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Merge branch 'develop' into features/mchmmer
[jalview.git]
/
src
/
jalview
/
hmmer
/
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
2017-08-14
TZVanaalten
JAL-2629 remove annotation when exporting for hmmbuild
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 validation for HMMER path
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 add force alphabet type for HMMER commands
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
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commitdiff
2017-08-10
TZVanaalten
JAL-2629 hmmalign now correctly creates a new frame
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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-2629 buffers are now temporary files
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2629 add ability to select hmmer binaries folder
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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
2017-08-04
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
2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
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commitdiff