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JAL-3664 hmm related TODOs
[jalview.git] / src / jalview / io / FileLoader.java
2020-06-22 Jim ProcterJAL-3664 hmm related TODOs jims/work_on_2_12/JAL-3664_hmmer_ux blob | commitdiff
2020-06-22 Jim ProcterJAL-3664 update colours to enable HMM colouring options... blob | commitdiff | diff to current
2019-06-06 tvaJAL-3285 fix FileLoader failing to load HMMER file blob | commitdiff | diff to current
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer blob | commitdiff | diff to current
2019-03-19 Ben SoaresJAL-3130 Merge of JAL-3130_Java_11_investigations-Ben... blob | commitdiff | diff to current
2019-03-01 gmungocMerge branch 'feature/JAL-3093wrappedModeTooltips'... blob | commitdiff | diff to current
2018-12-13 Ben SoaresJAL-3130 Attempting to fix 8 tests that pass on a Mac... blob | commitdiff | diff to current
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... blob | commitdiff | diff to current
2018-10-04 gmungocJAL-3132 set status message when over sequence id or... blob | commitdiff | diff to current
2018-09-19 gmungocJAL-3063 use JAXB for 'Save as Project' and load projec... blob | commitdiff | diff to current
2018-05-29 gmungocJAL-3005 refactor updateRecentlyOpened to enable reuse blob | commitdiff | diff to current
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not... blob | commitdiff | diff to current
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... blob | commitdiff | diff to current
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications blob | commitdiff | diff to current
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer blob | commitdiff | diff to current
2017-10-27 gmungocJAL-1793 spike branch updated to latest blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-01 gmungocJAL-2488 remove finalize methods blob | commitdiff | diff to current
2017-08-29 osboxesJAL-2629 HMMs dropped on the alignment now map to the... blob | commitdiff | diff to current
2017-08-28 TZVanaaltenJAL-2629 fix issue where HMM would not be added to... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 fix for NPE caused by incorrect initiation... blob | commitdiff | diff to current
2017-08-23 tzvanaaltenJAL-2629 selected HMM is now a sequence, not a HMM blob | commitdiff | diff to current
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer blob | commitdiff | diff to current
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-08-15 tzvanaaltenJAL-2629 fix file loading issues on Mac blob | commitdiff | diff to current
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu blob | commitdiff | diff to current
2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment blob | commitdiff | diff to current
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence blob | commitdiff | diff to current
2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too... blob | commitdiff | diff to current
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu... blob | commitdiff | diff to current
2017-05-26 tcofoegbuJAL-2465 Improvement to re-instate storing recently... blob | commitdiff | diff to current
2017-05-26 tcofoegbuJAL-2465 fix to prevent files loaded from the system... blob | commitdiff | diff to current
2017-05-15 tcofoegbuJAL-2520 improvement to use URL leaf name for creating... blob | commitdiff | diff to current
2017-05-09 tcofoegbuJAL-2520 improvement to download and update structure... blob | commitdiff | diff to current
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... blob | commitdiff | diff to current
2017-01-11 gmungocJAL-2344 separated AlignmentFileI into AlignmentFileRea... blob | commitdiff | diff to current
2017-01-11 gmungocJAL-2344 FileFormats singleton for formats, FileFormatI... blob | commitdiff | diff to current
2016-11-28 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2016-11-25 gmungocJAL-2344 use .equals() to compare FileFormatI objects blob | commitdiff | diff to current
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane blob | commitdiff | diff to current
2016-11-24 gmungocFileFormatI further tweaks, clean compile blob | commitdiff | diff to current
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch blob | commitdiff | diff to current
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... blob | commitdiff | diff to current
2016-07-12 gmungocFileFormat enum wip changes blob | commitdiff | diff to current
2016-07-11 gmungocfile format enum wip changes blob | commitdiff | diff to current
2016-03-23 tcofoegbuJAL-2009 added programmatic custom feature setting... blob | commitdiff | diff to current
2015-12-22 gmungocJAL-653 set showSequenceFeatures=true on loading a... blob | commitdiff | diff to current
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or... blob | commitdiff | diff to current
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 blob | commitdiff | diff to current
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright blob | commitdiff | diff to current
2015-10-05 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch blob | commitdiff | diff to current
2015-09-29 tcofoegbuJAL-1896 fixed NPE for RNA Helice without equivalent... blob | commitdiff | diff to current
2015-09-28 tcofoegbuJAL-1896 revised implementation to construct a ColourSc... blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports blob | commitdiff | diff to current
2015-09-02 gmungocJAL-1355 User error text externalised to message bundle blob | commitdiff | diff to current
2015-08-21 tcofoegbuJAL-1443 bug fix for loading pasted alignments from... blob | commitdiff | diff to current
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... blob | commitdiff | diff to current
2015-07-30 tcofoegbuJAL-1443 modified exception notifications blob | commitdiff | diff to current
2015-07-21 tcofoegbuJAL-1443 bugfix to prevent loading of unidentifiable... blob | commitdiff | diff to current
2015-07-08 gmungocJAL-1759 merge from develop blob | commitdiff | diff to current
2015-07-02 tcofoegbuJAL-1443 data validation for empty content before loadi... blob | commitdiff | diff to current
2015-06-30 tcofoegbuJAL-1641 round trip test/refactoring blob | commitdiff | diff to current
2015-06-25 Jim ProcterJAL-1780 JAL-653 JAL-1892 brackets in wrong place broke... blob | commitdiff | diff to current
2015-06-17 Jim ProcterMerge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments blob | commitdiff | diff to current
2015-06-15 Jim ProcterJAL-1775 FileLoader javadoc blob | commitdiff | diff to current
2015-06-15 Jim ProcterJAL-1775 fix regression from commit 70f9c4700f20a8fa57e... blob | commitdiff | diff to current
2015-06-12 tcofoegbuJAL-1641 refactor blob | commitdiff | diff to current
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and... blob | commitdiff | diff to current
2015-06-05 Jim ProcterJAL-653 JAL-966 TODO and avoid NPE when desktop instanc... blob | commitdiff | diff to current
2015-05-20 tcofoegbuJAL-1541 minor code clean up, and added test for BioJsH... blob | commitdiff | diff to current
2015-05-19 tcofoegbuJAL-1641 Further refactoring of JSON export option... blob | commitdiff | diff to current
2015-05-11 tcofoegbuJAL-1641 cherry-picked changes into develop compatible... blob | commitdiff | diff to current
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch blob | commitdiff | diff to current
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... blob | commitdiff | diff to current
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... blob | commitdiff | diff to current
2015-01-07 gmungocJAL-1588 refactoring to StructureViewerBase and related blob | commitdiff | diff to current
2014-12-15 Jim ProcterJAL-1620 version bump and release notes blob | commitdiff | diff to current
2014-11-12 Charles OfoegbuExcluded HtmlFile.java dependencies from AppletFomatAdapter blob | commitdiff | diff to current
2014-11-12 Charles OfoegbuModified biojs exporter/importer to preserve SequenceFe... blob | commitdiff | diff to current
2014-10-30 Jim ProcterJAL-674 register PDB IDs when ever they are resolved... blob | commitdiff | diff to current
2014-10-30 Jim ProcterJAL-1551 format and tidy blob | commitdiff | diff to current
2014-09-23 darolmarJAL-1355 blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 source formatting blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch blob | commitdiff | diff to current
2014-05-22 Jim ProcterJAL-1503 update version in GPL header blob | commitdiff | diff to current
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop blob | commitdiff | diff to current
2014-02-03 Jim ProcterMerge branch 'Release_2_8_1_Branch_i18n' into try_r20b1... blob | commitdiff | diff to current
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge blob | commitdiff | diff to current
2014-01-29 Jim ProcterJAL-1432 updated copyright notices blob | commitdiff | diff to current
2013-12-25 darolmarJAL-1355 (basic i18n support) blob | commitdiff | diff to current
2013-10-14 Jim ProcterMerge branch 'develop' into dev_from_2_8_1 blob | commitdiff | diff to current
2013-08-29 darolmari18n blob | commitdiff | diff to current
2013-06-07 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' into... blob | commitdiff | diff to current
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