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JAL-1632 add score model params to PCAModel and PCA constructors
[jalview.git]
/
src
/
jalview
/
datamodel
/
2014-04-25
Jim Procter
Merge branch 'JAL-1177_prop_rnasecstr' into develop
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commitdiff
2014-04-25
Jim Procter
JAL-1177 propagate sequence associated annotation to...
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commitdiff
2014-04-21
Jim Procter
Merge branch 'jims_marckhacks' into develop
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commitdiff
2014-04-21
Jim Procter
JAL-1473 refactor score matrices and tree score calcula...
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commitdiff
2014-02-18
Jim Procter
Merge branch 'JAL-1445' into develop
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commitdiff
2014-02-03
Jim Procter
Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
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commitdiff
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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commitdiff
2013-10-15
Jim Procter
JAL-1159 Merging 2.8.1 patches and Anne Menards work...
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commitdiff
2013-10-14
Jim Procter
Merge branch 'develop' into dev_from_2_8_1
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commitdiff
2013-10-11
Jim Procter
Merge branch 'JAL-1164_disorderforselection' into Relea...
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commitdiff
2013-10-11
Jim Procter
JAL-1114 javadoc
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commitdiff
2013-10-11
Jim Procter
JAL-1114 promote start/end attributes to gettable field...
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commitdiff
2013-10-11
Jim Procter
JAL-1114 API javadoc
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commitdiff
2013-10-04
Jim Procter
fix for JAL-1380 and efficiency todo for JAL-1381
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commitdiff
2013-09-02
Jim Procter
Merge branch 'JAL-1373_precision' into develop
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commitdiff
2013-09-02
Jim Procter
JAL-1373 pass size of sequence set to consensus renderi...
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commitdiff
2013-08-30
Jim Procter
JAL-1367 promote the existing representative sequence...
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commitdiff
2013-07-11
Jim Procter
Merge branch 'JAL-1347' into develop
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commitdiff
2013-07-11
Jim Procter
JAL-1347 make it efficient to call getConsensus to...
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commitdiff
2013-07-07
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
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commitdiff
2013-06-23
Jim Procter
Merge branch 'bug/JAL-1230' into develop
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commitdiff
2013-06-23
Jim Procter
JAL-1230 proxy method for synchronising internal Alignm...
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commitdiff
2013-06-21
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
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commitdiff
2013-06-21
Jim Procter
Merge branch 'JAL-1294_iupredexportimport' into develop
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 bugfix equals
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commitdiff
2013-06-21
Jim Procter
JAL-1294 JAL-1325 test annotation threshold line equiva...
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commitdiff
2013-06-18
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
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commitdiff
2013-06-17
Jim Procter
Merge branch 'JAL-1312_ambiguity_na' into develop
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commitdiff
2013-06-17
Jim Procter
JAL-1312 patch for regression noticed after patch to...
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commitdiff
2013-06-07
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
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commitdiff
2013-06-07
Jim Procter
Merge branch 'JAL-1161_optimisingAnnotationPanel' into...
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commitdiff
2013-05-31
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
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commitdiff
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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commitdiff
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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commitdiff
2013-05-24
Jim Procter
JAL-1295 relaxed test for Annotation element equivalenc...
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commitdiff
2013-05-24
Jim Procter
javadoc and formatting
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commitdiff
2013-05-24
Jim Procter
JAL-1297 JAL-1295 JAL-1294 sensible toString for benefi...
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commitdiff
2013-02-13
jprocter
fix merge conflicts for finess on JAL-1140 (introduced...
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commitdiff
2012-12-07
jprocter
revised renderer and annotation model to support differ...
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commitdiff
2012-12-07
jprocter
convenience function to get the RNA model for an annota...
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commitdiff
2012-12-07
jprocter
use new secstructure process algorithm
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commitdiff
2012-12-04
jprocter
JAL-1140 - IO classes should only raise generic IOExcep...
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commitdiff
2012-11-15
jprocter
Merge branch 'develop' into menard
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commitdiff
2012-11-08
jprocter
tidy imports
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commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
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commitdiff
2012-10-03
jprocter
formatting
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commitdiff
2012-09-25
jprocter
JAL-1179 note and patch for exceptions raised when...
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commitdiff
2012-09-03
jprocter
JAL-1153 ensure _linecolour is copied in copy constructor
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commitdiff
2012-08-31
jprocter
Merge branch 'develop' into menard
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commitdiff
2012-08-29
jprocter
JAL-1153 new runtime property set to first non-null...
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commitdiff
2012-08-28
jprocter
javadoc and note about broken semantics for findIndex
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commitdiff
2012-08-14
Anne Menard
last version stay many bugs ..
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commitdiff
2012-07-16
Anne Menard
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2012-07-10
Anne Menard
v2
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commitdiff
2012-07-05
Anne Menard
Add support RNAML format
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commitdiff
2012-07-03
jprocter
JAL-961 allow calcId to be specified independently...
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commitdiff
2012-06-15
jprocter
Merge branch 'JAL-1013_pca_rna_dna' into develop
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commitdiff
2012-06-13
jprocter
javatidy
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commitdiff
2012-06-12
jprocter
JAL-1115 refactor reordering code operating directly...
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commitdiff
2012-06-12
jprocter
JAL-1115 refactor base collection for Alignment from...
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commitdiff
2012-05-30
jprocter
JAL-1114 - refactor methods handling Vectors and Hashta...
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commitdiff
2012-05-24
jprocter
ensure annotation isn't added twice - note - this could...
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commitdiff
2012-05-23
jprocter
JAL-961 - annotatable datamodel objects can be queried...
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commitdiff
2012-05-22
jprocter
update the copy constructor
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commitdiff
2012-05-22
jprocter
Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...
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commitdiff
2011-12-08
jprocter
(JAL-1013) generalise binary sequence encoding scheme...
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commitdiff
2011-11-03
jprocter
(JAL-811) new 'annotation type' field for marking annot...
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commitdiff
2011-10-28
jprocter
JAL-580 ensure WUSS annotation string is up to date...
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commitdiff
2011-10-27
jprocter
(JAL-969) refactored alignmentViewport base class to...
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commitdiff
2011-10-21
jprocter
new base class to hold core visualization settings...
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commitdiff
2011-10-11
jprocter
normalised logo rendering (JAL-958)
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commitdiff
2011-10-10
jprocter
update author list in license for (JAL-826)
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commitdiff
2011-10-04
jprocter
Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...
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commitdiff
2011-09-27
jprocter
apply version 2.7 copyright
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commitdiff
2011-08-18
jprocter
fix for JAL-701 - ensure '<' appears in tooltip in...
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commitdiff
2011-08-17
jprocter
JAL-813 fix - check whether conservation is applied...
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commitdiff
2011-08-15
janengelhardt
JAL-891; Sorting of Structure logo implemented; bug...
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commitdiff
2011-08-11
janengelhardt
JAL-885; hasRNAStructure method was introduced to Align...
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commitdiff
2011-07-29
janengelhardt
JAL-885; Implementation of StructureFrequency.java...
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commitdiff
2011-07-25
janengelhardt
Further structure accessing feature
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commitdiff
2011-07-25
janengelhardt
Container for VARNA classes are created according to...
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commitdiff
2011-07-25
janengelhardt
'Update to Covariaton color scheme' merge; JAL-580
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commitdiff
2011-07-25
janengelhardt
Start merging of Laurens Code
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commitdiff
2011-07-08
jprocter
open each query result from an alignment datasource...
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commitdiff
2011-07-06
jprocter
ensure selseq is trimmed to just sequences included...
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commitdiff
2011-05-05
jprocter
uncommentable debug message for JAL-771
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commitdiff
2011-04-21
jprocter
allow an alignment annotation row to be removed and...
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commitdiff
2011-04-21
jprocter
allow an existing alignment annotation row to be bound...
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commitdiff
2011-02-27
jprocter
first patch for JAL-774 - ensure end is a valid bound...
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commitdiff
2011-01-05
jprocter
propagated groups trimmed to correct region on viscontig
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commitdiff
2011-01-05
jprocter
graphThreshold not being copied by constructor
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commitdiff
2010-12-17
jprocter
adjust start and end of intersecting group relative...
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commitdiff
2010-12-17
jprocter
1.1 compat
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commitdiff
2010-12-17
jprocter
1.1 compat
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commitdiff
2010-12-17
jprocter
refactored gap insert/visible view modification code...
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commitdiff
2010-12-17
jprocter
javadoc
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commitdiff
2010-12-10
jprocter
remove implicit non-1.1 compatible call
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commitdiff
2010-12-09
jprocter
java 1.1 patches
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commitdiff
2010-12-09
jprocter
java 1.1 patches
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commitdiff
2010-12-09
jprocter
new methods and test code for JAL-716
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