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Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950
[jalview.git] / src /
2018-07-18 Jim ProcterMerge branch 'features/mchmmer' into features/mchmmer_m... features/mchmmer_merge_JAL-1950 tree | commitdiff
2018-06-06 gmungocJAL-3013 resolve symlink to hmmer binaries folder features/mchmmer tree | commitdiff
2018-06-06 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-06-06 gmungocJAL-3013 ensure Chimera as a symlink gets resolved tree | commitdiff
2018-06-06 gmungocJAL-2956 don't load (non-existent) HMMER jar entry... tree | commitdiff
2018-06-05 gmungocJAL-3011 include annotation scores in sequence id toolt... tree | commitdiff
2018-06-05 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-06-04 gmungocJAL-3019 correctly form toRange of 'traversed' MapList tree | commitdiff
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3 tree | commitdiff
2018-06-01 Jim ProcterJAL-3012 JAL-2937 TODO avoid creating data copies by... tree | commitdiff
2018-06-01 Jim ProcterJAL-2937 hmmbuild input data generated via AlignmentVie... tree | commitdiff
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow individual groups to be remater... tree | commitdiff
2018-06-01 Jim ProcterJAL-1551 formatting tree | commitdiff
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of group without sequences... tree | commitdiff
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of sequences from group... tree | commitdiff
2018-05-31 Jim ProcterJAL-1950 JAL-2629 insert gaps into HMM used to search... tree | commitdiff
2018-05-31 Jim ProcterJAL-2629 (probably not right issue) JAL-1950 - make... tree | commitdiff
2018-05-31 Jim ProcterJAL-3011 JAL-2719 JAL-1958 add posterior probability... tree | commitdiff
2018-05-31 Jim ProcterJAL-3011 - show score in annotation row - looks like... tree | commitdiff
2018-05-31 Jim ProcterJAL-1958 use the annotation score for the sequence... tree | commitdiff
2018-05-31 Jim ProcterJAL-1950 JAL-1958 disable per-row score modulation... tree | commitdiff
2018-05-31 gmungocJAL-2808 don't capture or report min-max for mixed... tree | commitdiff
2018-05-31 Jim ProcterMerge branch 'spike/JAL-1950_hmmer3client' into feature... tree | commitdiff
2018-05-31 Jim ProcterMerge branch 'develop' into spike/JAL-1950_hmmer3client tree | commitdiff
2018-05-31 gmungocJAL-2808 pre-fill numeric inequality filter with min... tree | commitdiff
2018-05-30 gmungocJAL-2629 suppress 'Add Database' menu option in favour... tree | commitdiff
2018-05-30 gmungocJAL-3005 JAL-2629 file chooser argument for HMM search... tree | commitdiff
2018-05-30 gmungocJAL-3005 JAL-3008 render file chooser and radio button... tree | commitdiff
2018-05-30 gmungocJAL-3008 new parameter type RadioChoiceParameter tree | commitdiff
2018-05-30 gmungocJAL-3005 new argument type FileParameter for file chooser tree | commitdiff
2018-05-29 gmungocJAL-3005 refactor updateRecentlyOpened to enable reuse tree | commitdiff
2018-05-29 Mungo CarstairsJAL-2994 utility method to match a list of folder/file... tree | commitdiff
2018-05-28 gmungocJAL-2994 restrict search to \Program Files\Chimera* tree | commitdiff
2018-05-28 gmungocJAL-2994 use pattern matches to search for chimera.exe tree | commitdiff
2018-05-28 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-28 gmungocMerge branch 'bug/JAL-797' into develop tree | commitdiff
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-05-25 Jim ProcterMerge branch 'bug/JAL-2992panelHeight' into releases... tree | commitdiff
2018-05-25 Jim ProcterMerge branch 'bug/JAL-1460_dragndropWindows' into relea... tree | commitdiff
2018-05-25 gmungocJAL-2992 simpler heuristic for available height bug/JAL-2992panelHeight tree | commitdiff
2018-05-25 Jim ProcterMerge branch 'bug/JAL-2991_exporttosvgwrapview' into... tree | commitdiff
2018-05-25 Jim ProcterJAL-2994 add a few future release points for good measu... feature/JAL-2994chimeraPath tree | commitdiff
2018-05-25 Jim ProcterJAL-1460 temp variable for clearer conditional and... bug/JAL-1460_dragndropWindows tree | commitdiff
2018-05-25 Jim ProcterJAL-1460 javadoc tree | commitdiff
2018-05-25 gmungocJAL-2995 tooltip on fields with double-click to browse... tree | commitdiff
2018-05-25 gmungocJAL-2994 temporary patch with paths to Chimera for... tree | commitdiff
2018-05-24 gmungocJAL-2997 additional tests tree | commitdiff
2018-05-24 Jim ProcterJAL-1460 tidied up the use of windows link file parser tree | commitdiff
2018-05-24 Jim ProcterJAL-1460 more complete drag'n'drop debugging info and... tree | commitdiff
2018-05-24 Jim ProcterJAL-1460 process .lnk files dragged to Jalview when... tree | commitdiff
2018-05-24 Jim ProcterJAL-1460 new data flavor for URLs added belt-and-braces... tree | commitdiff
2018-05-23 gmungocJAL-2993 AlignFrame listen for keystrokes in OverviewPanel tree | commitdiff
2018-05-23 Jim Procterfix for JAL-2991 - we could do better :/ bug/JAL-2991_exporttosvgwrapview tree | commitdiff
2018-05-23 gmungocJAL-2997 handle tab-delimited trailing column number... tree | commitdiff
2018-05-22 gmungocJAL-2716 fix to reset choice parameter on Revert tree | commitdiff
2018-05-22 gmungocJAL-2716 fix broken checkIfModified behaviour tree | commitdiff
2018-05-22 gmungocJAL-2629 method refactor and menu tidying tree | commitdiff
2018-05-21 gmungocJAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW bug/JAL-797 tree | commitdiff
2018-05-15 gmungocJAL-2719 parse bit score annotation from search results tree | commitdiff
2018-05-15 gmungocJAL-1264 exclude score-only from 'Add Reference Annotat... tree | commitdiff
2018-05-15 gmungocJAL-2629 JAL-2937 respect 'align automatically' option... tree | commitdiff
2018-05-14 gmungocJAL-2989 refactoring to reduce code duplication tree | commitdiff
2018-05-14 gmungocJAL-2711 show short file names in search database combo box tree | commitdiff
2018-05-14 gmungocJAL-2989 support value display names for Option or... tree | commitdiff
2018-05-14 gmungocJAL-2711 removed unused and flaky utility method tree | commitdiff
2018-05-14 gmungocJAL-2939 check for hmm present when processing groups tree | commitdiff
2018-05-11 gmungocJAL-2985 show label instead of checkbox for a required... tree | commitdiff
2018-05-11 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue... tree | commitdiff
2018-05-10 gmungocJAL-2629 revert to showing Profile parameter even if... tree | commitdiff
2018-05-10 gmungocJAL-2629 default HMMBuild to alignment if not specified... tree | commitdiff
2018-05-10 gmungocJAL-591 reduced updating by checking/setting 'updating... tree | commitdiff
2018-05-10 gmungocJAL-2629 handle decline 'Add Database' tree | commitdiff
2018-05-10 gmungocJAL-2629 adjust placement and optionality of arguments... tree | commitdiff
2018-05-10 gmungocJAL-591 show choice list with a single option tree | commitdiff
2018-05-10 Jim ProcterMerge branch 'bug/JAL-2920_uniprotvariantfeature' into... tree | commitdiff
2018-05-10 Jim ProcterJAL-2920 simplified logic and added corner cases for... tree | commitdiff
2018-05-09 gmungocJAL-2714 HMMSearch cutoff by E-Value, Score or None tree | commitdiff
2018-05-09 gmungocJAL-2984 add pdb as sequence(s) if associate structure... tree | commitdiff
2018-05-09 Jim ProcterMerge branch 'patch/JAL-2976_vaqua4_fallback' into... tree | commitdiff
2018-05-09 Jim ProcterJAL-2976 fixed bad equivalence check and implemented... tree | commitdiff
2018-05-08 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 ensure default is ‘parseImmediately=true’ tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 use configured values for structure derived... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 add secondary structure & temp factor if not... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 use StructureImportSettings singleton settings... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 isParseImmediately() allows the parse() method... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 allow JmolParser to be configured before parsi... tree | commitdiff
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-05-07 Jim ProcterJAL-2906 apply GPLv3 license source tree | commitdiff
2018-05-07 Jim ProcterJAL-2960 don’t override a swing method and create infin... tree | commitdiff
2018-05-04 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_... tree | commitdiff
2018-05-04 Jim ProcterJAL-2976 patch NPE when trying to open Uniprot FTS tree | commitdiff
2018-05-04 Jim ProcterJAL-2948 transfer features/annotation is now available... tree | commitdiff
2018-05-04 Jim ProcterJAL-2960 raise the structure view after adding structur... tree | commitdiff
2018-05-02 Jim ProcterJAL-2976 fallback to Vaqua for Macs that don’t work... tree | commitdiff
2018-05-01 Jim ProcterJAL-2899 colouring moved from SwingWorker to a backgrou... tree | commitdiff
2018-04-30 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_... tree | commitdiff
2018-04-25 Jim ProcterMerge branch 'features/JAL-2944_openStructuresInSelecte... tree | commitdiff
2018-04-24 gmungocJAL-2959 no Print dialog shown if Page Format is Cancelled tree | commitdiff
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