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JAL-2174 bug fixes + refactoring to allow + unit tests
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
2016-07-14
Jim Procter
JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
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2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
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2016-07-12
Jim Procter
JAL-2110 javadoc
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2016-07-12
Jim Procter
JAL-2110 scalability todo
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2016-07-12
Jim Procter
JAL-1381 JAL-2110 efficiency TODO
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2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
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2016-07-06
gmungoc
JAL-2110 AlignmentUtils.alignCdsAsProtein implemented
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2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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2016-07-04
gmungoc
JAL-2110 use shared dataset when copying alignment...
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2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
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2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
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2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
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2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
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2016-06-23
Jim Procter
Merge branch 'develop' into merge_JAL-2110
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2016-06-22
gmungoc
JAL-1982 defensive checks for null annotations array
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2016-06-16
Jim Procter
JAL-2110 throw implementation error if not given a...
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2016-06-14
gmungoc
JAL-2110 fixes to dbref resolution and mappings, use...
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2016-06-09
gmungoc
JAL-2110 work in progress
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2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
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2016-05-18
gmungoc
JAL-2049 set sequence feature group to "Jalview" for...
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2016-05-18
gmungoc
JAL-2049 use HGVS notation for variant on protein residue
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2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
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2016-04-14
gmungoc
JAL-2049 revised computePeptideVariants to transfer...
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2016-04-12
gmungoc
JAL-2049 separate protein variant per dna variant ...
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2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
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2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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2016-03-07
gmungoc
JAL-2023 CDS sequences added to / share alignment dataset
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2016-03-03
gmungoc
JAL-1705 include stop codons in derived CDS; support...
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2016-03-02
gmungoc
JAL-1705 include any unmapped protein start 'X' when...
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2016-03-01
gmungoc
JAL-1705 align CDS to transcripts
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2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
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2016-01-28
gmungoc
JAL-1705 refine feature copying to including 5' and...
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2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
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2016-01-23
gmungoc
JAL-1705 compute peptide variants from dna; add "conseq...
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2016-01-21
gmungoc
JAL-1705 transfer features to the dataset sequence...
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2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
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2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
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2015-11-30
gmungoc
JAL-653 small comment change only
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2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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2015-10-07
Jim Procter
JAL-1894 source formatting
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2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
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2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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2015-09-09
gmungoc
JAL-1619 'align protein as cDNA' now leaves unmapped...
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2015-09-07
gmungoc
JAL-1636 translate stop codon as '*', mouseover * as...
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2015-08-17
gmungoc
JAL-1800 separated SearchResults.getCharacters() from...
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2015-06-04
gmungoc
JAL-1544 spelling in javadoc only
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2015-05-12
gmungoc
JAL-1712 fixes/tests for Castor binding and 'show flank...
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2015-04-21
gmungoc
JAL-1693 mappings added back to the original alignment
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2015-04-14
gmungoc
JAL-1693 generate multiple exon sequences for 1-many...
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2015-04-13
gmungoc
JAL-1693 make exon alignment for get-xref splitframe...
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2015-03-30
gmungoc
JAL-1264 remove broken applet build dependencies
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2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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2014-11-27
Jim Procter
JAL-674 add sequence associated annotation rows to...
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2014-10-30
gmungoc
JAL-1152 prototype of new Annotations menu with sort...
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2014-06-06
Jim Procter
JAL-1517 source formatting
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2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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2014-04-21
Jim Procter
JAL-1466 don't include empty columns if no upstream...
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2014-04-21
Jim Procter
JAL-1466 improved test and patched off by one that...
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2014-04-21
Jim Procter
JAL-1466 new calculation menu option to recover the...
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