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2014-09-12	j.procter@dundee...	Merge branch 'Release_2_8_2_Branch' of https://source...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	Merge branch 'bug/JAL-1486_flatfile' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1486 JAL-1543 pushed alignment viewport->view-...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	formatting and organise imports	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1486 fix: pass selected region to jalview.io via...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1199 add stockholm output to list of AppletFormatAdapter...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1486 JAL-535 refactor code for trimming alignment...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-535 tidy interface definition and documentation	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1516 Annotation row score output script for jalview...	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	Merge branch 'features/JAL-1333' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 fix imports	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	Merge branch 'features/JAL-1333' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 log4j/slf additional jars	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 add log4j-slf4j bridge	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	Merge branch 'features/JAL-1333' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 finessing log4j and slf dependencies for strucviz...	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 JAL-1533 todo to get Chimera superposing properly...	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 more superposition debugging and deadlock...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1379 Jpred JABA client test harness	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1333 allow reuse of existing chimera for new or...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1333 more refinements - deadlocks still possible...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-674 futzing with bugs	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-795 take colour from annotation if colour is present	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	ensure the dataset is instantiated before materialising...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1379 new look JPred results	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1520 switch between Protein and non-canonical RNA...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1028 JAL-1142 refactor test to allow reuse of secondary...	commit \| commitdiff \| tree
2014-07-08	j.procter@dundee...	JAL-1333 allow reuse of existing viewers (of a specified...	commit \| commitdiff \| tree
2014-07-08	j.procter@dundee...	JAL-1333 more efficient color statement	commit \| commitdiff \| tree
2014-07-04	j.procter@dundee...	JAL-1333 more abstraction and refactoring and working...	commit \| commitdiff \| tree
2014-07-03	j.procter@dundee...	Merge branch 'Release_2_8_2_Branch' into features/JAL...	commit \| commitdiff \| tree
2014-07-03	j.procter@dundee...	Merge branch 'hotfix/JAL-1530' into Release_2_8_2_Branch	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
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
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