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JAL-2716 fix broken checkIfModified behaviour
[jalview.git]
/
src
/
2018-05-22
gmungoc
JAL-2716 fix broken checkIfModified behaviour
tree
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commitdiff
2018-05-22
gmungoc
JAL-2629 method refactor and menu tidying
tree
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commitdiff
2018-05-15
gmungoc
JAL-2719 parse bit score annotation from search results
tree
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commitdiff
2018-05-15
gmungoc
JAL-1264 exclude score-only from 'Add Reference Annotat...
tree
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commitdiff
2018-05-15
gmungoc
JAL-2629 JAL-2937 respect 'align automatically' option...
tree
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commitdiff
2018-05-14
gmungoc
JAL-2989 refactoring to reduce code duplication
tree
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commitdiff
2018-05-14
gmungoc
JAL-2711 show short file names in search database combo box
tree
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commitdiff
2018-05-14
gmungoc
JAL-2989 support value display names for Option or...
tree
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commitdiff
2018-05-14
gmungoc
JAL-2711 removed unused and flaky utility method
tree
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commitdiff
2018-05-14
gmungoc
JAL-2939 check for hmm present when processing groups
tree
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commitdiff
2018-05-11
gmungoc
JAL-2985 show label instead of checkbox for a required...
tree
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commitdiff
2018-05-11
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
tree
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commitdiff
2018-05-10
gmungoc
JAL-2629 revert to showing Profile parameter even if...
tree
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commitdiff
2018-05-10
gmungoc
JAL-2629 default HMMBuild to alignment if not specified...
tree
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commitdiff
2018-05-10
gmungoc
JAL-591 reduced updating by checking/setting 'updating...
tree
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commitdiff
2018-05-10
gmungoc
JAL-2629 handle decline 'Add Database'
tree
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commitdiff
2018-05-10
gmungoc
JAL-2629 adjust placement and optionality of arguments...
tree
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commitdiff
2018-05-10
gmungoc
JAL-591 show choice list with a single option
tree
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commitdiff
2018-05-09
gmungoc
JAL-2714 HMMSearch cutoff by E-Value, Score or None
tree
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commitdiff
2018-05-08
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-07
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2960 don’t override a swing method and create infin...
tree
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commitdiff
2018-05-04
Jim Procter
Merge branch 'bug/JAL-2899' into releases/Release_2_10_...
tree
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commitdiff
2018-05-04
Jim Procter
JAL-2976 patch NPE when trying to open Uniprot FTS
tree
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commitdiff
2018-05-04
Jim Procter
JAL-2948 transfer features/annotation is now available...
tree
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commitdiff
2018-05-04
Jim Procter
JAL-2960 raise the structure view after adding structur...
tree
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commitdiff
2018-05-02
Jim Procter
JAL-2976 fallback to Vaqua for Macs that don’t work...
tree
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commitdiff
2018-05-01
Jim Procter
JAL-2899 colouring moved from SwingWorker to a backgrou...
tree
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commitdiff
2018-04-30
Jim Procter
Merge branch 'bug/JAL-2899' into releases/Release_2_10_...
tree
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commitdiff
2018-04-25
Jim Procter
Merge branch 'features/JAL-2944_openStructuresInSelecte...
tree
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commitdiff
2018-04-24
gmungoc
JAL-2959 no Print dialog shown if Page Format is Cancelled
tree
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commitdiff
2018-04-24
gmungoc
JAL-2939 exit calc thread if no HMM in alignment
tree
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commitdiff
2018-04-24
gmungoc
JAL-591 use constant for Preferences key
tree
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commitdiff
2018-04-24
gmungoc
JAL-2616 unused field removed
tree
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commitdiff
2018-04-23
gmungoc
JAL-2956 save/restore HMMER profile to/from Jalview...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2954 more efficient SearchResults.markColumns
tree
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commitdiff
2018-04-23
gmungoc
JAL-2952 set negative TempFactor values as AlignmentAnn...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2957 don't validate input on arrow keys
tree
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commitdiff
2018-04-23
gmungoc
JAL-591 ensure slider hidden if text input field only
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commitdiff
2018-04-20
gmungoc
JAL-591 slider scale factor now derived from min-max...
tree
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commitdiff
2018-04-20
gmungoc
JAL-591 tidy and comment code
tree
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commitdiff
2018-04-20
gmungoc
JAL-591 OptionBox FlowLayout, tweaks to wrapping of...
tree
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commitdiff
2018-04-19
gmungoc
JAL-591 utility method renamed and slightly generalised
tree
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commitdiff
2018-04-18
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-04-18
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-04-18
gmungoc
JAL-2593 render 'duplicate' features if transparency...
tree
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commitdiff
2018-04-18
gmungoc
JAL-2629 corrected cutoff parameter passing to hmmsearch
tree
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commitdiff
2018-04-17
gmungoc
Merge branch 'features/mchmmer' of https://source.jalvi...
tree
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commitdiff
2018-04-17
gmungoc
JAL-2629 choice of hmm profile now a parameter not...
tree
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commitdiff
2018-04-17
Mungo Carstairs
JAL-2937 working Cygwin bash execution of hmmbuild...
tree
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commitdiff
2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
tree
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commitdiff
2018-04-16
gmungoc
JAL-2937 use preferences for presets, simplify some...
tree
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commitdiff
2018-04-13
gmungoc
Merge branch 'features/JAL-2944_openStructuresInSelecte...
features/JAL-2944_openStructuresInSelectedView
tree
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commitdiff
2018-04-12
gmungoc
JAL-2223 don't add duplicate mappings to StructureSelec...
tree
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commitdiff
2018-04-12
gmungoc
JAL-1847 minor post-review updates
tree
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commitdiff
2018-04-12
gmungoc
JAL-2944 tidies for review comments
tree
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commitdiff
2018-04-11
Jim Procter
JAL-2946 catch unexpected SIFTS mapping exceptions...
tree
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2937 Cygwin path preference, method refactoring
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2629 more error checking
tree
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2937 extract reusable utility method
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2069 typo
tree
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commitdiff
2018-04-09
Jim Procter
JAL-2944 ’new view’ and ‘add to view’ button rather...
tree
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commitdiff
2018-04-09
Jim Procter
JAL-1847 superpose checkbox in structure chooser
tree
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commitdiff
2018-04-09
Jim Procter
JAL-1847 JAL-2944 make superposition step a configurabl...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2945 resolve model as PDB file. Need to verify...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2945 provide access to last highlighted results
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 open selected structures in existing or a...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 combo box to pick which viewer to load structu...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 methods to check existence and get a title...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 allow StructureViewer proxy to be created...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 get viewer’s title via toString()
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 expose UI update methods in api
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 remove modal prompt logic and expose methods...
tree
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commitdiff
2018-04-05
Jim Procter
JAL-2944 pull up structure viewer discovery routine...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2599 MapList from HMM nodes to consensus dataset...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2629 tidy code, factory methods for param sets
tree
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commitdiff
2018-03-30
gmungoc
JAL-2629 use correct gap character, revised deletion...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2629 Javadoc updates
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commitdiff
2018-03-30
gmungoc
JAL-2629 combine with/without defaults in one method...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 field/method naming more consistent
tree
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commitdiff
2018-03-30
gmungoc
JAL-2629 ensure hmm consensus sequence set on alignment...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2941 'map hmm to RF' removed pending clarifications
tree
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commitdiff
2018-03-30
gmungoc
JAL-2938 revisions to implementation details
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commitdiff
2018-03-30
gmungoc
JAL-2939 remove commented out code
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commitdiff
2018-03-30
gmungoc
JAL-2599 move utility method to MappingUtils
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commitdiff
2018-03-30
gmungoc
JAL-2939 simplified way of getting hmm consensus residue
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commitdiff
2018-03-30
gmungoc
JAL-2629 add title to output alignment window
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commitdiff
2018-03-30
gmungoc
JAL-2629 select HMM selects sequence under cursor
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commitdiff
2018-03-29
gmungoc
JAL-2907 bug fix redone on HMMER branch
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commitdiff
2018-03-28
gmungoc
JAL-1265 output all dbrefs in Stockholm (+tests) (...
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 unused action handler methods removed
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 no need to recalc HMM annotation for show...
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 always store Information profile
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commitdiff
2018-03-23
gmungoc
JAL-2629 pad gaps when exporting alignment as 'database...
tree
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commitdiff
2018-03-23
gmungoc
JAL-2937 unused field removed
tree
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commitdiff
2018-03-23
gmungoc
JAL-2938 update colour schemes enum for class name...
tree
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commitdiff
2018-03-23
gmungoc
JAL-2938 extracted base class for Hmmer colour schems
tree
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commitdiff
2018-03-22
gmungoc
JAL-2929 unit test, tidy unused/unneeded fields/parameters
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commitdiff
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