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Merge branch 'develop' into develop_m2_8_1_2
[jalview.git]
/
src
/
jalview
/
io
/
2013-06-07
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
tree
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commitdiff
2013-06-07
Jim Procter
Merge branch 'JAL-1161_optimisingAnnotationPanel' into...
tree
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commitdiff
2013-05-24
Jim Procter
Merge branch 'menard' into develop_m2_8_1_2
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commitdiff
2013-05-24
Jim Procter
patch for JAL-1300 fixes JAL-1294: read and write COMBI...
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commitdiff
2013-05-24
Jim Procter
JAL-381 Desktop.addInternalFrame cannot be called in...
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commitdiff
2013-05-24
Jim Procter
JAL-1299 fix: ensure a new graphGroup is created if...
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commitdiff
2013-05-24
Jim Procter
fix for JAL-1297: COMBINE output now follows specificat...
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commitdiff
2013-05-24
Jim Procter
JAL-1070 - [ not a real patch ] - include offending...
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commitdiff
2013-05-13
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStre...
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commitdiff
2013-04-12
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStre...
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commitdiff
2013-02-14
Jim Procter
Merge branch 'JAL-1199-Stk_writing' into rnaml_test
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commitdiff
2013-02-14
Jim Procter
JAL-1140 reinstate the simpler version of parsing code...
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commitdiff
2013-02-13
Jim Procter
Merge branch 'jims_annotate3d_update' into menard_final...
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commitdiff
2013-02-13
jprocter
fix merge conflicts for finess on JAL-1140 (introduced...
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commitdiff
2013-02-13
jprocter
JAL-1213 JAL-674 - import a PDB file using Jmol data...
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commitdiff
2013-02-11
jprocter
patch for 'This parser does not support specification...
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commitdiff
2013-02-06
jprocter
JAL-1265 basic support for parsing database accessions...
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commitdiff
2013-02-06
jprocter
JAL-1199 refactored stockholm test code from main class...
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commitdiff
2013-02-05
jprocter
formatting
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commitdiff
2012-12-17
Natasha
test for output a file in Stockholm format
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commitdiff
2012-12-12
Natasha
Output accession number for file in stockholm format
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commitdiff
2012-12-07
jprocter
Anne's refined RNAML parser. Seems to have some bugs...
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commitdiff
2012-12-07
jprocter
Anne reinstated general stockholm parser code but exten...
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commitdiff
2012-12-07
jprocter
formatting and error report cleanup
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commitdiff
2012-12-07
jprocter
proxy commit for Anne Menard <menard.annec@gmail.com...
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commitdiff
2012-12-04
jprocter
JAL-1140 - handled VARNA specific RNA exceptions within...
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commitdiff
2012-12-04
jprocter
JAL-1140 - handle VARNA specific RNA exceptions within...
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commitdiff
2012-12-04
jprocter
JAL-1140 - IO classes should only raise generic IOExcep...
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commitdiff
2012-12-04
jprocter
JAL-1213 JAL-674 - import a PDB file using Jmol data...
tree
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commitdiff
2012-11-23
Natasha
stockholm file output code developed by Natasha Sherstneva
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commitdiff
2012-11-17
jprocter
Merge branch 'develop' into menard
tree
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commitdiff
2012-11-17
jprocter
FileParse adapter for reading directly from inputstreams
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commitdiff
2012-11-17
jprocter
format adapter should return AlignmentI
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commitdiff
2012-11-17
jprocter
formatting
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commitdiff
2012-11-17
jprocter
sequence numbering from 1
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commitdiff
2012-11-17
jprocter
formatting
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commitdiff
2012-11-17
jprocter
formatting
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commitdiff
2012-11-15
Paolo Di Tommaso
Fixed T-Coffee file scores parser to support extended...
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commitdiff
2012-11-15
jprocter
allow .rnaml as a filename extension
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commitdiff
2012-11-15
jprocter
comment on jalview.io.AlignFile architecture
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commitdiff
2012-11-15
jprocter
source formatting
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commitdiff
2012-11-15
jprocter
Merge branch 'develop' into menard
tree
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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
2012-08-31
jprocter
Merge branch 'develop' into menard
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commitdiff
2012-08-31
jprocter
JAL-1015 resolve dataset sequence before searching...
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commitdiff
2012-08-31
jprocter
JAL-1015 refactor tooltip html generation code to jalvi...
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commitdiff
2012-08-20
jprocter
JAL-1140 bugfix - getDataName throws errors - prefer...
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commitdiff
2012-08-20
jprocter
JAL-1140 use the Reader provided by the jalview.io...
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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
2012-07-01
jprocter
JAL-1117 alleviate lock starvation
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commitdiff
2012-06-13
jprocter
JAL-1116 - location where vamsas sync failure occurs
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commitdiff
2012-06-13
jprocter
javatidy
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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
JAL-1065 per sequence and per-alignment scores added...
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commitdiff
2012-05-24
jprocter
JAL-1065 - ensure null entries in annotation row so...
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commitdiff
2012-05-23
jprocter
JAL-1067, JAL-1105 - refactor parser to fit Jalview...
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commitdiff
2012-05-23
jprocter
todo: blocked by JAL-1104
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commitdiff
2012-05-22
jprocter
Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...
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commitdiff
2012-03-02
jprocter
(JAL-1052) todo for output of RNA consensus lines
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commitdiff
2012-03-02
jprocter
(JAL-1052) basic consensus line parsing to rna structur...
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commitdiff
2012-03-02
jprocter
(JAL-1052) make RNA secondary structure string parsing...
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commitdiff
2011-10-21
jprocter
todo
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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
2011-08-30
jprocter
ensure parsing errors and 'lack of data' errors are...
tree
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commitdiff
2011-08-19
jprocter
JAL-908 JAL-701 refactored HTML escape/unescape code...
tree
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commitdiff
2011-07-25
janengelhardt
some print statements to test things
tree
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commitdiff
2011-07-25
janengelhardt
JAL-878; Additional structures with a 'GR' tag in Stock...
tree
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commitdiff
2011-07-25
janengelhardt
JAL-841; Structure trigger token in jalview.io.Alignmen...
tree
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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
2011-07-21
jprocter
ensure contents of hash is extended JAL-876
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commitdiff
2011-06-24
jprocter
fix to preserve sequence numbering in MSF (JAL-847)
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commitdiff
2011-05-17
jprocter
refactor to allow distinct StructureSelectionManager...
tree
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commitdiff
2011-02-17
jprocter
classCast exception - attempting to update registry...
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commitdiff
2011-01-21
jprocter
relaxed ID matching parameter JAL-753
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commitdiff
2011-01-07
jprocter
check for all http protocols
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commitdiff
2011-01-05
jprocter
JAL-727
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commitdiff
2011-01-05
jprocter
JAL-727
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commitdiff
2010-12-17
jprocter
JAL-715
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commitdiff
2010-12-15
jprocter
update modification state flag according to parsing...
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commitdiff
2010-12-15
jprocter
getters and modification state flag
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commitdiff
2010-12-15
jprocter
more accurate determination of annotation modification
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commitdiff
2010-12-15
jprocter
refactored key calc for hash to separate function
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commitdiff
2010-12-14
jprocter
1.1 compat
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commitdiff
2010-12-14
jprocter
1.1 compat
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commitdiff
2010-12-14
jprocter
always provide reference to hashtable so feature settin...
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commitdiff
2010-12-14
jprocter
refactored and patched for JAL-721
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commitdiff
2010-12-10
jprocter
mime types and handler
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commitdiff
2010-12-09
jprocter
dataIn.ready() is not a test of data source validity!
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commitdiff
2010-12-09
jprocter
initial list of mime-type bindings to jalview data...
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commitdiff
2010-12-09
jprocter
initial implementation for JAL-718
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