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JAL-2629 add basic parameter adjustment to hmmsearch/align
[jalview.git]
/
src
/
jalview
/
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
2017-07-24
tzvanaalten
JAL-2616 add ability to change location of family and...
tree
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commitdiff
2017-07-24
tzvanaalten
JAL-2599 .hmm parser should now accept older .hmm files
tree
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commitdiff
2017-07-22
gmungoc
JAL-2624 check feature colour threshold when colouring...
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
2017-07-21
TZVanaalten
JAL-2616 add ability to sort Pfam families and HMMs...
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 small code improvements
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2616 add documentation for probability analyser
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2616 add probability distribution analyser class
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
kiramt
JAL-2611 Tidies, initial unit tests
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
TZVanaalten
JAL-2599 complete documentation for HMM and HMMFile...
tree
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commitdiff
2017-07-18
kiramt
JAL-2611 Better
tree
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commitdiff
2017-07-18
TZVanaalten
JAL-2599 modified state transition probability storage
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
Merge branch 'feature/JAL-2613' into feature/JAL-2611
tree
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commitdiff
2017-07-14
kiramt
JAL-2611 Pre-merge checkin
tree
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commitdiff
2017-07-13
kiramt
JAL-2611 Added overview dimensions test for position...
tree
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commitdiff
2017-07-13
kiramt
JAL-2613 Unit tests and a fix. Phew.
tree
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commitdiff
2017-07-12
kiramt
JAL-2613 Centre alignment at click point
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-147 prevent vertical Overview box movement in wrapp...
tree
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commitdiff
2017-07-06
gmungoc
JAL-147 unit test for hide/show sequences update Viewpo...
tree
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commitdiff
2017-07-06
gmungoc
JAL-2605 ensure correct scale width calculation
tree
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commitdiff
2017-07-05
gmungoc
JAL-147 don't update overview for column selection...
tree
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commitdiff
2017-07-05
gmungoc
JAL-147 additions to unit test, check for negative...
tree
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commitdiff
2017-07-05
gmungoc
JAL-147 prevent overview box move up over hidden first...
tree
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commitdiff
2017-07-04
gmungoc
JAL-147 revised update of startSeq, endSeq on unhide...
tree
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commitdiff
2017-07-04
gmungoc
JAL-147 unit tests added, unused setEndRes removed
tree
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commitdiff
2017-07-04
gmungoc
JAL-147 corrected update of ViewportRanges for show...
tree
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commitdiff
2017-07-04
gmungoc
JAL-147 update ViewportRanges height after show/hide...
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
2017-07-04
gmungoc
JAL-147 extract local variable for ease of debugging
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 don't scroll Overview box outside panel dimensions
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
Merge branch 'bug/JAL-2597' into develop
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
2017-06-30
gmungoc
JAL-2602 same fix for applet
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
add information content calculations
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
kiramt
JAL-2597 Fix and unit test
bug/JAL-2597
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
test HMMER colour scheme
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
2017-06-20
TZVanaalten
restructure file exporter
tree
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commitdiff
2017-06-15
gmungoc
Merge branch 'bug/JAL-2386groupConservationColouring...
tree
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commitdiff
2017-06-15
TZVanaalten
add HMMFile class to read and write HMM files
tree
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commitdiff
2017-06-15
TZVanaalten
Update HiddenMarkovModel class
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
kiramt
JAL-2591 Updates following code review
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
TZVanaalten
Add HiddenMarkovModel class
tree
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commitdiff
2017-06-09
gmungoc
JAL-2589 render colour scheme gap colour in overview
bug/JAL-2589gapColour
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
gmungoc
JAL-2386 JAL-2570 use ResidueShader copy constructor...
bug/JAL-2386groupConservationColouring
tree
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commitdiff
2017-06-08
kiramt
Merge branch 'bug/JAL-2586' into develop
tree
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commitdiff
2017-06-08
kiramt
JAL-2586 Clarification to URL link code
bug/JAL-2586
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 Made redraw flag in OverviewRenderer volatile
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 made redraw volatile
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 Hidden columns regions can be output to string...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 updated HiddenColumns::findHiddenRegionPositio...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 ported to applet
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Overview changes ported to applet
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 More rationalising of hiddencols
tree
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commitdiff
2017-06-07
gmungoc
JAL-2386 ensure group conservation shading is applied...
tree
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commitdiff
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