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2014-11-03	Jim Procter	fix for JAL-1579 create threshold object for annotation...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1578 test property accessors/copy constructor	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1578 JAL-674 store/restore alignment annotation...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1578 formatting and imports	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-674 peptide structure input so test is not dependent...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-674 JAL-961 JAL-1578 accessors and copy constructor...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	javadoc	commit \| commitdiff \| tree
2014-10-31	Jim Procter	JAL-674 JAL-961 pass row reference to handler to check...	commit \| commitdiff \| tree
2014-10-31	Jim Procter	JAL-674 JAL-961 properties to stash additional information...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	Merge branch 'develop' into features/ssFromPDBEntry	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 hang on to sequences created by secondary parsiing...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 count number of annotation transferred in test	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 propagate annotation onto mapped sequence and...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 register PDB IDs when ever they are resolved...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 use PDB ID<>File registry to look up correct...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 return original and replacement sequences and...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 helpful javadoc for remap method	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 flag and proxy method to distinguish setMapping...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 map on StructureSelectionManager to record...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	patch for JAL-795 - use base secondary structure colour...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 patch test to verify presence of annotation...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-1551 format and tidy	commit \| commitdiff \| tree
2014-10-29	Jim Procter	JAL-1264 JAL-674 test to exercise the AlignmentAnnotation...	commit \| commitdiff \| tree
2014-10-29	Jim Procter	JAL-1264 JAL-674 method to copy annotation on structure...	commit \| commitdiff \| tree
2014-10-29	Jim Procter	JAL-674 JAL-1264 remap method to allow annotation positions...	commit \| commitdiff \| tree
2014-10-27	Jim Procter	Merge branch 'Release_2_8_2_Branch' into merge_r282_dev	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 develop	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
2014-06-12	Jim Procter	Merge branch 'feature/JAL-1379' into develop	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	Merge branch 'Release_2_8_2_Branch' into develop	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1520 fix unicode translation errors.	commit \| commitdiff \| tree
2014-06-06	Jim Procter	Merge branch 'Release_2_8_2_Branch' into develop	commit \| commitdiff \| tree
2014-06-06	Jim Procter	JAL-1520 fix unicode translation errors.	commit \| commitdiff \| tree
2014-06-06	Jim Procter	Merge branch 'Release_2_8_2_Branch' into develop	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
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	commit \| commitdiff \| tree
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	commit \| commitdiff \| tree
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1503 typo	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'develop' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1503 update author list for 2.8.1	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-690 JAL-1503 make file associations optional for...	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-952 fixed unresolved conflict breaking build	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Jalview 2.8.2 release branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-952 fixed unresolved conflict breaking build	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1503 tweak whatsNew document	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1503 JAL-690 document .jvp in release notes	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1514 - add jalview.org and dundee to explore if...	commit \| commitdiff \| tree
2014-06-04	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1503 tidying docs	commit \| commitdiff \| tree
2014-06-04	Jim Procter	JAL-1355 key typo	commit \| commitdiff \| tree
2014-06-03	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 documentation and release notes	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-690 jvp rather than jar for save/restore state...	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-690 JAL-1503 update file types/extensions in Jalview...	commit \| commitdiff \| tree
2014-06-03	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 update version/branch version for this branch	commit \| commitdiff \| tree
2014-06-03	Jim Procter	regress fix on JAL-690 - insert association elements...	commit \| commitdiff \| tree
2014-06-03	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 whats new and release history for 2.8.1 (still...	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 JAL-1350 rework documentation for 2.8.1	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1164 note that feature introduced in 2.8.0b1	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 JAL-1355 documentation	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1473 exclude score models not compatible with PCA...	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 gui changes (score models, flanking regions...	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 formatting	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 additional tree score functions	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 PAM250 documentation	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 document updated PCA interface	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-690 add .jvp as default jalview project filetype	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 formatting	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1503 formatting build file	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1512 comment out for 2.8.1 release	commit \| commitdiff \| tree
2014-06-03	Jim Procter	JAL-1512 fix calculation once again and include score...	commit \| commitdiff \| tree
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