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JAL-4065 update citations for Pfam and Rfam and added the Interpro citation
[jalview.git]
/
src
/
jalview
/
analysis
/
2016-08-25
Jim Procter
JAL-2154 JAL-2106 transfer primary refs to CDS for...
tree
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commitdiff
2016-08-25
Jim Procter
JAL-2154 copy and paste error
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'refactor/JAL-2106_sourceDbRef_revision...
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'develop' into refactor/JAL-2106_sourceDbR...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 propagate from contig to CDS after constructin...
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 should only add mappings between dataset sequences
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 - only copy DBRef from contig to new CDS seque...
tree
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commitdiff
2016-08-23
Jim Procter
Merge branch 'develop' into bug/JAL-2154projectMappings
tree
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commitdiff
2016-08-22
Jim Procter
JAL-2154 verify recovered xref sequence not already...
tree
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commitdiff
2016-08-22
Jim Procter
JAL-2154 regression warning - should never recover...
tree
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commitdiff
2016-08-22
gmungoc
JAL-2011 adjust method to fix failing unit test
tree
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commitdiff
2016-08-18
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-17
gmungoc
JAL-2172 reverted to not sorting column selection
tree
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commitdiff
2016-08-17
gmungoc
JAL-2172 handle case where column selection is not...
tree
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commitdiff
2016-08-16
Jim Procter
JAL-2154 make sure any new sequences via DBRefEntry...
tree
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commitdiff
2016-08-16
Jim Procter
JAL-2154 always resolve dataset sequences when creating...
tree
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commitdiff
2016-08-16
gmungoc
JAL-2171 matching bracket default character for rna...
tree
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commitdiff
2016-08-12
gmungoc
JAL-1841 count (logo height) is valid pairs only; detec...
tree
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commitdiff
2016-08-12
gmungoc
JAL-1841, bug fix in rna SS consensus, additions to...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 make sure codon mappings between sequences...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 todo
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 use convenience method
tree
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commitdiff
2016-07-20
gmungoc
JAL-2023 JAL-1681 fixed bug in computing '+' for co...
tree
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commitdiff
2016-07-19
gmungoc
JAL-391 corrected handling of gapped sequences
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2145 improvement: ensure conservation calculation...
tree
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commitdiff
2016-07-14
Jim Procter
JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 javadoc
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 scalability todo
tree
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commitdiff
2016-07-12
Jim Procter
JAL-1381 JAL-2110 efficiency TODO
tree
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commitdiff
2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
tree
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commitdiff
2016-07-07
gmungoc
JAL-2110 field 'cf' moved to stack
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 AlignmentUtils.alignCdsAsProtein implemented
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 use shared dataset when copying alignment...
tree
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commitdiff
2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 bug fix / test for searchDataset mappings...
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
tree
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commitdiff
2016-06-23
Jim Procter
Merge branch 'develop' into merge_JAL-2110
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 make indirect xref searches work by not filter...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 warning message when routine finds non-ds...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 clarify javadoc
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 refactor to split SequenceFetcher from x-ref...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 use SequenceI.isProtein()
tree
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commitdiff
2016-06-22
gmungoc
JAL-1982 defensive checks for null annotations array
tree
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commitdiff
2016-06-22
Jim Procter
JAL-2110 remove hardwired detection of search context...
tree
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commitdiff
2016-06-19
Jim Procter
JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
tree
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commitdiff
2016-06-16
Jim Procter
JAL-2110 throw implementation error if not given a...
tree
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commitdiff
2016-06-14
gmungoc
JAL-2110 fixes to dbref resolution and mappings, use...
tree
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commitdiff
2016-06-09
gmungoc
JAL-2110 work in progress
tree
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commitdiff
2016-06-03
gmungoc
JAL-2110 random stuff
tree
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commitdiff
2016-06-02
gmungoc
Merge branch 'develop' into features/JAL-2110_makeSense...
tree
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commitdiff
2016-06-01
Jim Procter
JAL-2038 ensure bare Strings are lowercased before...
tree
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commitdiff
2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
tree
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commitdiff
2016-05-30
tcofoegbu
JAL-2038 fix to enable case-insensitive file name ...
tree
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commitdiff
2016-05-26
gmungoc
JAL-1797 non-case-sensitive counting of residues /...
tree
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commitdiff
2016-05-25
gmungoc
JAL-2110 wip CrossRefs rewrite of CrossRef
tree
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commitdiff
2016-05-20
gmungoc
JAL-2110 unit tests for and minor refactoring of CrossRef
tree
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commitdiff
2016-05-18
gmungoc
JAL-2049 set sequence feature group to "Jalview" for...
tree
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commitdiff
2016-05-18
gmungoc
JAL-2049 use HGVS notation for variant on protein residue
tree
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commitdiff
2016-04-29
gmungoc
JAL-2051 better checking of retrieved / duplicated...
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 fix: use AlignmentView.getVisibleContigs and...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2049 revised computePeptideVariants to transfer...
tree
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commitdiff
2016-04-13
Jim Procter
JAL-2046 fix: patched SeqsetUtils so sequence features...
tree
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commitdiff
2016-04-12
gmungoc
JAL-2049 separate protein variant per dna variant ...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
tree
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commitdiff
2016-03-21
gmungoc
JAL-2029 further fixes to get correct xrefs and xrefs...
tree
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commitdiff
2016-03-21
gmungoc
JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
tree
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commitdiff
2016-03-11
gmungoc
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2016-03-11
gmungoc
JAL-1270 unit test for SequenceIdMatcher.SeqIdName
tree
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commitdiff
2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
tree
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commitdiff
2016-03-07
gmungoc
JAL-2023 CDS sequences added to / share alignment dataset
tree
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commitdiff
2016-03-03
gmungoc
JAL-1705 include stop codons in derived CDS; support...
tree
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commitdiff
2016-03-02
gmungoc
JAL-1705 include any unmapped protein start 'X' when...
tree
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commitdiff
2016-03-01
gmungoc
JAL-1705 align CDS to transcripts
tree
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commitdiff
2016-02-19
gmungoc
JAL-1705 refactor show products, set initial split...
tree
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commitdiff
2016-02-12
gmungoc
JAL-1705 various refactoring towards Uniprot-to-Ensembl...
tree
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commitdiff
2016-02-12
gmungoc
JAL-2008 updates for String[] to List<String> change
tree
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commitdiff
2016-02-12
gmungoc
JAL-2008 avoid unnecessary repaints; signatures changed...
tree
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commitdiff
2016-02-04
gmungoc
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2016-02-04
gmungoc
JAL-2005 added (stable) sort methods parameterised by
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commitdiff
2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
tree
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commitdiff
2016-01-28
gmungoc
JAL-1705 refine feature copying to including 5' and...
tree
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
tree
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commitdiff
2016-01-27
gmungoc
JAL-1705 add exon name to features and render on peptid...
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 compute peptide variants from dna; add "conseq...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 transfer features to the dataset sequence...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 get xrefs only for dna/peptide; code tidy
tree
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commitdiff
2015-12-22
gmungoc
JAL-391 new Calculate options to Reverse, Reverse Compl...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
tree
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commitdiff
2015-11-30
gmungoc
JAL-1421 generics loop syntax; 'bug?' comment added
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 small comment change only
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