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JAL-2629 add basic parameter adjustment to hmmsearch/align
[jalview.git]
/
src
/
jalview
/
gui
/
2017-08-25
TZVanaalten
JAL-2629 add basic parameter adjustment to hmmsearch...
tree
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commitdiff
2017-08-23
tzvanaalten
JAL-2629 selected HMM is now a sequence, not a HMM
tree
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commitdiff
2017-08-23
tzvanaalten
JAL-2629 add logarithmic parameter for logarithmic...
tree
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commitdiff
2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
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-2629 add hmmbuild validation check which also gets...
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 the HMMER tab is now disabled when HMMER is...
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
2017-08-13
TZVanaalten
JAL-2629 hmmalign can now be run from the sequence...
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 add HMMER tab in preferences menu
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
JAL-2629 fix files permission issue on Mac
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 removed unnecessary exception throws from...
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-2629 add ability to select hmmer binaries folder
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 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 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 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
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
gmungoc
JAL-2622 don't vertical scroll wrapped alignment id...
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
2017-07-25
TZVanaalten
JAL-2629 add non-functional HMMER menu
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
2017-07-22
gmungoc
JAL-2623 initialise colour threshold slider correctly
tree
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commitdiff
2017-07-22
kiramt
Merge branch 'develop' into feature/JAL-2611
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2616 remove statistical analysis from AlignFrame
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2599 add ability to process RNA HMMer files
tree
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commitdiff
2017-07-18
gmungoc
JAL-147 don't scroll up beyond startRes = 0
bug/JAL-147scrollWrappedView
tree
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commitdiff
2017-07-18
gmungoc
JAL-147 corrected calculation of vertical scroll positi...
tree
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commitdiff
2017-07-18
gmungoc
JAL-147 draw up to last position of wrapped alignment!
tree
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commitdiff
2017-07-18
kiramt
JAL-2611 Better
tree
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commitdiff
2017-07-17
kiramt
JAL-2611 Still not happy with behaviour
tree
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commitdiff
2017-07-14
TZVanaalten
add partial button fix to annotation and statistics...
features/hmmer_statistics
tree
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commitdiff
2017-07-14
kiramt
JAL-2611 First pass, not thrilled with hidden column...
tree
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commitdiff
2017-07-14
kiramt
JAL-2611 Pre-merge checkin
tree
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commitdiff
2017-07-12
TZVanaalten
test HMM annotaTION
tree
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commitdiff
2017-07-11
TZVanaalten
complete Information Content annotation
tree
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commitdiff
2017-07-06
gmungoc
JAL-2605 ensure correct scale width calculation
tree
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commitdiff
2017-07-04
gmungoc
JAL-147 remove redundant calls to update overview panel
tree
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commitdiff
2017-07-04
gmungoc
JAL-2608 tidy up OverviewPanel when closed
tree
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commitdiff
2017-07-04
gmungoc
JAL-147 call method that sets visible width when drawin...
tree
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commitdiff
2017-07-03
gmungoc
Merge branch 'develop' into bug/JAL-147scrollWrappedView
tree
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commitdiff
2017-07-03
gmungoc
JAL-147 correct width out-by-one drawing ids
tree
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commitdiff
2017-07-03
gmungoc
JAL-147 ViewportRanges calculate wrapped vertical scrol...
tree
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commitdiff
2017-07-03
gmungoc
JAL-147 don't draw ScalePanel when in wrapped mode
tree
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commitdiff
2017-07-03
gmungoc
JAL-2034 don't refresh Overview for selection in id...
tree
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commitdiff
2017-06-30
gmungoc
JAL-147 don't page up above origin, repaint ids for...
tree
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commitdiff
2017-06-30
gmungoc
JAL-2602 pulled up identical methods to base class
tree
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commitdiff
2017-06-29
gmungoc
JAL-147 improved wrapped scrolling (including Overview...
tree
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commitdiff
2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
tree
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commitdiff
2017-06-29
gmungoc
JAL-2605 exclude left/right scale in sequence column...
tree
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commitdiff
2017-06-28
gmungoc
Merge branch 'bug/JAL-2600resizeflicker' into develop
tree
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commitdiff
2017-06-28
kiramt
JAL-2600 Tidies
bug/JAL-2600resizeflicker
tree
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commitdiff
2017-06-28
kiramt
JAL-2600 updates following review
tree
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commitdiff
2017-06-27
kiramt
JAL-2600 Tidies
tree
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commitdiff
2017-06-27
kiramt
JAL-2600 Abandoned fastpaint for resize; now full repai...
tree
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commitdiff
2017-06-27
gmungoc
JAL-2602 check for null or empty description when copyi...
tree
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commitdiff
2017-06-27
kiramt
JAL-2600 Add in IdCanvas and checks for 0 size images
tree
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commitdiff
2017-06-27
kiramt
JAL-2600 vertical fast paint too
tree
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commitdiff
2017-06-27
kiramt
JAL-2600 fast painting on resize
tree
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commitdiff
2017-06-26
kiramt
JAL-2600 reinstate original behaviour
tree
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commitdiff
2017-06-23
TZVanaalten
add HMMER colour scheme
tree
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commitdiff
2017-06-22
TZVanaalten
fully integrate HMMER3 file format into Jalview
tree
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commitdiff
2017-06-15
gmungoc
Merge branch 'bug/JAL-2386groupConservationColouring...
tree
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commitdiff
2017-06-15
kiramt
Merge remote-tracking branch 'origin/develop' into...
bug/JAL-2591
tree
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commitdiff
2017-06-15
gmungoc
Merge branch 'bug/JAL-2589gapColour' into develop
tree
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commitdiff
2017-06-12
gmungoc
JAL-2577 mirror select/hide by annotation in split...
tree
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commitdiff
2017-06-12
gmungoc
JAL-2577 mirror hide/select columns by annotation acros...
tree
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commitdiff
2017-06-09
gmungoc
JAL-2592 distinguish "User Defined" (scheme name) from...
bug/JAL-2592userDefinedScheme
tree
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commitdiff
2017-06-09
gmungoc
JAL-2594 avoid stack trace creating feature on gapped...
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 Refactor HiddenColumns to use ArrayList instea...
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 More HiddenColumns refactoring. Tests passing.
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Further refactoring (still incomplete)
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 More refactoring (incomplete)
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 updated HiddenColumns::findHiddenRegionPositio...
tree
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commitdiff
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