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JAL-3878 Clear services list on reload.
[jalview.git]
/
src
/
jalview
/
hmmer
/
2021-10-06
Mateusz Warowny
JAL-3899 Update usages of uniquify and deuniquify.
tree
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commitdiff
2020-05-18
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 can now choose number of jackhmmer iterations
merge/JAL-3285_mchmmer_with_211_develop
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 fix faulty label in a MessageManager.getString...
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 hmmer searches now read domain rather than...
tree
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commitdiff
2019-07-11
Thomas
JAL-2629 hmmer searches include seqs past inclusion...
tree
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commitdiff
2019-07-11
Thomas
JAL-2629 hmm search UI and structural improvements...
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix hmmsearch/jackhmmer assigning incorrect...
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix hmsearch and jackhmmer not being able...
tree
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commitdiff
2019-07-10
tva
JAL-2629 hmmsearch # of new sequences now only displaye...
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix incorrect hmmbuild on groups behaviour
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix hmmsearch/jackhmmer being unable to search...
tree
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commitdiff
2019-07-05
tva
JAL-2629 uniquify all hmmer command sequence outputs
tree
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commitdiff
2019-07-05
tva
JAL-2629 fix file format issues preventing hmmsearch...
tree
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commitdiff
2019-07-03
tva
JAL-2629 fix search scores being read in incorrectly
tree
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commitdiff
2019-07-03
tva
JAL-2629 fix hmm on alignment being deleted upon runnin...
tree
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commitdiff
2019-07-03
tva
JAL-2629 can now filter by sequence e-value or bit...
tree
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commitdiff
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
tree
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commitdiff
2019-06-28
tva
JAL-3336 add better method of determining where data...
tree
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commitdiff
2019-06-28
tva
JAL-3336 fix hmmsearch failing when parsing score table
tree
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commitdiff
2019-06-28
tva
JAL-2629 add HMM Match Score colour scheme
tree
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commitdiff
2019-06-10
tva
JAL-3297 pad gaps in alignment to ensure hmmalign runs
tree
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commitdiff
2019-06-06
tva
JAL-3285 fix incorrect file paths on HMMAlign/Search...
tree
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commitdiff
2019-06-06
tva
JAL-3285 add Cygwin environment path fix for Windows
tree
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commitdiff
2019-06-05
tva
JAL-3285 method call change to HMMBuild not included...
tree
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commitdiff
2018-07-18
Jim Procter
Merge branch 'features/mchmmer' into features/mchmmer_m...
features/mchmmer_merge_JAL-1950
tree
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commitdiff
2018-06-06
gmungoc
JAL-3013 resolve symlink to hmmer binaries folder
features/mchmmer
tree
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commitdiff
2018-06-01
Jim Procter
JAL-3012 JAL-2937 TODO avoid creating data copies by...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-2937 hmmbuild input data generated via AlignmentVie...
tree
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commitdiff
2018-05-31
Jim Procter
JAL-1950 JAL-2629 insert gaps into HMM used to search...
tree
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commitdiff
2018-05-31
Jim Procter
JAL-2629 (probably not right issue) JAL-1950 - make...
tree
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commitdiff
2018-05-31
Jim Procter
JAL-3011 JAL-2719 JAL-1958 add posterior probability...
tree
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commitdiff
2018-05-30
gmungoc
JAL-3005 JAL-2629 file chooser argument for HMM search...
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-2629 JAL-2937 respect 'align automatically' option...
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
2018-05-10
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-2629 adjust placement and optionality of arguments...
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
2018-04-20
gmungoc
JAL-591 slider scale factor now derived from min-max...
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
2018-04-09
Mungo Carstairs
JAL-2937 Cygwin path preference, method refactoring
tree
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2629 more error checking
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
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-2629 add title to output alignment window
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
tree
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commitdiff
2018-03-23
gmungoc
JAL-2629 pad gaps when exporting alignment as 'database...
tree
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commitdiff
2018-03-21
gmungoc
JAL-2629 tweaks to Information annotation updating
tree
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commitdiff
2018-03-20
gmungoc
JAL-2629 InformationThread.findOrCreateAnnotation and...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
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commitdiff
2018-02-28
gmungoc
JAL-2629 some tidying of Hmmer commands (wip)
tree
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commitdiff
2018-02-27
gmungoc
JAL-2717 JAL-2668 fixes to HMMER colour scheme display...
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy tests, refactor hmmer node mapping slightly
tree
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commitdiff
2018-02-21
gmungoc
JAL-2629 simplifying method signatures in Hmmer command...
tree
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commitdiff
2018-02-20
gmungoc
JAL-2629 removed SequenceI.get/setLastPosition and...
tree
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commitdiff
2018-02-19
gmungoc
JAL-2629 partial refactoring of Hmmer command classes
tree
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commitdiff
2018-02-19
gmungoc
JAL-2629 formatting only
tree
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commitdiff
2017-09-01
TZVanaalten
JAL-2629 fix hmmbuild failing due to RF longer than...
features/hmmer
tree
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commitdiff
2017-09-01
TZVanaalten
JAL-2629 manual curation of HMMs via reference annotati...
tree
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commitdiff
2017-08-30
TZVanaalten
JAL-2629 fix issue where HMM sequence would be longer...
tree
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commitdiff
2017-08-30
TZVanaalten
JAL-2629 for multi-job hmmbuilds, group names are now...
tree
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commitdiff
2017-08-28
TZVanaalten
JAL-2629 HMMER alignment background colour scheme is...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 hmmsearch now adds the E-value as an annotation
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 hmmbuild runs on the alignment by default
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 fix for hmmbuild failing due to whitespace...
tree
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commitdiff
2017-08-25
TZVanaalten
Revert "jal-2629 fix for hmmbuild failing due to whites...
tree
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commitdiff
2017-08-25
TZVanaalten
jal-2629 fix for hmmbuild failing due to whitespace...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add multiple options for running hmmbuild...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add adjustable parameters to hmmbuild
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 adjust log parameter slightly and reduce granu...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 hmmsearch no longer throws an error if no...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 adjust parameter min and max to better suit...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 fix for NPE caused by incorrect initiation...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 hmmsearch now works for different databases
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add ability to add and select a DB for hmmsearch
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add basic parameter adjustment to hmmsearch...
tree
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commitdiff
2017-08-23
tzvanaalten
JAL-2629 fix for addHMMConsensus failing if no HMM...
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
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-2629 add documentation to previous work
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 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
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