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Merge branch 'develop' into develop_m2_8_1_2
[jalview.git]
/
src
/
2013-05-31
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
tree
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commitdiff
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
tree
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commitdiff
2013-05-24
Jim Procter
Merge branch 'menard' into develop_m2_8_1_2
tree
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commitdiff
2013-05-21
Jim Procter
JAL-1140 JAL-674 process with annotate3d and Jmol to...
tree
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commitdiff
2013-05-21
Jim Procter
JAL-674 ensure annotation is properly annotated
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commitdiff
2013-05-21
Jim Procter
JAL-1231 add chain ID
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commitdiff
2013-05-21
Jim Procter
JAL-1231 allow Jmol file handler to read from a stream
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commitdiff
2013-05-13
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStre...
tree
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commitdiff
2013-05-13
Jim Procter
Merge branch 'JAL-1289_initCallBack' into develop
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commitdiff
2013-05-13
Jim Procter
JAL-1289 call oninit callback even if no alignment...
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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
2013-02-14
Jim Procter
patch for bizarre ConcurrentModificationException that...
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commitdiff
2013-02-13
Jim Procter
Merge branch 'jims_annotate3d_update' into menard_final...
tree
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commitdiff
2013-02-13
jprocter
fix merge conflicts for finess on JAL-1140 (introduced...
tree
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commitdiff
2013-02-13
jprocter
JAL-1216 switch to official release of VARNA 3.9
tree
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commitdiff
2013-02-13
jprocter
JAL-1214 todo
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commitdiff
2013-02-13
jprocter
JAL-1213 JAL-674 - import a PDB file using Jmol data...
tree
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commitdiff
2013-02-13
jprocter
JAL-674 commented out annotate3d calling code for Jmol...
tree
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commitdiff
2013-02-13
jprocter
JAL-1028 JAL-674 hooks to call external processing...
tree
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commitdiff
2013-02-11
jprocter
patch for 'This parser does not support specification...
tree
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commitdiff
2013-02-11
jprocter
upgrade to latest paradise services model using JSon...
tree
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commitdiff
2013-02-06
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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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
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
tree
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commitdiff
2013-02-05
jprocter
formatting
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commitdiff
2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
tree
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commitdiff
2013-01-20
jprocter
Merge branch 'Dbfetch_hotfix-JAL-1238' into develop
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commitdiff
2013-01-18
jprocter
JAL-1238 order to place primary sources before lower...
tree
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commitdiff
2013-01-18
jprocter
JAL-1238 method to test if DAS source is a primary...
tree
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commitdiff
2013-01-18
jprocter
JAL-1238 tier index indicating distance of a source...
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commitdiff
2013-01-18
jprocter
Merge branch 'JAL-1254-hotfix' into develop
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commitdiff
2013-01-18
jprocter
JAL-1255 don't show 'Right click to add annotations...
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commitdiff
2013-01-18
jprocter
JAL-1254 patch for NPE in annotation renderer when...
tree
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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
2012-12-11
jprocter
JAL-1217 check and avoid NPE if no datastore object...
tree
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commitdiff
2012-12-11
jprocter
JAL-1217 report exception for service when no datastore...
tree
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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
2012-12-07
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
typing
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commitdiff
2012-12-07
jprocter
consensus secondary structure algorithm (possibly came...
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commitdiff
2012-12-07
jprocter
revised RNA stem/loop processing code that copes with...
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commitdiff
2012-12-07
jprocter
update authors for RNA processing routines
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commitdiff
2012-12-07
jprocter
menu for choosing between 'protein' and 'RNA' mode...
tree
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commitdiff
2012-12-07
jprocter
formatting and error report cleanup
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commitdiff
2012-12-07
jprocter
gui hooks for contrafold and RNAfold services. commente...
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commitdiff
2012-12-07
jprocter
Exception signature change (will be overwritten by...
tree
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commitdiff
2012-12-07
jprocter
formatting
tree
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commitdiff
2012-12-07
jprocter
tidy import
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commitdiff
2012-12-07
jprocter
remove mentions of non-functional RNAInteraction colour...
tree
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commitdiff
2012-12-07
jprocter
tidy debug messages
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commitdiff
2012-12-07
jprocter
proxy commit for Anne Menard <menard.annec@gmail.com...
tree
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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...
tree
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commitdiff
2012-12-04
jprocter
JAL-1140 - IO classes should only raise generic IOExcep...
tree
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commitdiff
2012-12-04
jprocter
JAL-1216 switch to official release of VARNA 3.9
tree
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commitdiff
2012-12-04
jprocter
JAL-1214 todo
tree
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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
2012-12-04
jprocter
JAL-674 commented out annotate3d calling code for Jmol...
tree
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commitdiff
2012-12-04
jprocter
JAL-1028 JAL-674 hooks to call external processing...
tree
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commitdiff
2012-12-04
jprocter
JAL-1028 tidy and refactor external processing and...
tree
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commitdiff
2012-11-23
Natasha
stockholm file output code developed by Natasha Sherstneva
tree
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commitdiff
2012-11-19
jprocter
bugfix
tree
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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
tree
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commitdiff
2012-11-17
jprocter
return alignmentI created from pdbfile class directly...
tree
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commitdiff
2012-11-17
jprocter
return annotated rna sequences from rnaml returned...
tree
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commitdiff
2012-11-17
jprocter
store chainid on pdbentry
tree
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commitdiff
2012-11-17
jprocter
format adapter should return AlignmentI
tree
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commitdiff
2012-11-17
jprocter
formatting
tree
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commitdiff
2012-11-17
jprocter
call annotate3d service and parse rnaml to alignment
tree
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commitdiff
2012-11-17
jprocter
formatting
tree
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commitdiff
2012-11-17
jprocter
sequence numbering from 1
tree
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commitdiff
2012-11-17
jprocter
formatting
tree
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commitdiff
2012-11-17
jprocter
store chaincode on pdbentry
tree
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commitdiff
2012-11-17
jprocter
formatting
tree
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commitdiff
2012-11-17
jprocter
simple HTTP multipart entity poster - may not be useful
tree
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commitdiff
2012-11-17
jprocter
openjdk7 returns null for default value selected format...
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commitdiff
2012-11-17
jprocter
method to construct sequence mapping for matching posit...
tree
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commitdiff
2012-11-17
jprocter
convenience method for performing pairwise alignment
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commitdiff
2012-11-17
jprocter
formatting and javadoc
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commitdiff
2012-11-15
Paolo Di Tommaso
Fixed T-Coffee file scores parser to support extended...
tree
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commitdiff
2012-11-15
jprocter
don't set background colour for menu bar
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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
2012-11-09
jprocter
constructor takes settings from any existing feature...
tree
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commitdiff
2012-11-08
jprocter
JAL-1193 ensure the 'loadedComplete' method gets called...
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commitdiff
2012-11-08
jprocter
remember to close input file!
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commitdiff
2012-11-08
jprocter
tidy imports
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commitdiff
2012-11-07
jprocter
JAL-957 manual update to applet authorlist - need to...
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commitdiff
2012-10-24
jprocter
JAL-1193 call setLoadingFromArchiveFinished(true) for...
tree
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commitdiff
2012-10-24
jprocter
JAL-1193 patch prevents JalviewJmolBinding from handlin...
tree
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commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
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commitdiff
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