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2022-01-17	Jim Procter	Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files...	commit \| commitdiff \| tree
2022-01-17	Jim Procter	JAL-3940 fix issues in release notes	commit \| commitdiff \| tree
2022-01-17	Jim Procter	JAL-3940 bump version and update release notes - release...	commit \| commitdiff \| tree
2022-01-17	Jim Procter	JAL-3940 update release notes for JAL-3702,JAL-3935...	commit \| commitdiff \| tree
2022-01-06	Jim Procter	JAL-3934 update whats new	commit \| commitdiff \| tree
2022-01-06	Jim Procter	Merge branch 'task/JAL-3934_update_log4j_again' into...	commit \| commitdiff \| tree
2022-01-06	Jim Procter	JAL-3934 trigger patch release for log4j version bump	commit \| commitdiff \| tree
2021-12-20	Jim Procter	JAL-3842 remove replacement tokens in html text - not...	commit \| commitdiff \| tree
2021-12-20	Jim Procter	JAL-3842 patch what’s new text	commit \| commitdiff \| tree
2021-12-20	Jim Procter	JAL-3842 release 2.11.1.5 release notes	commit \| commitdiff \| tree
2021-12-20	Jim Procter	Merge branch 'critical/JAL-3933_log4shell_mitigation...	commit \| commitdiff \| tree
2021-12-15	Jim Procter	JAL-3933 remove obsolete Castor logging configuration	commit \| commitdiff \| tree
2021-12-15	Jim Procter	JAL-3933 configure root logger console appender to...	commit \| commitdiff \| tree
2021-07-13	Jim Procter	JAL-3842 fix automatic what's new link for custom version...	commit \| commitdiff \| tree
2021-06-30	Jim Procter	JAL-3842 JAL-3746 (need to cherry pick to develop)...	commit \| commitdiff \| tree
2014-10-23	Jim Procter	Merge branch 'hotfix/JAL-1521' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-10-23	Jim Procter	JAL-1521 patch is to remove xerces from classpath....	commit \| commitdiff \| tree
2014-10-23	Jim Procter	JAL-1521 test to check registry is returning sources	commit \| commitdiff \| tree
2014-10-23	Jim Procter	Merge branch 'Release_2_8_1_Branch'	commit \| commitdiff \| tree
2014-10-23	Jim Procter	patch fixes JAL-1558	commit \| commitdiff \| tree
2014-10-23	Jim Procter	Merge branch 'Release_2_8_1_Branch'	commit \| commitdiff \| tree
2014-10-23	Jim Procter	JAL-1503 tag 2.8.1b1 hotfix - last in 2.8.1 line	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'forpush/JAL-674_dssp' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 check for null vector before ...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'patch_sjf4j_typo' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1216 update varna dependency string in jalviewLite...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'patch_sjf4j_typo' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JWS-59 JAL-1216 patch broken InstallAnywhere build	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'forpush/JAL-674_dssp' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 reinstate missing import	commit \| commitdiff \| tree
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
2014-10-10	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 develop	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 develop	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 develop	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 develop	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 develop	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
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