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2014-10-21	Jim Procter	JAL-674 initial implementation - only need to extract...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 crlf	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 JAL-1551 imports dropped during merge	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1216 update to VARNA 3.91	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 remove any spurious PDBEntrys generated by...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 methods and test for PDB derived annotation...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 store ID in MCview.PDBfile calcId string, not...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 don't create multiple secondary structure lines...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test for the test for presence of annotation...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test for presence of annotation derived from...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 patch for duplicate row bug	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test for duplicate alignment annotation rows...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 patch to ensure existing annotation is properly...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test to ensure sequence and annotation on sequence...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 source formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 JAL-207 getTers for aligned sequences in dataset...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 refactor method to match and transfer annotation...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'features/JAL-1264_showHideAnnotations...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 crlf changes	commit \| commitdiff \| tree
2014-10-16	Jim Procter	Merge branch 'feature/JAL-674_dssp' into features/JAL...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	Merge branch 'jims_crlf_hell_JAL-1551' of https://source...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-1551 crlf changes due to checkout with text=auto	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-1551 crlf changes due to checkout with text=auto	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 always try to extract secondary structure when...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 support preservation of any annotation created...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 make transferAnnotation method static	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-348 JAL-674 JAL-1564 TODO and implementation error...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 patch logic to test whether old and new sequence...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 JAL-1305 JAL-348 new liftOver method and test...	commit \| commitdiff \| tree
2014-10-14	gmungoc	JAL-1551 CRLF handling	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 employ new signature in Annotate3D service...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 disable secondary structure annotation when...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 typo	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 new constructors to pass flags about annotating...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 parser flag to control secondary structure...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 change jalview.io.AlignFile to allow parsing...	commit \| commitdiff \| tree
2014-10-09	Jim Procter	Merge branch 'bug/JAL-1558' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-09	Jim Procter	patch fixes JAL-1558	commit \| commitdiff \| tree
2014-10-07	Jim Procter	Merge branch 'bugs/JAL-1151' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-07	Jim Procter	JAL-1557 partial implementation - need to think about...	commit \| commitdiff \| tree
2014-10-07	Jim Procter	patch for JAL-1151 - select whole sequence when double...	commit \| commitdiff \| tree
2014-10-07	Jim Procter	JAL-1421 remove Vector and pass a list	commit \| commitdiff \| tree
2014-10-07	Jim Procter	JAL-1151 source tidy	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'JAL-429_phylip-file-support' into Release_2_8_...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'patch/JAL-848' into JAL-429_phylip-file...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'patch/JAL-848' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-848 reinstate netbeans files from Phylip patch...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'JAL-429_phylip-file-support' into Release_2_8_...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'Release_2_8_2_Branch' into JAL-429_phylip...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'patch/JAL-1286_JAL-1265' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-1286 missing file for testcase where file ends...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-1500 JAL-1265 patch to parse PDB database refs...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'feature/JAL-654_dssp' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 remove any annotation rows for chain specific...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 updated pdb db fetcher test to verify the number...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 JAL-1264 sequence associated annotation is...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 format and refactor test demonstrating PDB...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-1115 TODO remove use of java.util.Vector	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 javadoc createDatasetSequence and transferAnnotation	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654_dssp formatting and javadoc	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'Release_2_8_2_Branch_i18n' into Release_2_8_2_...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	JAL-1355 removed all top level html tags from message...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'Release_2_8_2_Branch' into Release_2_8_2_Branc...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-03	Jim Procter	JAL-1338 note added #fridaycommits not actually connected...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-03	Jim Procter	JAL-1499 simple test to check JABA client can	commit \| commitdiff \| tree
2014-07-03	Jim Procter	fixes JAL-1530	commit \| commitdiff \| tree
2014-07-02	Jim Procter	revalidate appears to have gone away ?? (java 1.7 upgrade...	commit \| commitdiff \| tree
2014-07-02	Jim Procter	formatting	commit \| commitdiff \| tree
2014-07-02	Jim Procter	JAL-1333 JAL-1527 refactors to create core structure...	commit \| commitdiff \| tree
2014-07-02	Jim Procter	JAL-1333 test suite for key functionality of java interface...	commit \| commitdiff \| tree
2014-07-02	Jim Procter	JAL-1333 Chimera specific code extracted from the...	commit \| commitdiff \| tree
2014-07-01	Jim Procter	Merge branch 'feature/JAL-1333' into features/JAL-1333	commit \| commitdiff \| tree
2014-06-23	Jim Procter	Merge branch 'JAL-1526' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-06-23	Jim Procter	JAL-1526 simple function to write a snapshot of the...	commit \| commitdiff \| tree
2014-06-12	Jim Procter	Merge branch 'hotfix/JAL-1524' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-06-12	Jim Procter	Merge branch 'hotfix/JAL-1524' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-12	Jim Procter	JAL-1524 fix	commit \| commitdiff \| tree
2014-06-10	Jim Procter	Merge branch 'feature/JAL-1379' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-06-10	Jim Procter	JAL-1379 a JPred v3.0.1 client via JABA 2.1	commit \| commitdiff \| tree
2014-06-10	Jim Procter	JAL-1379 allow services with an MSA interface to create...	commit \| commitdiff \| tree
2014-06-10	Jim Procter	tidy source	commit \| commitdiff \| tree
2014-06-10	Jim Procter	JAL-1379 allow JABA2 tests to run on local or default...	commit \| commitdiff \| tree
2014-06-10	Jim Procter	JAL-1379 refactor Jws2 service client so dynamic services...	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1520 fix unicode translation errors.	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1520 fix unicode translation errors.	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1519 make the splash screen larger/more readable	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1519 - tidy build properties management code	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1519 fix author update issue (doh)	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1140 Add Anne Menard to author list	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1517 copyright and formatting	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1518 drop Jalopy from utils directory	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1517 copyright and formatting	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1517 source formatting	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1518 drop Jalopy from utils directory	commit \| commitdiff \| tree
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