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[jalview.git] / src / MCview / PDBfile.java

2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff
2016-07-21	tcofoegbu	JAL-2148 fix to heuristically determine chain terminati...	blob \| commitdiff \| diff to current
2016-07-08	tcofoegbu	JAL-1919 Fixed failing tests, enabled HETATM processing...	blob \| commitdiff \| diff to current
2016-03-15	tcofoegbu	JAL-1919 refined structure view annotation settings...	blob \| commitdiff \| diff to current
2016-03-03	tcofoegbu	JAL-1919 PDBfile and JmolParser refactor	blob \| commitdiff \| diff to current
2016-02-25	tcofoegbu	JAL-1919 initial support for mmCIF using JMol API....	blob \| commitdiff \| diff to current
2016-01-21	tcofoegbu	JAL-1919 basic support for importing and viewing mmCIF...	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...	blob \| commitdiff \| diff to current
2015-10-29	tcofoegbu	JAL-1926 JAL-1479 updated PDBfile fetcher to add source...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-08-07	tcofoegbu	JAL-1824 updated caching procedure for pdb entries...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-653 JAL-1780 reorder imports	blob \| commitdiff \| diff to current
2015-06-08	gmungoc	JAl-1421 fix method reflection argument (properly this...	blob \| commitdiff \| diff to current
2015-06-08	gmungoc	JAL-1421 undid premature 'improvement' of method parame...	blob \| commitdiff \| diff to current
2015-06-04	gmungoc	JAL-1421 generic collections in MCView package (+unit...	blob \| commitdiff \| diff to current
2015-05-22	tcofoegbu	JAL-1745, JAL-1717 improvement to ensure cached PDB...	blob \| commitdiff \| diff to current
2015-04-30	tcofoegbu	JAL-1717 updated the PDBEntry model and updated the...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-26	Jim Procter	JAL-674 employ the provided DNA/Protein matrix string...	blob \| commitdiff \| diff to current
2014-11-18	Jim Procter	JAL-674 make temperature factor, local secondary struct...	blob \| commitdiff \| diff to current
2014-10-31	Jim Procter	JAL-674 JAL-961 pass row reference to handler to check...	blob \| commitdiff \| diff to current
2014-10-30	Jim Procter	JAL-674 hang on to sequences created by secondary parsi...	blob \| commitdiff \| diff to current
2014-10-30	Jim Procter	JAL-1551 format and tidy	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-674 check for null vector before ...	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-674 remove any spurious PDBEntrys generated by...	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-674 methods and test for PDB derived annotation...	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-674 store ID in MCview.PDBfile calcId string, not...	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-674 test for presence of annotation derived from...	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-1551 formatting	blob \| commitdiff \| diff to current
2014-10-21	Jim Procter	JAL-674 refactor method to match and transfer annotatio...	blob \| commitdiff \| diff to current
2014-10-15	Jim Procter	JAL-674 support preservation of any annotation created...	blob \| commitdiff \| diff to current
2014-10-15	Jim Procter	JAL-674 make transferAnnotation method static	blob \| commitdiff \| diff to current
2014-10-10	Jim Procter	JAL-674 typo	blob \| commitdiff \| diff to current
2014-10-10	Jim Procter	JAL-674 new constructors to pass flags about annotating...	blob \| commitdiff \| diff to current
2014-10-10	Jim Procter	JAL-674 parser flag to control secondary structure...	blob \| commitdiff \| diff to current
2014-10-06	Jim Procter	JAL-654_dssp formatting and javadoc	blob \| commitdiff \| diff to current
2014-09-26	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into develop	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-10-15	Jim Procter	workaround for JAL-1395	blob \| commitdiff \| diff to current
2013-06-09	Jim Procter	Merge branch 'develop' into develop_m2_8_1_2	blob \| commitdiff \| diff to current
2013-06-09	Jim Procter	JAL-674 avoid runtime dependency on annotate3d webservi...	blob \| commitdiff \| diff to current
2013-05-21	Jim Procter	JAL-1140 JAL-674 process with annotate3d and Jmol to...	blob \| commitdiff \| diff to current
2013-02-13	jprocter	fix merge conflicts for finess on JAL-1140 (introduced...	blob \| commitdiff \| diff to current
2013-02-13	jprocter	JAL-1214 todo	blob \| commitdiff \| diff to current
2013-02-13	jprocter	JAL-674 commented out annotate3d calling code for Jmol...	blob \| commitdiff \| diff to current
2013-02-13	jprocter	JAL-1028 JAL-674 hooks to call external processing...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	proxy commit for Anne Menard <menard.annec@gmail.com...	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-1140 - IO classes should only raise generic IOExcep...	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-1214 todo	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-674 commented out annotate3d calling code for Jmol...	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-1028 JAL-674 hooks to call external processing...	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-1028 tidy and refactor external processing and...	blob \| commitdiff \| diff to current
2012-11-19	jprocter	bugfix	blob \| commitdiff \| diff to current
2012-11-17	jprocter	return annotated rna sequences from rnaml returned...	blob \| commitdiff \| diff to current
2012-11-17	jprocter	store chainid on pdbentry	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-14	Anne Menard	last version stay many bugs ..	blob \| commitdiff \| diff to current
2012-07-16	Anne Menard	Last version	blob \| commitdiff \| diff to current
2012-07-10	Anne Menard	v2	blob \| commitdiff \| diff to current
2012-07-05	Anne Menard	Add support RNAML format	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-01-06	jprocter	JAL-730	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-10-30	jprocter	na pdb: detect P backbone	blob \| commitdiff \| diff to current
2009-10-12	jprocter	ensure id string doesn't get set to the empty string...	blob \| commitdiff \| diff to current
2009-06-08	jprocter	patch for wierd format header lines and apply gpl devel...	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-01-29	jprocter	FileParse object can be re-used to read different files...	blob \| commitdiff \| diff to current
2007-06-17	jprocter	fix modeller generated PDB file reading bug (missing...	blob \| commitdiff \| diff to current
2007-04-20	jprocter	adds annotation for display (with flag to set alignment...	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	formatting	blob \| commitdiff \| diff to current
2007-01-19	jprocter	PDBChain maintains reference to dataset of sequences...	blob \| commitdiff \| diff to current
2007-01-18	jprocter	transfer and update of sequenceFeatures for associated...	blob \| commitdiff \| diff to current
2006-11-20	amwaterhouse	Memory check on PDB file	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-08-11	amwaterhouse	inFile might be null if PDB was pasted	blob \| commitdiff \| diff to current
2006-07-26	amwaterhouse	PDB file MUST have an id	blob \| commitdiff \| diff to current
2006-07-25	amwaterhouse	Extends AlignFile, dataset has PDBEntry added	blob \| commitdiff \| diff to current
2006-03-08	amwaterhouse	Can read from zip file	blob \| commitdiff \| diff to current
2005-12-09	amwaterhouse	All colours added to Structure viewer	blob \| commitdiff \| diff to current
2005-12-06	amwaterhouse	PDB structure viewer updated	blob \| commitdiff \| diff to current
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