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JAL-2629 fix for addHMMConsensus failing if no HMM sequences found
[jalview.git]
/
src
/
2017-08-23
tzvanaalten
JAL-2629 fix for addHMMConsensus failing if no HMM...
tree
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commitdiff
2017-08-23
tzvanaalten
JAL-2629 add logarithmic parameter for logarithmic...
tree
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commitdiff
2017-08-22
TZVanaalten
JAL-2629 add hmmsearch class
tree
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commitdiff
2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
tree
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commitdiff
2017-08-18
TZVanaalten
JAL-2668 add tests for HMMER commands, annotation and io
tree
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commitdiff
2017-08-18
TZVanaalten
JAL-2668 HMMFile export method moved to print method
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2599 move fillSymbol method to HMFile
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2599 some slight renaming of variables and methods
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2599 HMM annotation now shows consensus characters...
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2599 fix background frequency storage and correct...
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2629 fix for hmmbuild not loading a HMM onto the...
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2629 add hmmbuild validation check which also gets...
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 prevent hmmbuild from running if there are...
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 configure file chooser to select either a...
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 add checks for executing hmmer commands as...
tree
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commitdiff
2017-08-15
tzvanaalten
JAL-2629 fix file loading issues on Mac
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 add HMMER version check
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 selected HMM name now shown in HMMER menu
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 exported HMMs are now named correctly
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 fix uniquified sequence names appearing when...
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2599 fix HMMER scheme not colouring inserts and...
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 the HMMER tab is now disabled when HMMER is...
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 remove annotation when exporting for hmmbuild
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 remove gap padding, and now has option to...
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 add insert sequence at method on alignment
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 fix expected length error for hmmbuild by...
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 add padding for .sto annotations to fix issues...
tree
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commitdiff
2017-08-14
Jim Procter
JAL-2335 choose appropriate alphabet for filtering...
tree
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commitdiff
2017-08-14
Jim Procter
JAL-2335 source formatting
tree
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commitdiff
2017-08-14
Jim Procter
JAL-2335 filterNonStandardResidues configurable for...
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 remove redundant options from HMMER menu
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 add validation for HMMER path
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 fix incorrect gap insertions on HMM sequence
tree
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commitdiff
2017-08-14
Jim Procter
Merge branch 'patch/JAL-2663_filterAACons' into develop
tree
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commitdiff
2017-08-14
Jim Procter
JAL-2663 flag and filter to exclude non-standard amino...
tree
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commitdiff
2017-08-14
Jim Procter
JAL-2663 source formatting
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 fix issue where trim termini setting would...
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 hmmalign can now be run from the sequence...
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 add force alphabet type for HMMER commands
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 fix issue where HMM sequences would be too...
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 add HMMER tab in preferences menu
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2629 delete unnecessary buffer files for hmmer...
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2629 add ability to build a HMM from a group
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2629 add ability to select HMMs
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2599 HMMs can now be dropped onto the desktop
tree
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commitdiff
2017-08-10
TZVanaalten
JAL-2629 hmmalign now correctly creates a new frame
tree
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commitdiff
2017-08-10
gmungoc
JAL-2660 used saved value of ignoreGapsInConsensus...
tree
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commitdiff
2017-08-10
tzvanaalten
Merge branch 'features/hmmer' of https://source.jalview...
tree
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commitdiff
2017-08-10
tzvanaalten
JAL-2629 fix files permission issue on Mac
tree
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commitdiff
2017-08-09
Jim Procter
JAL-2426 Rfam download suffix
tree
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commitdiff
2017-08-09
Jim Procter
JAL-2426 JAL-1270 report Xfam download URL used if...
tree
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commitdiff
2017-08-09
Jim Procter
JAL-2425 raw stockholm download URLs
tree
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commitdiff
2017-08-09
Jim Procter
JAL-2425 remove overloaded getSequenceRecords method...
tree
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commitdiff
2017-08-09
TZVanaalten
JAL-2599 fix for issue where info annot would not display
tree
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commitdiff
2017-08-09
tzvanaalten
JAL-2599 fix for issue where info annot would not display
tree
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commitdiff
2017-08-09
TZVanaalten
JAL-2629 buffers are now temporary files
tree
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commitdiff
2017-08-09
TZVanaalten
JAL-2629 removed unnecessary exception throws from...
tree
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commitdiff
2017-08-09
Jim Procter
Merge branch 'bug/JAL-2634' into develop
tree
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commitdiff
2017-08-09
Jim Procter
Merge branch 'documentation/JAL-2418_release2102' into...
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2616 fix allowing clan sorting to work
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2629 add ability to select hmmer binaries folder
tree
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commitdiff
2017-08-08
gmungoc
JAL-2560 alternative fix (reinstate lost line of code)
tree
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commitdiff
2017-08-08
gmungoc
JAL-2649 JAL-2650 wait for Conservation calc to complet...
tree
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commitdiff
2017-08-08
gmungoc
JAL-2650 configure new viewport settings before selecti...
tree
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commitdiff
2017-08-07
TZVanaalten
JAL-2629 fixed hmmalign failing due to differing sequen...
tree
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commitdiff
2017-08-07
TZVanaalten
JAL-2629 current hmmer commands are now executed in...
tree
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commitdiff
2017-08-07
Jim Procter
Merge branch 'bug/JAL-2592userDefinedScheme' into develop
tree
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commitdiff
2017-08-04
TZVanaalten
JAL-2599 fixed information annotation buttons not working
tree
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commitdiff
2017-08-04
TZVanaalten
JAL-2629 hmmbuild now runs on alignments of different...
tree
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commitdiff
2017-08-04
TZVanaalten
JAL-2629 multiple HMMs can now be dropped onto an alignment
tree
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commitdiff
2017-08-03
gmungoc
JAL-2435 test for 'mirror font' option visible (not...
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix for HMM logo not normalising correctly
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix issue where parser exported map annotation...
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix for information annotation buttons
tree
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commitdiff
2017-08-01
Jim Procter
Merge branch 'bug/JAL-2632' into develop
tree
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commitdiff
2017-08-01
gmungoc
JAL-2611 reinstate missed merge - again!
tree
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commitdiff
2017-08-01
gmungoc
Merge branch 'feature/JAL-2611' into develop
tree
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commitdiff
2017-08-01
gmungoc
Merge branch 'bug/JAL-2630gradColourUpdateOverview...
tree
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commitdiff
2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
tree
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commitdiff
2017-07-31
kiramt
JAL-2634 Make overview box full height when alignment...
bug/JAL-2634
tree
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commitdiff
2017-07-31
gmungoc
JAL-2623 updated Overview/structure on input of thresho...
bug/JAL-2630gradColourUpdateOverview
tree
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commitdiff
2017-07-31
kiramt
JAL-2634 Added null test for graphics in AnnotationPane...
tree
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commitdiff
2017-07-31
gmungoc
JAL-2622 don't vertical scroll wrapped alignment id...
tree
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commitdiff
2017-07-31
gmungoc
JAL-2623 JAL-2015 set Below Threshold on FeatureColour...
tree
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commitdiff
2017-07-31
gmungoc
JAL-2630 applet update overview on release of threshold...
tree
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commitdiff
2017-07-28
kiramt
JAL-2632 Added paintAlignment(true) to show cols code
tree
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commitdiff
2017-07-28
gmungoc
JAL-147 corrected status bar message for wrapped scroll...
tree
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commitdiff
2017-07-28
gmungoc
JAL-2622 no vertical scroll of wrapped alignment from...
tree
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commitdiff
2017-07-28
gmungoc
JAL-2006 squash rounding errors at min/max threshold...
tree
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commitdiff
2017-07-28
gmungoc
JAL-2630 update Overview/structure from graduated colou...
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 moved HMM storage location to placeholder...
tree
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commitdiff
2017-07-26
TZVanaalten
JAL-2629 HMMs now map to reference annotation if exists
tree
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commitdiff
2017-07-25
TZVanaalten
JAL-2629 add non-functional HMMER menu
tree
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commitdiff
2017-07-25
TZVanaalten
JAL-2616 add ability to perform random alignments withi...
tree
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commitdiff
2017-07-24
tzvanaalten
JAL-2616 add placeholder sequence for HMM, does not...
tree
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commitdiff
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