 James ProcterMerge branch 'develop' into features/JAL-34_comparing_msas features/JAL-34_comparing_msas commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 invokeAndWait to avoid hang whilst calling... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'features/JAL-4366_foldseek_3di_viewing... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4371 minimal test and move PDBEntryUtils to correct... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 invokeAndWait to avoid hang whilst calling... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 uniprotkb - try to avoid another redirect... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 use rest.uniprot.org as fetch domain commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignor... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'bug/JAL-4368_default_colourscheme_applied... commit | commitdiff | tree | snapshot
2024-01-19 Ben SoaresJAL-4373 Setting the jvmmempc and jvmmemmax strings... bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch commit | commitdiff | tree | snapshot
2024-01-19 Ben SoaresJAL-4373 Fix Main-Class and other attribute settings... commit | commitdiff | tree | snapshot
2024-01-18 James ProcterJAL-34 fix up comparison annotation so it gets shown... commit | commitdiff | tree | snapshot
2024-01-18 James ProcterJAL-34 mouse over ruler in one alignment highlights... commit | commitdiff | tree | snapshot
2024-01-17 James ProcterJAL-34 - quick hack to see how we can do alignment... commit | commitdiff | tree | snapshot
2024-01-16 James ProcterJAL-4366 JAL-728 show 3di-Mat based quality in the... commit | commitdiff | tree | snapshot
2024-01-16 James ProcterJAL-4366 JAL-728 simple hack to use 3di matrix when... commit | commitdiff | tree | snapshot
2024-01-15 James ProcterJAL-4366 JAL-4371 allow cruft after inferred pdb ids... commit | commitdiff | tree | snapshot
2024-01-14 James ProcterJAL-4366 JAL-3947 avoid ambiguity for multi character... commit | commitdiff | tree | snapshot
2024-01-14 James ProcterJAL-4366 JAL-4371 tighten up detection of chain code... commit | commitdiff | tree | snapshot
2024-01-14 James ProcterJAL-4366 revive broken alignDNAasDNA test commit | commitdiff | tree | snapshot
2024-01-14 James ProcterJAL-4366 JAL-4371 fix imports commit | commitdiff | tree | snapshot
2024-01-14 James ProcterJAL-4366 avoid corrupting map when no complete mapping... commit | commitdiff | tree | snapshot
2024-01-14 James ProcterJAL-4366 JAL-4371 refactor and fix up code inferring... commit | commitdiff | tree | snapshot
2024-01-12 James ProcterJAL-4366 provide options for updating (or not) the... commit | commitdiff | tree | snapshot
2024-01-12 James ProcterJAL-4366 fixed wrinkles in reconstructing peptide align... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 fix reconstruction of peptide alignment... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 test reconstruction of peptide alignment given... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 use dataset sequences for building the mapping commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4371 make the PDB fetcher use simple naming 1xyzA... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-3466 higher ‘crummy alignment’ threshold when decid... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 remove some tortuous repetition in computeMapp... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 incomplete test verifying a 3di alignment... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 new mapping type for 3di/protein sequence... commit | commitdiff | tree | snapshot
2024-01-11 James ProcterJAL-4366 allow a 3di alignment to be loaded and shown... commit | commitdiff | tree | snapshot
2024-01-05 Ben SoaresJAL-4368 Only set a colour scheme if --colour is given... bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately commit | commitdiff | tree | snapshot
2023-12-17 James ProcterJAL-4366 account for 3dmat matrix in tests commit | commitdiff | tree | snapshot
2023-12-16 James ProcterJAL-4366 1:1 mapping requires exact sequence length... commit | commitdiff | tree | snapshot
2023-12-16 James ProcterJAL-789 pairwise alignment via calculations dialog... commit | commitdiff | tree | snapshot
2023-12-16 James ProcterJAL-4366 mat3di score model commit | commitdiff | tree | snapshot
2023-12-15 James ProcterJAL-4366 hacked in a 1:1 mapping commit | commitdiff | tree | snapshot
2023-12-15 James ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2023-12-15 James ProcterJAL-4366 build a mapping to a PDBChain with an arbitrar... commit | commitdiff | tree | snapshot
2023-12-15 James ProcterJAL-4366 compute coverage on each side of the pairwise... commit | commitdiff | tree | snapshot
2023-12-14 James ProcterJAL-4356 update release notes commit | commitdiff | tree | snapshot
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
2023-12-14 James ProcterJAL-4353 wait for files to be written fully before... commit | commitdiff | tree | snapshot
2023-12-14 James ProcterJAL-4217 singleThread all tests commit | commitdiff | tree | snapshot
2023-12-14 James ProcterMerge branch 'bug/JAL-2934proportionalScrolling' into... commit | commitdiff | tree | snapshot
2023-12-14 James ProcterMerge branch 'develop' into bug/JAL-2934proportionalScr... bug/JAL-2934proportionalScrolling commit | commitdiff | tree | snapshot
2023-12-12 Ben SoaresJAL-4353 bigger tighter test commit | commitdiff | tree | snapshot
2023-12-12 James ProcterJAL-4217 don’t try and export an image when Jmol is... commit | commitdiff | tree | snapshot
2023-12-12 Ben SoaresMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
2023-12-12 James ProcterMerge branch 'develop' into bug/JAL-4353_cannot_output_... commit | commitdiff | tree | snapshot
2023-12-12 James ProcterJAL-4217 close internal frame on the swing thread to... commit | commitdiff | tree | snapshot
2023-12-12 Ben SoaresJAL-4353 helper method and test for primary/secondary... commit | commitdiff | tree | snapshot
2023-12-12 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
2023-12-12 James ProcterJAL-4353 failing test commit | commitdiff | tree | snapshot
2023-12-12 James ProcterJAL-4353 fix assert that successive test output files... commit | commitdiff | tree | snapshot
2023-12-11 James ProcterJAL-4192 more specific info about versions needed commit | commitdiff | tree | snapshot
2023-12-06 Ben SoaresJAL-4353 re-used random color code commit | commitdiff | tree | snapshot
2023-12-06 Ben SoaresJAL-4353 Preserve the user given 'linkedId' with ArgVal... commit | commitdiff | tree | snapshot
2023-12-06 James ProcterJAL-4356 bump RELEASE commit | commitdiff | tree | snapshot
2023-12-06 James ProcterJAL-4356 new release notes and whats new for 2.11.3... commit | commitdiff | tree | snapshot
2023-12-06 James ProcterMerge branch 'patch/JAL-840_clustalx_docs_fix' into... commit | commitdiff | tree | snapshot
2023-12-06 James ProcterMerge branch 'bug/JAL-2934proportionalScrolling' into... commit | commitdiff | tree | snapshot
2023-12-06 Ben SoaresJAL-4353 Add a 'random' colour to produce a random... commit | commitdiff | tree | snapshot
2023-12-05 Ben SoaresJAL-4353 Add secondary Types for Args, for STRUCTUREIMA... commit | commitdiff | tree | snapshot
2023-12-01 Ben SoaresJAL-4243 Updated bio.tools record and JSON (version... commit | commitdiff | tree | snapshot
2023-11-30 James ProcterJAL-4351 update release notes for JAL-4342 commit | commitdiff | tree | snapshot
2023-11-30 James ProcterMerge branch 'patch/JAL-4342_emptyannotationsexport... commit | commitdiff | tree | snapshot
2023-11-30 James ProcterJAL-4342 test and patch checking annotation csv export... patch/JAL-4342_emptyannotationsexport commit | commitdiff | tree | snapshot
2023-11-30 James ProcterPatch fixes JAL-4165 - added to release notes JAL-4351 commit | commitdiff | tree | snapshot
2023-11-30 James ProcterJAL-4351 2.11.3.2 scheduled for 1st December release commit | commitdiff | tree | snapshot
2023-11-30 James ProcterMerge branch 'bug/JAL-4344_structureimage_cl_arg_only_c... commit | commitdiff | tree | snapshot
2023-11-30 Ben SoaresJAL-4344 careful application of -Djava.awt.headless... commit | commitdiff | tree | snapshot
2023-11-22 James ProcterJAL-4343 fix insufficient-caffeine error - add whats... commit | commitdiff | tree | snapshot
2023-11-22 James ProcterJAL-4343 release today, update notes for JAL-4348 and... commit | commitdiff | tree | snapshot
2023-11-22 James ProcterMerge branch 'patch/JAL-4345_pae_epas1_doubleclick... commit | commitdiff | tree | snapshot
2023-11-21 James ProcterJAL-4345 patch and release notes patch/JAL-4345_pae_epas1_doubleclick commit | commitdiff | tree | snapshot
2023-11-20 Ben SoaresJAL-4348 Add newer versions of Chimera and ChimeraX... commit | commitdiff | tree | snapshot
2023-11-20 James ProcterJAL-4343 patch for JAL-4347 uniprot non-pos feature... commit | commitdiff | tree | snapshot
2023-11-17 James ProcterJAL-4343 release notes for JAL-4340 and JAL-4243 commit | commitdiff | tree | snapshot
2023-11-17 James ProcterJAL-4343 bump version commit | commitdiff | tree | snapshot
2023-11-16 Ben SoaresJAL-4243 Updated bio.tools record for 2.11.3.0 commit | commitdiff | tree | snapshot
2023-11-16 Ben SoaresJAL-4340 Change launch scripts to be xresources to... commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 JAL-4334 patch in release notes commit | commitdiff | tree | snapshot
2023-11-15 James ProcterMerge branch 'bug/JAL-4334_unknownstartenduniprotfeatur... commit | commitdiff | tree | snapshot
2023-11-15 James ProcterMerge branch 'patch/JAL-4222_100s_timeout_on_imagexport... commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4273 actually pass startSeq etc on to rendering... commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 fix up release notes new known issues commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4222 bail if we wait too long for Jmol to save... patch/JAL-4222_100s_timeout_on_imagexport commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 blocker patch JAL-3772 tidy up groovy console... commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 JAL-4334 position status when start, end or... bug/JAL-4334_unknownstartenduniprotfeatures commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 JAL-4338 known defect commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 release 15th November 2023 commit | commitdiff | tree | snapshot
2023-11-15 James ProcterJAL-4090 JAL-3858 fix up PAE docs - drop the EBI image... commit | commitdiff | tree | snapshot
2023-11-13 James ProcterJAL-4090 JAL-1551 source license commit | commitdiff | tree | snapshot
2023-11-13 James ProcterJAL-4090 relese date 14th Nov 2023 commit | commitdiff | tree | snapshot
2023-11-13 James ProcterJAL-4236 don’t look for headers in JalviewJS commit | commitdiff | tree | snapshot
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