Log of /biojava-live/trunk/biojava3-structure

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Revision 10104 - Directory Listing
Modified Wed Mar 27 17:57:10 2013 UTC (7 weeks, 2 days ago) by andreas

making atomcache more extensible.  Now can be extended by DB-based implementation, rather than file system based.

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Revision 10103 - Directory Listing
Modified Tue Mar 26 17:21:15 2013 UTC (7 weeks, 3 days ago) by andreas

making sure this ends with the correct URL

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Revision 10102 - Directory Listing
Modified Fri Mar 22 17:53:35 2013 UTC (8 weeks ago) by andreas

propagaingt server config to the remote domain lookup services

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Revision 10101 - Directory Listing
Modified Fri Mar 22 17:42:05 2013 UTC (8 weeks ago) by andreas

now threads sleep longer

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Revision 10100 - Directory Listing
Modified Wed Mar 20 23:59:58 2013 UTC (8 weeks, 2 days ago) by blivens

Minor bug fixes in AlignmentTools (rmsd calculation) 

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Revision 10097 - Directory Listing
Modified Tue Mar 19 04:23:50 2013 UTC (8 weeks, 4 days ago) by andreas

updated toString method

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Revision 10096 - Directory Listing
Modified Tue Mar 19 04:01:43 2013 UTC (8 weeks, 4 days ago) by andreas

new flag to update remediated files

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Revision 10095 - Directory Listing
Modified Tue Mar 19 04:00:51 2013 UTC (8 weeks, 4 days ago) by andreas

new flag to update remediated files

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Revision 10094 - Directory Listing
Modified Mon Mar 18 22:07:10 2013 UTC (8 weeks, 4 days ago) by andreas

fixing a problem with 2F03

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Revision 10092 - Directory Listing
Modified Sat Mar 16 17:58:22 2013 UTC (2 months ago) by andreas

using new cache path for storing chemp comps

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Revision 10091 - Directory Listing
Modified Sat Mar 16 17:55:10 2013 UTC (2 months ago) by andreas

using new cache path for storing chemp comps

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Revision 10090 - Directory Listing
Modified Fri Mar 15 18:01:08 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10089 - Directory Listing
Modified Fri Mar 15 18:00:57 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10088 - Directory Listing
Modified Fri Mar 15 18:00:43 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10087 - Directory Listing
Modified Fri Mar 15 18:00:15 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10086 - Directory Listing
Modified Fri Mar 15 17:59:48 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10085 - Directory Listing
Modified Fri Mar 15 17:59:22 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10084 - Directory Listing
Modified Fri Mar 15 17:58:43 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10083 - Directory Listing
Modified Fri Mar 15 17:57:51 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10082 - Directory Listing
Modified Fri Mar 15 17:57:41 2013 UTC (2 months ago) by andreas

adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

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Revision 10078 - Directory Listing
Modified Wed Mar 6 02:25:29 2013 UTC (2 months, 1 week ago) by blivens

Added static methods to calculate rotation angle quickly

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Revision 10077 - Directory Listing
Modified Wed Mar 6 01:25:19 2013 UTC (2 months, 1 week ago) by blivens

Visualize screw translation in RotationAxis

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Revision 10076 - Directory Listing
Modified Wed Mar 6 00:28:33 2013 UTC (2 months, 1 week ago) by blivens

Fixed bug with RotationAxis effecting a small fraction of 180 deg rotations

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Revision 10075 - Directory Listing
Modified Tue Mar 5 18:24:29 2013 UTC (2 months, 1 week ago) by andreas

new SparseSquareMatrix implementation

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Revision 10074 - Directory Listing
Modified Tue Mar 5 02:17:53 2013 UTC (2 months, 1 week ago) by dmyerstu

Fixed a ArrayIndexOutBoundsException in CeCPMain resulting from a empty alignment and a similar issue in RotationAxis.

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Revision 10072 - Directory Listing
Modified Sat Mar 2 17:18:24 2013 UTC (2 months, 2 weeks ago) by andreas

demo for how load secstruc assignment from pdb file

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Revision 10069 - Directory Listing
Modified Fri Mar 1 02:25:21 2013 UTC (2 months, 2 weeks ago) by blivens

Fixed bug in RotationAxis position

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Revision 10068 - Directory Listing
Modified Fri Mar 1 01:46:12 2013 UTC (2 months, 2 weeks ago) by blivens

Refactored RotationAxis & added documentation

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Revision 10067 - Directory Listing
Modified Fri Mar 1 01:45:47 2013 UTC (2 months, 2 weeks ago) by blivens

Made AtomCache exception messages slightly more palatable, although they still get caught and rethrown multiple times

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Revision 10066 - Directory Listing
Modified Thu Feb 28 18:22:47 2013 UTC (2 months, 2 weeks ago) by andreas

better error message

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Revision 10065 - Directory Listing
Modified Thu Feb 28 17:57:46 2013 UTC (2 months, 2 weeks ago) by andreas

checking for non-existing chem comps

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Revision 10058 - Directory Listing
Modified Tue Feb 26 00:23:55 2013 UTC (2 months, 2 weeks ago) by dmyerstu

Forgot to commit AtomPositionMap's test; adding it now.

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Revision 10057 - Directory Listing
Modified Tue Feb 26 00:22:41 2013 UTC (2 months, 2 weeks ago) by dmyerstu

Small improvements to ResidueRange, AtomPosition, and ResidueNumber; added a few useful methods. No bug fixes.

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Revision 10018 - Directory Listing
Modified Thu Feb 21 01:00:22 2013 UTC (2 months, 3 weeks ago) by blivens

Added RotationAxis, which calculates (and displays) the axis of rotation for alignments.

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Revision 10010 - Directory Listing
Modified Tue Feb 12 20:14:59 2013 UTC (3 months ago) by andreas

updating docu text

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Revision 10008 - Directory Listing
Modified Tue Feb 12 01:39:50 2013 UTC (3 months ago) by andreas

now setting custom user file name correctly

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Revision 10007 - Directory Listing
Modified Tue Feb 12 01:39:41 2013 UTC (3 months ago) by andreas

now setting custom user file name correctly

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Revision 10006 - Directory Listing
Modified Tue Feb 12 00:49:00 2013 UTC (3 months ago) by andreas

better naming of user provided file

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Revision 10001 - Directory Listing
Modified Mon Feb 11 18:54:51 2013 UTC (3 months ago) by andreas

now accepting new parameters searchFile and nrCPU

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Revision 10000 - Directory Listing
Modified Mon Feb 11 18:49:52 2013 UTC (3 months ago) by andreas

now accepting new parameters searchFile and nrCPU

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Revision 9999 - Directory Listing
Modified Mon Feb 11 18:49:24 2013 UTC (3 months ago) by andreas

new utility classes for checking and downloading PDB files

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Revision 9998 - Directory Listing
Modified Mon Feb 11 18:49:04 2013 UTC (3 months ago) by andreas

refactoring DB search code to be independent of UI

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Revision 9997 - Directory Listing
Modified Mon Feb 11 16:43:31 2013 UTC (3 months ago) by andreas

updated about text

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Revision 9991 - Directory Listing
Modified Thu Feb 7 19:33:53 2013 UTC (3 months, 1 week ago) by andreas

now with support for PdbxChemCompDescriptor category

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Revision 9990 - Directory Listing
Modified Wed Feb 6 01:13:57 2013 UTC (3 months, 1 week ago) by andreas

making field a string for now

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Revision 9989 - Directory Listing
Modified Wed Feb 6 00:39:08 2013 UTC (3 months, 1 week ago) by andreas

adding support for new chemp comp object types for entries in the BIRD dictionary

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Revision 9988 - Directory Listing
Modified Wed Feb 6 00:38:54 2013 UTC (3 months, 1 week ago) by andreas

adding support for new chemp comp object types for entries in the BIRD dictionary

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Revision 9969 - Directory Listing
Modified Thu Jan 24 17:26:22 2013 UTC (3 months, 3 weeks ago) by andreas

fixing special case is one letter code of nonstandard amino acid = ?

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Revision 9967 - Directory Listing
Modified Fri Jan 18 23:26:22 2013 UTC (3 months, 4 weeks ago) by andreas

fix, if something goes wrong with ChemComps...

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Revision 9966 - Directory Listing
Modified Fri Jan 18 23:22:34 2013 UTC (3 months, 4 weeks ago) by andreas

requesting a structure by PDB ID does not reduce it any longer

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Revision 9965 - Directory Listing
Modified Fri Jan 18 22:04:27 2013 UTC (3 months, 4 weeks ago) by pwrose

Made sure that CrystallographicInfo is copied.

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Revision 9964 - Directory Listing
Modified Fri Jan 18 21:39:56 2013 UTC (3 months, 4 weeks ago) by pwrose

Added copying of CrystallographicInfo to clone().

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Revision 9963 - Directory Listing
Modified Wed Jan 16 22:17:28 2013 UTC (4 months ago) by andreas

turning off debug mode

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Revision 9962 - Directory Listing
Modified Wed Jan 16 20:03:54 2013 UTC (4 months ago) by andreas

update to parser to make sure 2BGJ , 2J4Z, 2JBP are being parsed correctly. (probably there are more)

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Revision 9961 - Directory Listing
Modified Wed Jan 16 19:49:35 2013 UTC (4 months ago) by andreas

update to parser to make sure 2BGJ , 2J4Z, 2JBP are being parsed correctly. (probably there are more)

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Revision 9960 - Directory Listing
Modified Wed Jan 16 00:52:01 2013 UTC (4 months ago) by andreas

Probable fix for endless loop in eigenvector calculations. See http://cio.nist.gov/esd/emaildir/lists/jama/msg00834.html

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Revision 9959 - Directory Listing
Modified Wed Jan 16 00:50:48 2013 UTC (4 months ago) by andreas

Probable fix for endless loop in eigenvector calculations. See http://cio.nist.gov/esd/emaildir/lists/jama/msg00834.html

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Revision 9958 - Directory Listing
Modified Wed Jan 16 00:06:02 2013 UTC (4 months ago) by andreas

making sure the atomcache is using a local tmp dir, not a hardcoded path

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Revision 9957 - Directory Listing
Modified Thu Jan 10 00:27:21 2013 UTC (4 months ago) by andreas

fixing hard coded tmp path

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Revision 9956 - Directory Listing
Modified Wed Jan 2 07:43:22 2013 UTC (4 months, 2 weeks ago) by dmyerstu

Committed ResidueRange and AtomPositionMap, and their test cases.

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Revision 9955 - Directory Listing
Modified Mon Dec 17 21:57:31 2012 UTC (4 months, 4 weeks ago) by andreas

now using the standard UserConfiguration to get the PDB File path...

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Revision 9954 - Directory Listing
Modified Mon Dec 17 21:52:10 2012 UTC (4 months, 4 weeks ago) by andreas

more clear warning message

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Revision 9953 - Directory Listing
Modified Mon Dec 17 19:45:35 2012 UTC (4 months, 4 weeks ago) by andreas

less verbose

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Revision 9952 - Directory Listing
Modified Wed Dec 12 19:27:56 2012 UTC (5 months ago) by andreas

need to set flag that this is a biological assembly...

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Revision 9951 - Directory Listing
Modified Wed Dec 12 19:21:08 2012 UTC (5 months ago) by andreas

actually that flag is not needed

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Revision 9950 - Directory Listing
Modified Wed Dec 12 19:18:01 2012 UTC (5 months ago) by andreas

now correctly setting NMR flag...

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Revision 9949 - Directory Listing
Modified Wed Dec 12 18:55:56 2012 UTC (5 months ago) by andreas

adding a couple of more utility methods

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Revision 9947 - Directory Listing
Modified Tue Dec 11 00:00:36 2012 UTC (5 months ago) by andreas

more print...

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Revision 9946 - Directory Listing
Modified Mon Dec 10 23:50:17 2012 UTC (5 months ago) by andreas

making error message readable

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Revision 9945 - Directory Listing
Modified Sun Dec 9 19:29:43 2012 UTC (5 months, 1 week ago) by dmyerstu

Removed getSuppressed() call so it can compile with Java 1.6 (and cleaned the error messages up a little).

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Revision 9944 - Directory Listing
Modified Sun Dec 9 18:40:39 2012 UTC (5 months, 1 week ago) by andreas

changing specification for URL (so cruisecontrol can resolve it)

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Revision 9943 - Directory Listing
Modified Sun Dec 9 06:25:27 2012 UTC (5 months, 1 week ago) by dmyerstu

Commited the RCSB RESTful package, org.biojava.bio.structure.rcsb, along with a unit test and its resources.

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Revision 9941 - Directory Listing
Modified Fri Nov 30 18:52:08 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 9939 - Directory Listing
Modified Fri Nov 30 18:52:01 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.5

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Revision 9937 - Directory Listing
Modified Fri Nov 30 06:47:44 2012 UTC (5 months, 2 weeks ago) by andreas

setting group name for nucleotides and catching a NPE

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Revision 9936 - Directory Listing
Modified Fri Nov 30 06:32:48 2012 UTC (5 months, 2 weeks ago) by andreas

setting group name for nucleotides

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Revision 9934 - Directory Listing
Modified Fri Nov 30 00:59:02 2012 UTC (5 months, 2 weeks ago) by andreas

now also testing for nr of models

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Revision 9933 - Directory Listing
Modified Fri Nov 30 00:58:06 2012 UTC (5 months, 2 weeks ago) by andreas

making sure that multiple copies of the same chain are in different models

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Revision 9932 - Directory Listing
Modified Thu Nov 29 22:16:27 2012 UTC (5 months, 2 weeks ago) by andreas

less verbose

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Revision 9930 - Directory Listing
Modified Wed Nov 28 20:03:10 2012 UTC (5 months, 2 weeks ago) by andreas

making sure to test parsing with seqres alignments on

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Revision 9929 - Directory Listing
Modified Wed Nov 28 20:01:45 2012 UTC (5 months, 2 weeks ago) by andreas

a junit test to make sure that cloning of structures works correctly

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Revision 9928 - Directory Listing
Modified Wed Nov 28 20:01:25 2012 UTC (5 months, 2 weeks ago) by andreas

some minor refactoring, so the ChainImpl can access this for cloning SEQRES records

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Revision 9927 - Directory Listing
Modified Wed Nov 28 20:00:45 2012 UTC (5 months, 2 weeks ago) by andreas

now with correct cloning of seqres groups

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Revision 9926 - Directory Listing
Modified Wed Nov 28 18:24:45 2012 UTC (5 months, 2 weeks ago) by andreas

cleanup to avoid memory leak

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Revision 9925 - Directory Listing
Modified Wed Nov 28 18:23:09 2012 UTC (5 months, 2 weeks ago) by andreas

also setting cache in underlying provider

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Revision 9924 - Directory Listing
Modified Wed Nov 28 18:18:46 2012 UTC (5 months, 2 weeks ago) by andreas

now accepts external fileparsing parameters via AtomCache

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Revision 9923 - Directory Listing
Modified Wed Nov 28 18:17:48 2012 UTC (5 months, 2 weeks ago) by andreas

now accepts external fileparsing parameters via AtomCache

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Revision 9922 - Directory Listing
Modified Wed Nov 28 18:14:31 2012 UTC (5 months, 2 weeks ago) by andreas

clone() now also clones seqres groups

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Revision 9921 - Directory Listing
Modified Wed Nov 28 18:14:03 2012 UTC (5 months, 2 weeks ago) by andreas

PDB ID are now converted to all-lowercase (just as in the files on the wwpdb ftp site)

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Revision 9920 - Directory Listing
Modified Wed Nov 28 18:05:51 2012 UTC (5 months, 2 weeks ago) by andreas

more useful error message

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Revision 9919 - Directory Listing
Modified Wed Nov 28 18:04:59 2012 UTC (5 months, 2 weeks ago) by andreas

biounit data providers can now accept external atom caches...

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Revision 9918 - Directory Listing
Modified Wed Nov 28 17:44:28 2012 UTC (5 months, 2 weeks ago) by andreas

default provider is PDB based...

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Revision 9917 - Directory Listing
Modified Tue Nov 27 18:13:40 2012 UTC (5 months, 2 weeks ago) by andreas

more logging if something goes wrong

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Revision 9916 - Directory Listing
Modified Tue Nov 27 18:13:08 2012 UTC (5 months, 2 weeks ago) by andreas

more logging if something goes wrong

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Revision 9913 - Directory Listing
Modified Mon Nov 26 19:27:24 2012 UTC (5 months, 2 weeks ago) by andreas

ignore parsing of ligands for multi-chain domains in SCOP

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Revision 9902 - Directory Listing
Modified Tue Nov 20 02:11:37 2012 UTC (5 months, 3 weeks ago) by andreas

demo how to use StructureIO for accessing structures...

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Revision 9900 - Directory Listing
Modified Tue Nov 20 01:25:33 2012 UTC (5 months, 3 weeks ago) by andreas

a demo for how to access CATH

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Revision 9899 - Directory Listing
Modified Tue Nov 20 01:24:58 2012 UTC (5 months, 3 weeks ago) by andreas

now with support for accessing CATH domains

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Revision 9898 - Directory Listing
Modified Tue Nov 20 00:40:55 2012 UTC (5 months, 3 weeks ago) by andreas

new utility method to look up current PDB IDs

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Revision 9892 - Directory Listing
Modified Mon Nov 19 08:01:41 2012 UTC (5 months, 4 weeks ago) by aalhossary

fixing a warning

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Revision 9891 - Directory Listing
Modified Mon Nov 19 08:00:56 2012 UTC (5 months, 4 weeks ago) by aalhossary

Locale, Formatter, and StringBuilder

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Revision 9890 - Directory Listing
Modified Sat Nov 17 00:05:01 2012 UTC (6 months ago) by blivens

Changing default symmetry order to 1 (from -1 sentinal)

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Revision 9884 - Directory Listing
Modified Sat Nov 10 18:03:47 2012 UTC (6 months ago) by andreas

should take distribution config from parent

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Revision 9876 - Directory Listing
Modified Sat Nov 10 17:57:29 2012 UTC (6 months ago) by andreas

snapshot repository config was missing

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Revision 9866 - Directory Listing
Modified Sat Nov 10 01:34:42 2012 UTC (6 months, 1 week ago) by andreas

CathTest now in IntegrationTests

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Revision 9863 - Directory Listing
Modified Fri Nov 9 21:14:49 2012 UTC (6 months, 1 week ago) by andreas

typo

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Revision 9862 - Directory Listing
Modified Fri Nov 9 20:54:45 2012 UTC (6 months, 1 week ago) by andreas

less verbose

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Revision 9861 - Directory Listing
Modified Fri Nov 9 19:17:55 2012 UTC (6 months, 1 week ago) by andreas

do we need to initialize cath all the time?

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Revision 9857 - Directory Listing
Modified Fri Nov 9 18:11:10 2012 UTC (6 months, 1 week ago) by andreas

surefire config is coming from parent, no need to repeat

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Revision 9855 - Directory Listing
Modified Fri Nov 9 17:52:12 2012 UTC (6 months, 1 week ago) by andreas

print memory usage for debugging

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Revision 9854 - Directory Listing
Modified Fri Nov 9 02:31:15 2012 UTC (6 months, 1 week ago) by andreas

fixing typo

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Revision 9853 - Directory Listing
Modified Fri Nov 9 02:30:42 2012 UTC (6 months, 1 week ago) by andreas

version upgrade of surefire plugin

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Revision 9851 - Directory Listing
Modified Fri Nov 9 02:24:26 2012 UTC (6 months, 1 week ago) by andreas

prob. need to declare memory for each module... cath tests seem to require more ram...

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Revision 9850 - Directory Listing
Modified Fri Nov 9 02:09:07 2012 UTC (6 months, 1 week ago) by andreas

adding missing annotation

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Revision 9848 - Directory Listing
Modified Fri Nov 9 01:57:59 2012 UTC (6 months, 1 week ago) by andreas

less verbose

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Revision 9847 - Directory Listing
Modified Fri Nov 9 01:55:46 2012 UTC (6 months, 1 week ago) by andreas

cleanup

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Revision 9846 - Directory Listing
Modified Fri Nov 9 01:54:43 2012 UTC (6 months, 1 week ago) by andreas

less verbose

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Revision 9845 - Directory Listing
Modified Fri Nov 9 01:49:56 2012 UTC (6 months, 1 week ago) by andreas

less verbose

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Revision 9844 - Directory Listing
Modified Fri Nov 9 01:48:41 2012 UTC (6 months, 1 week ago) by andreas

more clear method name

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Revision 9843 - Directory Listing
Modified Fri Nov 9 01:43:50 2012 UTC (6 months, 1 week ago) by andreas

now printing the time it took to download cath

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Revision 9842 - Directory Listing
Modified Fri Nov 9 01:33:47 2012 UTC (6 months, 1 week ago) by andreas

less verbose

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Revision 9840 - Directory Listing
Modified Fri Nov 9 01:29:41 2012 UTC (6 months, 1 week ago) by andreas

now with support for downloading and parsing of CATH files. Thanks to Daniel Asarnow for providing the patch

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Revision 9839 - Directory Listing
Modified Fri Nov 9 01:28:35 2012 UTC (6 months, 1 week ago) by andreas

now with support for downloading and parsing of CATH files. Thanks to Daniel Asarnow for providing the patch

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Revision 9838 - Directory Listing
Modified Fri Nov 9 01:27:40 2012 UTC (6 months, 1 week ago) by andreas

starting to add support for CATH domain definitions

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Revision 9819 - Directory Listing
Modified Fri Nov 2 06:23:53 2012 UTC (6 months, 2 weeks ago) by blivens

AlignmentTools: Added a parameter to applyAlignment, improved docs

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Revision 9818 - Directory Listing
Modified Fri Nov 2 02:40:40 2012 UTC (6 months, 2 weeks ago) by blivens

Added PDBDomainParser constructor to allow alternate source URLs

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Revision 9817 - Directory Listing
Modified Fri Nov 2 02:39:21 2012 UTC (6 months, 2 weeks ago) by blivens

Added applyAlignent method to AlignmentTools. Improved tests substantially.

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Revision 9813 - Directory Listing
Modified Mon Oct 29 05:20:31 2012 UTC (6 months, 2 weeks ago) by andreas

new utility classes for calculating sec struc

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Revision 9812 - Directory Listing
Modified Mon Oct 29 04:49:55 2012 UTC (6 months, 2 weeks ago) by andreas

much closer to real DSSP results now, but still mismatches

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Revision 9806 - Directory Listing
Modified Tue Oct 23 19:12:49 2012 UTC (6 months, 3 weeks ago) by andreas

tries to guess PDB file path

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Revision 9805 - Directory Listing
Modified Tue Oct 23 19:11:58 2012 UTC (6 months, 3 weeks ago) by andreas

updating legend

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Revision 9804 - Directory Listing
Modified Tue Oct 23 19:10:54 2012 UTC (6 months, 3 weeks ago) by andreas

making field public

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Revision 9803 - Directory Listing
Modified Tue Oct 23 19:09:48 2012 UTC (6 months, 3 weeks ago) by andreas

mmcif files can now be auto-updated

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Revision 9802 - Directory Listing
Modified Tue Oct 23 19:08:56 2012 UTC (6 months, 3 weeks ago) by andreas

now supports the pdb1 files provided by PDB

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Revision 9798 - Directory Listing
Modified Tue Oct 23 18:40:14 2012 UTC (6 months, 3 weeks ago) by andreas

Provide Bio assemblies based on the pdb1 files provided by the PDB

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Revision 9797 - Directory Listing
Modified Tue Oct 23 18:10:21 2012 UTC (6 months, 3 weeks ago) by andreas

turn off debug mode

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Revision 9796 - Directory Listing
Modified Tue Oct 23 18:07:52 2012 UTC (6 months, 3 weeks ago) by andreas

turn off debug mode

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Revision 9795 - Directory Listing
Modified Tue Oct 23 00:19:49 2012 UTC (6 months, 3 weeks ago) by andreas

cleanup

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Revision 9794 - Directory Listing
Modified Mon Oct 22 20:45:23 2012 UTC (6 months, 3 weeks ago) by andreas

making atom cache a protected field

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Revision 9792 - Directory Listing
Modified Fri Oct 12 15:52:28 2012 UTC (7 months ago) by andreas

cleanup

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Revision 9791 - Directory Listing
Modified Fri Oct 12 15:48:38 2012 UTC (7 months ago) by andreas

cleanup

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Revision 9790 - Directory Listing
Modified Fri Oct 12 15:47:24 2012 UTC (7 months ago) by andreas

cleanup

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Revision 9789 - Directory Listing
Modified Fri Oct 12 05:38:09 2012 UTC (7 months ago) by andreas

the most difficult bio assembly that I have found so far

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Revision 9788 - Directory Listing
Modified Fri Oct 12 05:30:24 2012 UTC (7 months ago) by andreas

manually verified that test ok

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Revision 9787 - Directory Listing
Modified Fri Oct 12 05:02:55 2012 UTC (7 months ago) by andreas

changing rows and columns

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Revision 9786 - Directory Listing
Modified Wed Oct 10 18:22:04 2012 UTC (7 months ago) by andreas

changing row/column order

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Revision 9785 - Directory Listing
Modified Wed Oct 10 17:44:32 2012 UTC (7 months ago) by andreas

more generalization of different biological unit providers

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Revision 9784 - Directory Listing
Modified Wed Oct 10 17:44:23 2012 UTC (7 months ago) by andreas

more generalization of different biological unit providers

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Revision 9783 - Directory Listing
Modified Wed Oct 10 01:37:20 2012 UTC (7 months, 1 week ago) by andreas

Major bug fix for dealing with rare biological assemblies, such as 4A1I bio assembly 2

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Revision 9782 - Directory Listing
Modified Wed Oct 10 01:37:10 2012 UTC (7 months, 1 week ago) by andreas

Major bug fix for dealing with rare biological assemblies, such as 4A1I bio assembly 2

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Revision 9781 - Directory Listing
Modified Wed Oct 10 01:36:53 2012 UTC (7 months, 1 week ago) by andreas

Major bug fix for dealing with rare biological assemblies, such as 4A1I bio assembly 2

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Revision 9780 - Directory Listing
Modified Tue Oct 9 22:45:10 2012 UTC (7 months, 1 week ago) by andreas

transformations have higher precision...

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Revision 9779 - Directory Listing
Modified Thu Oct 4 00:13:27 2012 UTC (7 months, 1 week ago) by andreas

not showing chain ID for now

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Revision 9776 - Directory Listing
Modified Fri Sep 28 00:05:59 2012 UTC (7 months, 2 weeks ago) by andreas

fixing failing unit test

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Revision 9775 - Directory Listing
Modified Thu Sep 27 00:24:57 2012 UTC (7 months, 2 weeks ago) by andreas

improved comparisons between residueNumbers, as provided by Douglas

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Revision 9774 - Directory Listing
Modified Tue Sep 25 18:29:53 2012 UTC (7 months, 3 weeks ago) by andreas

making sure NMR structures with bio assemblies are dealt with correctly

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Revision 9773 - Directory Listing
Modified Tue Sep 25 18:29:37 2012 UTC (7 months, 3 weeks ago) by andreas

making sure NMR structures with bio assemblies are dealt with correctly

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Revision 9772 - Directory Listing
Modified Tue Sep 25 18:29:08 2012 UTC (7 months, 3 weeks ago) by andreas

new utility method to remove all models

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Revision 9771 - Directory Listing
Modified Tue Sep 25 18:04:57 2012 UTC (7 months, 3 weeks ago) by andreas

fixing a bug with resetting a counter

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Revision 9770 - Directory Listing
Modified Tue Sep 25 16:53:40 2012 UTC (7 months, 3 weeks ago) by andreas

adding new cif categories

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Revision 9769 - Directory Listing
Modified Tue Sep 25 00:04:15 2012 UTC (7 months, 3 weeks ago) by andreas

fix wrongly formatted  groups names

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Revision 9768 - Directory Listing
Modified Mon Sep 24 17:57:21 2012 UTC (7 months, 3 weeks ago) by andreas

extending test to compare with access of flat file downloads

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Revision 9767 - Directory Listing
Modified Mon Sep 24 17:33:11 2012 UTC (7 months, 3 weeks ago) by andreas

now really returning the first bio assembly, rather than the asym unit

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Revision 9766 - Directory Listing
Modified Sat Sep 22 17:40:48 2012 UTC (7 months, 3 weeks ago) by andreas

docu update and changing access for some fields

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Revision 9755 - Directory Listing
Modified Thu Aug 9 00:09:47 2012 UTC (9 months, 1 week ago) by andreas

fixing a confusion between family and superfamily levels

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Revision 9754 - Directory Listing
Modified Thu Aug 9 00:09:28 2012 UTC (9 months, 1 week ago) by andreas

fixing a confusion between family and superfamily levels

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Revision 9744 - Directory Listing
Modified Tue Jul 3 00:33:08 2012 UTC (10 months, 2 weeks ago) by andreas

extending the name convention system to support biol units

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Revision 9742 - Directory Listing
Modified Fri Jun 29 20:58:11 2012 UTC (10 months, 2 weeks ago) by andreas

more logging if we get a KILL message from server

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Revision 9740 - Directory Listing
Modified Fri Jun 29 20:55:31 2012 UTC (10 months, 2 weeks ago) by andreas

junit tests for quaternary structure providers

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Revision 9739 - Directory Listing
Modified Fri Jun 29 20:55:06 2012 UTC (10 months, 2 weeks ago) by andreas

now supports parsing of REMARK 350 records

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Revision 9738 - Directory Listing
Modified Fri Jun 29 20:54:44 2012 UTC (10 months, 2 weeks ago) by andreas

major improvements to parsing of biological assembly / REMARK 350 records

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Revision 9737 - Directory Listing
Modified Fri Jun 29 20:54:04 2012 UTC (10 months, 2 weeks ago) by andreas

major improvements to parsing of biological assembly / REMARK 350 records

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Revision 9736 - Directory Listing
Modified Fri Jun 29 20:53:41 2012 UTC (10 months, 2 weeks ago) by andreas

now supports parsing of REMARK 350 records

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Revision 9735 - Directory Listing
Modified Fri Jun 29 20:53:21 2012 UTC (10 months, 2 weeks ago) by andreas

new utility class to parse biological assembly info - REMARK 350 records in PDB files

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Revision 9734 - Directory Listing
Modified Fri Jun 29 20:52:34 2012 UTC (10 months, 2 weeks ago) by andreas

new flag if biological assembly properties should be parsed

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Revision 9733 - Directory Listing
Modified Fri Jun 29 20:51:56 2012 UTC (10 months, 2 weeks ago) by andreas

now correctly setting the transformation rules for recreating biol assemblies in PDBHeader

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Revision 9732 - Directory Listing
Modified Thu Jun 28 23:11:26 2012 UTC (10 months, 2 weeks ago) by andreas

changing default bio assembly provider to mmcif for now...

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Revision 9731 - Directory Listing
Modified Thu Jun 28 22:55:38 2012 UTC (10 months, 2 weeks ago) by andreas

mmcif consumer now correctly detects element type of atoms

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Revision 9730 - Directory Listing
Modified Wed Jun 27 21:40:27 2012 UTC (10 months, 2 weeks ago) by andreas

switching to new way of loading biol assembly data

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Revision 9729 - Directory Listing
Modified Wed Jun 27 21:33:52 2012 UTC (10 months, 2 weeks ago) by andreas

refactoring classes for recreating biological assemblies

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Revision 9728 - Directory Listing
Modified Wed Jun 27 21:33:31 2012 UTC (10 months, 2 weeks ago) by andreas

refactoring classes for recreating biological assemblies

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Revision 9721 - Directory Listing
Modified Thu Jun 21 23:38:54 2012 UTC (10 months, 3 weeks ago) by blivens

Added PDBDomainProvider, which fetches domain info through the PDB's REST API.

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Revision 9711 - Directory Listing
Modified Wed Jun 13 23:07:39 2012 UTC (11 months ago) by andreas

new utility method getAllAtomArray(structure)

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Revision 9710 - Directory Listing
Modified Wed Jun 13 23:04:49 2012 UTC (11 months ago) by andreas

more renaming of classes

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Revision 9709 - Directory Listing
Modified Wed Jun 13 23:04:27 2012 UTC (11 months ago) by andreas

more renaming of classes

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Revision 9708 - Directory Listing
Modified Wed Jun 13 23:03:39 2012 UTC (11 months ago) by andreas

now allowing to set path

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Revision 9707 - Directory Listing
Modified Wed Jun 13 18:21:25 2012 UTC (11 months ago) by andreas

improving naming of class and interface names

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Revision 9706 - Directory Listing
Modified Wed Jun 13 18:13:16 2012 UTC (11 months ago) by andreas

some cleanup

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Revision 9705 - Directory Listing
Modified Wed Jun 13 18:11:54 2012 UTC (11 months ago) by andreas

fixing some issues related to correctly transforming the chains

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Revision 9704 - Directory Listing
Modified Wed Jun 13 17:09:31 2012 UTC (11 months ago) by andreas

matrix was getting parsed in the wrong way...

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Revision 9703 - Directory Listing
Modified Tue Jun 12 17:56:06 2012 UTC (11 months ago) by andreas

better catching of problems with identifying correct compounds (e.g. 3J0U, 3J10)

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Revision 9702 - Directory Listing
Modified Tue Jun 12 01:46:22 2012 UTC (11 months ago) by andreas

some cleanup, adding getGroups method

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Revision 9701 - Directory Listing
Modified Mon Jun 11 16:00:15 2012 UTC (11 months ago) by andreas

making public accessible

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Revision 9700 - Directory Listing
Modified Mon Jun 11 01:55:08 2012 UTC (11 months ago) by andreas

now also storing omega

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Revision 9699 - Directory Listing
Modified Mon Jun 11 01:54:29 2012 UTC (11 months ago) by andreas

new method to calc dihedral angs

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Revision 9698 - Directory Listing
Modified Wed Jun 6 05:13:52 2012 UTC (11 months, 1 week ago) by andreas

more rules for what resources to include

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Revision 9693 - Directory Listing
Modified Wed Jun 6 04:26:02 2012 UTC (11 months, 1 week ago) by andreas

adding a showStructure method

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Revision 9692 - Directory Listing
Modified Wed Jun 6 00:53:03 2012 UTC (11 months, 1 week ago) by andreas

fixing broken maven timestamp display

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Revision 9690 - Directory Listing
Modified Wed Jun 6 00:23:09 2012 UTC (11 months, 1 week ago) by andreas

adding more checks to this test, to make sure we also look at RNAs

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Revision 9689 - Directory Listing
Modified Wed Jun 6 00:03:34 2012 UTC (11 months, 1 week ago) by andreas

now can deal also with RNA sequences

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Revision 9688 - Directory Listing
Modified Tue Jun 5 23:49:13 2012 UTC (11 months, 1 week ago) by andreas

new wrapper method for showing DB results

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Revision 9686 - Directory Listing
Modified Tue Jun 5 22:05:52 2012 UTC (11 months, 1 week ago) by andreas

also track build nr. in About menu

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Revision 9685 - Directory Listing
Modified Tue Jun 5 22:05:33 2012 UTC (11 months, 1 week ago) by andreas

new properties file for tracking build number

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Revision 9684 - Directory Listing
Modified Tue Jun 5 22:05:14 2012 UTC (11 months, 1 week ago) by andreas

now printing version number and build date at startup

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Revision 9681 - Directory Listing
Modified Tue Jun 5 18:47:43 2012 UTC (11 months, 1 week ago) by andreas

now using resource filtering to update version number in properties file

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Revision 9679 - Directory Listing
Modified Tue Jun 5 17:18:38 2012 UTC (11 months, 1 week ago) by andreas

removing a trailing null string

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Revision 9678 - Directory Listing
Modified Tue Jun 5 17:08:53 2012 UTC (11 months, 1 week ago) by andreas

now correctly print all of the DB search column headers

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Revision 9676 - Directory Listing
Modified Tue Jun 5 17:08:20 2012 UTC (11 months, 1 week ago) by andreas

making sure to write the algorithm name to the output file

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Revision 9674 - Directory Listing
Modified Sat Jun 2 19:23:42 2012 UTC (11 months, 2 weeks ago) by andreas

adding check for null

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Revision 9673 - Directory Listing
Modified Sat Jun 2 14:43:48 2012 UTC (11 months, 2 weeks ago) by Peter Rose

fixed bug in getOneLetterCode. It was returning "?" in some cases (i.e., for YNM in PDB 2WS6), now it always returns X for any non-standard residue.

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Revision 9670 - Directory Listing
Modified Wed May 30 18:29:16 2012 UTC (11 months, 2 weeks ago) by andreas

better javadoc

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Revision 9668 - Directory Listing
Modified Wed May 30 18:14:37 2012 UTC (11 months, 2 weeks ago) by andreas

adding a new unit test for the StructureIO class

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Revision 9667 - Directory Listing
Modified Wed May 30 18:07:41 2012 UTC (11 months, 2 weeks ago) by andreas

adding a new StructureIO class for easy access to structure related methods. Behavior for the framework can be configured via factories. Starting to add a new factory interface for accessing biological units from either mmCif files or via webservices.

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Revision 9665 - Directory Listing
Modified Tue May 29 18:47:34 2012 UTC (11 months, 2 weeks ago) by andreas

adding new field

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Revision 9663 - Directory Listing
Modified Tue May 29 18:34:20 2012 UTC (11 months, 2 weeks ago) by andreas

moving slow running junit tests to new integrationtest module. They can be called by using mvn verify

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Revision 9660 - Directory Listing
Modified Tue May 29 18:31:41 2012 UTC (11 months, 2 weeks ago) by andreas

moving slow running junit tests to new integrationtest module. They can be called by using mvn verify

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Revision 9658 - Directory Listing
Modified Tue May 29 18:27:16 2012 UTC (11 months, 2 weeks ago) by andreas

moving slow running junit tests to new integrationtest module. They can be called by using mvn verify

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Revision 9654 - Directory Listing
Modified Tue May 29 18:18:22 2012 UTC (11 months, 2 weeks ago) by andreas

moving slow running tests to new integrationtest module

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Revision 9652 - Directory Listing
Modified Tue May 29 17:40:00 2012 UTC (11 months, 2 weeks ago) by andreas

BioJava now can reconstruct the quaternary structures of proteins! So far only works when using mmCif files as a source.

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Revision 9651 - Directory Listing
Modified Tue May 29 17:08:24 2012 UTC (11 months, 2 weeks ago) by andreas

fixing eclipse warnings

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Revision 9650 - Directory Listing
Modified Tue May 29 17:06:53 2012 UTC (11 months, 2 weeks ago) by andreas

adding support for storing internal chain ids, as are being used in mmCif files

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Revision 9649 - Directory Listing
Modified Fri May 25 17:57:39 2012 UTC (11 months, 3 weeks ago) by Peter Rose

Changed behavior of getSeqResSequence to always add an "X" for non-standard residues in the SEQRES record of a PDB file. So now the one-letter sequence matches the length of the SEQRES record in a PDB file.

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Revision 9647 - Directory Listing
Modified Tue May 22 05:19:32 2012 UTC (11 months, 3 weeks ago) by andreas

fixing typo

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Revision 9646 - Directory Listing
Modified Tue May 22 04:57:41 2012 UTC (11 months, 3 weeks ago) by andreas

improving SCOP demos

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Revision 9645 - Directory Listing
Modified Tue May 22 03:42:41 2012 UTC (11 months, 3 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 9643 - Directory Listing
Modified Tue May 22 03:42:34 2012 UTC (11 months, 3 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.4

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Revision 9642 - Directory Listing
Modified Fri May 18 01:24:38 2012 UTC (12 months ago) by andreas

https://redmine.open-bio.org/issues/3355 fix for this issue

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Revision 9641 - Directory Listing
Modified Fri May 18 00:59:36 2012 UTC (12 months ago) by andreas

https://redmine.open-bio.org/issues/3355 junit test for this ticket

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Revision 9636 - Directory Listing
Modified Tue May 15 00:14:52 2012 UTC (12 months ago) by andreas

https://redmine.open-bio.org/issues/3351 adding missing standard chem comp groups

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Revision 9634 - Directory Listing
Modified Mon May 7 21:41:00 2012 UTC (12 months, 1 week ago) by andreas

new request to fetch all representative domain names from remote

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Revision 9633 - Directory Listing
Modified Mon May 7 21:19:41 2012 UTC (12 months, 1 week ago) by andreas

just some small cleanup

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Revision 9632 - Directory Listing
Modified Mon May 7 21:09:52 2012 UTC (12 months, 1 week ago) by andreas

now supports changing the SCOP download location

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Revision 9631 - Directory Listing
Modified Mon May 7 18:58:26 2012 UTC (12 months, 1 week ago) by andreas

now with support for accessing the latest scop update from Berkeley

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Revision 9630 - Directory Listing
Modified Thu May 3 18:21:40 2012 UTC (12 months, 2 weeks ago) by andreas

no need to force init of domainProvider, unless actually requested.

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Revision 9628 - Directory Listing
Modified Tue May 1 18:53:09 2012 UTC (12 months, 2 weeks ago) by andreas

add an interface for PDP domain providers. (so we can have multiple implementations of this, not only the remote one)

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Revision 9627 - Directory Listing
Modified Tue May 1 18:52:16 2012 UTC (12 months, 2 weeks ago) by andreas

add an interface for PDP domain providers. (so we can have multiple implementations of this, not only the remote one)

---

Revision 9626 - Directory Listing
Modified Tue May 1 00:54:33 2012 UTC (12 months, 2 weeks ago) by andreas

now serializable

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Revision 9624 - Directory Listing
Modified Wed Apr 25 18:46:47 2012 UTC (12 months, 3 weeks ago) by andreas

pdpprovider is now a protected field

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Revision 9623 - Directory Listing
Modified Wed Apr 25 00:45:31 2012 UTC (12 months, 3 weeks ago) by andreas

allowing CECP to be called from command line

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Revision 9622 - Directory Listing
Modified Fri Apr 20 18:00:33 2012 UTC (12 months, 3 weeks ago) by andreas

new junit test for correct parsing of RNA/nucleotides

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Revision 9621 - Directory Listing
Modified Wed Apr 18 20:31:03 2012 UTC (12 months, 4 weeks ago) by Peter Rose

Modifications to support crystallographic information.

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Revision 9620 - Directory Listing
Modified Wed Apr 18 20:24:57 2012 UTC (12 months, 4 weeks ago) by Peter Rose

Modifications to support crystallographic information.

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Revision 9619 - Directory Listing
Modified Wed Apr 18 20:24:40 2012 UTC (12 months, 4 weeks ago) by Peter Rose

Modifications to support crystallographic information.

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Revision 9618 - Directory Listing
Modified Wed Apr 18 20:24:02 2012 UTC (12 months, 4 weeks ago) by Peter Rose

New class to hold crystallographic information.

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Revision 9616 - Directory Listing
Modified Thu Mar 29 17:06:05 2012 UTC (13 months, 2 weeks ago) by andreas

enhanced test

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Revision 9615 - Directory Listing
Modified Thu Mar 29 17:01:06 2012 UTC (13 months, 2 weeks ago) by andreas

junit test for https://redmine.open-bio.org/issues/3334 

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Revision 9614 - Directory Listing
Modified Thu Mar 29 17:00:43 2012 UTC (13 months, 2 weeks ago) by andreas

fix for https://redmine.open-bio.org/issues/3334 

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Revision 9612 - Directory Listing
Modified Wed Mar 28 06:43:40 2012 UTC (13 months, 2 weeks ago) by blivens

Removing debugging output.

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Revision 9611 - Directory Listing
Modified Wed Mar 28 06:42:58 2012 UTC (13 months, 2 weeks ago) by blivens

Added AlignmentTools.createAFPChain, which makes an AFPChain from a list of aligned ResidueNumbers.

---

Revision 9607 - Directory Listing
Modified Tue Mar 27 21:22:14 2012 UTC (13 months, 3 weeks ago) by blivens

Added StructureSequenceMatcher, which matches sequences to structures.
Added FastaStructureParser, which reads protein structures from FASTA files

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Revision 9590 - Directory Listing
Modified Fri Mar 16 22:28:32 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 9588 - Directory Listing
Modified Fri Mar 16 22:28:24 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.3

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Revision 9556 - Directory Listing
Modified Wed Mar 7 21:06:41 2012 UTC (14 months, 1 week ago) by blivens

Improved documentation

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Revision 9555 - Directory Listing
Modified Wed Mar 7 21:05:57 2012 UTC (14 months, 1 week ago) by blivens

Added CECP test for short CECP alignments

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Revision 9554 - Directory Listing
Modified Wed Mar 7 19:52:04 2012 UTC (14 months, 1 week ago) by andreas

Updating PDBFIleParser test to new Element symbol in toPDB method

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Revision 9553 - Directory Listing
Modified Wed Mar 7 19:46:47 2012 UTC (14 months, 1 week ago) by andreas

converting ELement R to X

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Revision 9552 - Directory Listing
Modified Wed Mar 7 19:46:43 2012 UTC (14 months, 1 week ago) by blivens

Bugfix: Short alignment blocks (<5 residues) will be ignored by CECP

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Revision 9551 - Directory Listing
Modified Wed Mar 7 19:20:41 2012 UTC (14 months, 1 week ago) by andreas

adding Element name toPDB method

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Revision 9550 - Directory Listing
Modified Wed Mar 7 19:01:17 2012 UTC (14 months, 1 week ago) by andreas

parser now ignores empty lines

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Revision 9549 - Directory Listing
Modified Tue Feb 28 19:50:12 2012 UTC (14 months, 2 weeks ago) by andreas

adding more details for SIFTs

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Revision 9548 - Directory Listing
Modified Tue Feb 28 17:08:34 2012 UTC (14 months, 2 weeks ago) by andreas

fixing some details about sifts parsing

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Revision 9547 - Directory Listing
Modified Mon Feb 27 18:31:54 2012 UTC (14 months, 2 weeks ago) by andreas

new framework for parsing EBI SIFTS files which provide PDB to UniProt mappings

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Revision 9542 - Directory Listing
Modified Fri Feb 24 16:39:35 2012 UTC (14 months, 3 weeks ago) by andreas

better error catching for downloads

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Revision 9540 - Directory Listing
Modified Thu Feb 23 18:41:55 2012 UTC (14 months, 3 weeks ago) by andreas

now uses the new FileDownload utility class

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Revision 9539 - Directory Listing
Modified Thu Feb 23 18:41:37 2012 UTC (14 months, 3 weeks ago) by andreas

new utility class for downloading content from URLs to Files

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Revision 9538 - Directory Listing
Modified Thu Feb 23 18:41:19 2012 UTC (14 months, 3 weeks ago) by andreas

less verbose

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Revision 9532 - Directory Listing
Modified Fri Feb 10 00:25:12 2012 UTC (15 months, 1 week ago) by andreas

making sure the max thresholds are set before we start parsing

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Revision 9531 - Directory Listing
Modified Fri Feb 10 00:17:23 2012 UTC (15 months, 1 week ago) by Peter Rose

making sure the MAX parameters are set correctly

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Revision 9530 - Directory Listing
Modified Wed Feb 8 19:33:06 2012 UTC (15 months, 1 week ago) by andreas

tiny cleanup

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Revision 9529 - Directory Listing
Modified Wed Feb 8 18:45:07 2012 UTC (15 months, 1 week ago) by aalhossary

added a small note to javadoc

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Revision 9527 - Directory Listing
Modified Wed Feb 8 00:28:00 2012 UTC (15 months, 1 week ago) by andreas

correct null check if file does not exist locally

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Revision 9526 - Directory Listing
Modified Wed Feb 8 00:27:18 2012 UTC (15 months, 1 week ago) by andreas

fixing broken altLoc parsing https://redmine.open-bio.org/issues/3307

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Revision 9525 - Directory Listing
Modified Wed Feb 8 00:26:57 2012 UTC (15 months, 1 week ago) by andreas

unit test for https://redmine.open-bio.org/issues/3307

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Revision 9524 - Directory Listing
Modified Tue Feb 7 01:36:02 2012 UTC (15 months, 1 week ago) by andreas

much faster way of downloading biol. unit files

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Revision 9523 - Directory Listing
Modified Sun Feb 5 12:08:34 2012 UTC (15 months, 1 week ago) by aalhossary

small code modification & comment

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Revision 9522 - Directory Listing
Modified Sun Feb 5 11:23:18 2012 UTC (15 months, 1 week ago) by aalhossary

removing unnecessary .append("") statements

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Revision 9519 - Directory Listing
Modified Fri Feb 3 22:49:53 2012 UTC (15 months, 1 week ago) by andreas

set structure names for user provided structures

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Revision 9518 - Directory Listing
Modified Fri Feb 3 22:48:46 2012 UTC (15 months, 1 week ago) by andreas

just some cleanup

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Revision 9517 - Directory Listing
Modified Fri Feb 3 22:47:55 2012 UTC (15 months, 1 week ago) by andreas

increasing version number

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Revision 9516 - Directory Listing
Modified Fri Feb 3 22:47:21 2012 UTC (15 months, 1 week ago) by andreas

This change should be slightly more memory efficient

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Revision 9515 - Directory Listing
Modified Fri Feb 3 22:46:13 2012 UTC (15 months, 1 week ago) by andreas

smarter caching of domain ranges

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Revision 9514 - Directory Listing
Modified Fri Feb 3 22:44:49 2012 UTC (15 months, 1 week ago) by andreas

always load the representative assignments from server (to make sure we always have the latest version)

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Revision 9513 - Directory Listing
Modified Fri Feb 3 22:44:02 2012 UTC (15 months, 1 week ago) by andreas

don't print ranges

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Revision 9512 - Directory Listing
Modified Fri Feb 3 22:43:26 2012 UTC (15 months, 1 week ago) by andreas

doing things step by step for readability

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Revision 9511 - Directory Listing
Modified Fri Feb 3 22:40:43 2012 UTC (15 months, 1 week ago) by andreas

track version of algorithm

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Revision 9510 - Directory Listing
Modified Fri Feb 3 22:40:13 2012 UTC (15 months, 1 week ago) by andreas

track version of algorithm

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Revision 9509 - Directory Listing
Modified Fri Jan 27 23:39:01 2012 UTC (15 months, 2 weeks ago) by andreas

moving the max nr of CA and max nr of atoms parameters to the FileParsingParameters

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Revision 9508 - Directory Listing
Modified Fri Jan 27 23:38:52 2012 UTC (15 months, 2 weeks ago) by andreas

moving the max nr of CA and max nr of atoms parameters to the FileParsingParameters

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Revision 9507 - Directory Listing
Modified Fri Jan 27 02:28:13 2012 UTC (15 months, 3 weeks ago) by andreas

new acceptedAtomNames FileParsingParameter

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Revision 9506 - Directory Listing
Modified Fri Jan 27 02:27:57 2012 UTC (15 months, 3 weeks ago) by andreas

new acceptedAtomNames FileParsingParameter

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Revision 9505 - Directory Listing
Modified Fri Jan 27 02:27:47 2012 UTC (15 months, 3 weeks ago) by andreas

testing the new acceptedAtomNames FileParsingParameter

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Revision 9504 - Directory Listing
Modified Thu Jan 19 23:12:11 2012 UTC (15 months, 4 weeks ago) by andreas

now support gzip compression

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Revision 9503 - Directory Listing
Modified Mon Jan 16 11:38:35 2012 UTC (16 months ago) by rthornton

Simplified boolean expressions.

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Revision 9499 - Directory Listing
Modified Thu Jan 12 03:10:34 2012 UTC (16 months ago) by rthornton

Removed null checks that were always true.  instanceof only returns true for non-null values.

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Revision 9498 - Directory Listing
Modified Wed Jan 11 17:01:21 2012 UTC (16 months ago) by andreas

fixing an issue with not caching domain ranges correctly

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Revision 9496 - Directory Listing
Modified Tue Jan 10 02:00:11 2012 UTC (16 months, 1 week ago) by andreas

fixing typo

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Revision 9495 - Directory Listing
Modified Tue Jan 10 01:59:28 2012 UTC (16 months, 1 week ago) by andreas

fixing recursion

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Revision 9493 - Directory Listing
Modified Tue Jan 10 01:49:52 2012 UTC (16 months, 1 week ago) by andreas

fixing self-assignment of parameters, as reported by Rob Thornton

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Revision 9492 - Directory Listing
Modified Tue Jan 10 01:23:46 2012 UTC (16 months, 1 week ago) by rthornton

Changed instances of String concatenation in StringBuffer to use append.

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Revision 9481 - Directory Listing
Modified Sun Dec 18 14:36:19 2011 UTC (16 months, 4 weeks ago) by aalhossary

updated POM and String Manipulation Test Helper (hoping not no crash the whole system)

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Revision 9480 - Directory Listing
Modified Sun Dec 18 14:25:00 2011 UTC (16 months, 4 weeks ago) by aalhossary

relaxing the default connection timeout to 15 seconds; to tolerate slow Internet connections (like mine ;) )

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Revision 9479 - Directory Listing
Modified Thu Dec 15 18:34:57 2011 UTC (17 months ago) by aalhossary

replacing < and > with &lt; and &gt; in order not to break HTML and enable generating .CHM files using http://jan.baresovi.cz/dr/en/javadoc-chm

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Revision 9475 - Directory Listing
Modified Tue Dec 6 01:19:17 2011 UTC (17 months, 1 week ago) by andreas

starting to refactor the CE dpAlign code

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Revision 9474 - Directory Listing
Modified Sun Dec 4 20:18:57 2011 UTC (17 months, 1 week ago) by andreas

reducing some GC overhead by allocating fewer temporary variables.

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Revision 9468 - Directory Listing
Modified Wed Nov 30 01:34:44 2011 UTC (17 months, 2 weeks ago) by blivens

Added AlignmentTools.getSymmetryOrder method which tries to find symmetry in alignments.

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Revision 9467 - Directory Listing
Modified Wed Nov 30 01:31:03 2011 UTC (17 months, 2 weeks ago) by blivens

[Minor] removed unused private method

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Revision 9466 - Directory Listing
Modified Sun Nov 27 22:19:15 2011 UTC (17 months, 2 weeks ago) by andreas

incorporating feedback from Elmar Krieger

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Revision 9412 - Directory Listing
Modified Thu Nov 10 21:47:25 2011 UTC (18 months, 1 week ago) by andreas

fixing problem with wrongly processed multi-fragment domains

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Revision 9411 - Directory Listing
Modified Thu Nov 10 04:24:04 2011 UTC (18 months, 1 week ago) by blivens

CeCPMain version 1.3: Ignore short CPs (under 5 res).

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Revision 9407 - Directory Listing
Modified Wed Nov 9 17:49:05 2011 UTC (18 months, 1 week ago) by andreas

setting version to 1.2

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Revision 9395 - Directory Listing
Modified Tue Nov 8 01:26:32 2011 UTC (18 months, 1 week ago) by blivens

Allow CECP results to display in FatCatCore format, dispite the format being unable to display CP residue numbers correctly.

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Revision 9394 - Directory Listing
Modified Tue Nov 8 01:24:32 2011 UTC (18 months, 1 week ago) by blivens

Bug fixes regarding structural alignment:

- Worked around a bug with reusing CE instances for multiple alignments which was causing OptimalCECP to give incorrect results.
- Much more thoroughly tested OptimalCECPMain.
- Changed the criteria for AFPChains to be considered equal. It now only looks at the alignment, not the algorithm or names.

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Revision 9393 - Directory Listing
Modified Tue Nov 8 01:19:08 2011 UTC (18 months, 1 week ago) by blivens

Refactored and cleaned up CeCPMain. No functional changes.

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Revision 9392 - Directory Listing
Modified Tue Nov 8 01:16:03 2011 UTC (18 months, 1 week ago) by blivens

Removed OptimalCECPMain from the StructureAlignmentFactory (and therefore the GUI).

If you want to run an OptimalCECPMain, just add an instance to the factory with addAlgorithm().

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Revision 9391 - Directory Listing
Modified Mon Nov 7 22:16:55 2011 UTC (18 months, 1 week ago) by andreas

better proxying of data

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Revision 9390 - Directory Listing
Modified Mon Nov 7 22:15:42 2011 UTC (18 months, 1 week ago) by andreas

code cleanup

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Revision 9389 - Directory Listing
Modified Mon Nov 7 22:14:53 2011 UTC (18 months, 1 week ago) by andreas

prevent an out of index error

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Revision 9388 - Directory Listing
Modified Mon Nov 7 22:14:23 2011 UTC (18 months, 1 week ago) by andreas

now tracks if alignment is circularly permuted

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Revision 9387 - Directory Listing
Modified Mon Nov 7 22:11:07 2011 UTC (18 months, 1 week ago) by andreas

now fetching all domains for representatives in one go

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Revision 9386 - Directory Listing
Modified Mon Nov 7 22:08:26 2011 UTC (18 months, 1 week ago) by andreas

not caching NULL values

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Revision 9384 - Directory Listing
Modified Mon Nov 7 22:07:50 2011 UTC (18 months, 1 week ago) by andreas

not caching NULL values

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Revision 9357 - Directory Listing
Modified Mon Oct 24 22:56:26 2011 UTC (18 months, 3 weeks ago) by andreas

setting correct paths for farm jobs.

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Revision 9356 - Directory Listing
Modified Mon Oct 24 22:55:57 2011 UTC (18 months, 3 weeks ago) by andreas

more transparent logging

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Revision 9355 - Directory Listing
Modified Mon Oct 24 22:38:26 2011 UTC (18 months, 3 weeks ago) by andreas

now also flushing scopDescriptionCache

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Revision 9354 - Directory Listing
Modified Mon Oct 24 22:37:46 2011 UTC (18 months, 3 weeks ago) by andreas

updating to latest file format

---

Revision 9353 - Directory Listing
Modified Mon Oct 24 22:19:25 2011 UTC (18 months, 3 weeks ago) by andreas

flush and cleanup memory of caches at shutdown

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Revision 9352 - Directory Listing
Modified Mon Oct 24 22:18:34 2011 UTC (18 months, 3 weeks ago) by andreas

now also tracking time it took for calculation

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Revision 9351 - Directory Listing
Modified Mon Oct 24 22:18:21 2011 UTC (18 months, 3 weeks ago) by andreas

now also tracking time it took for calculation

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Revision 9350 - Directory Listing
Modified Mon Oct 24 22:18:03 2011 UTC (18 months, 3 weeks ago) by andreas

now also tracking time it took for calculation

---

Revision 9349 - Directory Listing
Modified Mon Oct 24 22:17:37 2011 UTC (18 months, 3 weeks ago) by andreas

using new cachedremotescop

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Revision 9348 - Directory Listing
Modified Mon Oct 24 22:17:16 2011 UTC (18 months, 3 weeks ago) by andreas

Improved speed and caching behavior with new CachedRemoteScopInstallation

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Revision 9347 - Directory Listing
Modified Mon Oct 24 22:16:47 2011 UTC (18 months, 3 weeks ago) by andreas

Improved speed and caching behavior with new CachedRemoteScopInstallation

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Revision 9346 - Directory Listing
Modified Mon Oct 24 16:26:54 2011 UTC (18 months, 3 weeks ago) by andreas

catching nullpointer exception if alignment is too short.

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Revision 9337 - Directory Listing
Modified Thu Oct 20 21:48:26 2011 UTC (18 months, 4 weeks ago) by andreas

removing TmpAtomCache

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Revision 9334 - Directory Listing
Modified Wed Oct 19 00:58:15 2011 UTC (18 months, 4 weeks ago) by blivens

Deprecating TmpAtomCache. We don't need a special helper class for unit tests anymore.

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Revision 9333 - Directory Listing
Modified Wed Oct 19 00:57:14 2011 UTC (18 months, 4 weeks ago) by blivens

Added AlignmentTools.isSequentialAlignment(), which detects if an AFPChain is sequential (vs. permuted).

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Revision 9313 - Directory Listing
Modified Wed Oct 12 00:15:56 2011 UTC (19 months ago) by andreas

switching service provider

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Revision 9312 - Directory Listing
Modified Wed Oct 12 00:15:47 2011 UTC (19 months ago) by andreas

switching service provider

---

Revision 9311 - Directory Listing
Modified Mon Oct 10 22:01:41 2011 UTC (19 months, 1 week ago) by andreas

now valid XML

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Revision 9310 - Directory Listing
Modified Mon Oct 10 21:31:55 2011 UTC (19 months, 1 week ago) by andreas

setting description for domain ranges

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Revision 9309 - Directory Listing
Modified Mon Oct 10 21:30:29 2011 UTC (19 months, 1 week ago) by andreas

setting description for  SCOP domain based structures.

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Revision 9308 - Directory Listing
Modified Mon Oct 10 21:28:53 2011 UTC (19 months, 1 week ago) by andreas

set description in AFP chain

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Revision 9307 - Directory Listing
Modified Mon Oct 10 21:27:03 2011 UTC (19 months, 1 week ago) by andreas

update to new protocol for running large scale calculations with various algorithm names.

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Revision 9306 - Directory Listing
Modified Mon Oct 10 15:46:27 2011 UTC (19 months, 1 week ago) by andreas

less verbose

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Revision 9305 - Directory Listing
Modified Sat Oct 8 01:57:51 2011 UTC (19 months, 1 week ago) by blivens

Made SeqRes2AtomAligner#getFullAtomSequence static.

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Revision 9304 - Directory Listing
Modified Sat Oct 8 01:56:54 2011 UTC (19 months, 1 week ago) by blivens

Improved parsing of older SCOP versions.

Older versions sometimes omitted the chain ID from structures with only one chain. Parsing these no longer leads to an exception.

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Revision 9299 - Directory Listing
Modified Thu Oct 6 02:03:13 2011 UTC (19 months, 1 week ago) by andreas

making many fields protected so they can be accessed by extending classes.

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Revision 9284 - Directory Listing
Modified Mon Oct 3 16:04:25 2011 UTC (19 months, 2 weeks ago) by andreas

less verbose

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Revision 9283 - Directory Listing
Modified Mon Oct 3 16:03:57 2011 UTC (19 months, 2 weeks ago) by andreas

adding javascript

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Revision 9282 - Directory Listing
Modified Sat Oct 1 05:55:19 2011 UTC (19 months, 2 weeks ago) by andreas

update to latest version of AtomCache name conventions

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Revision 9281 - Directory Listing
Modified Fri Sep 30 17:34:15 2011 UTC (19 months, 2 weeks ago) by andreas

tracking a short description of the 2nd protein

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Revision 9280 - Directory Listing
Modified Thu Sep 29 22:23:13 2011 UTC (19 months, 2 weeks ago) by blivens

Added equals() and hashCode() methods to AFPChain. The methods do not test all properties extensively, but rather test for equality of the core alignment represented by an AFPChain.

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Revision 9274 - Directory Listing
Modified Mon Sep 26 21:10:16 2011 UTC (19 months, 3 weeks ago) by andreas

setting description of Structure

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Revision 9271 - Directory Listing
Modified Mon Sep 26 20:33:41 2011 UTC (19 months, 3 weeks ago) by andreas

more informative exception

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Revision 9270 - Directory Listing
Modified Mon Sep 26 20:32:50 2011 UTC (19 months, 3 weeks ago) by andreas

flushing now all remote providers

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Revision 9269 - Directory Listing
Modified Sat Sep 24 23:32:32 2011 UTC (19 months, 3 weeks ago) by andreas

making sure there is no null values to be written. (could be the result of an external error)

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Revision 9268 - Directory Listing
Modified Sat Sep 24 23:29:22 2011 UTC (19 months, 3 weeks ago) by andreas

improved caching of remote data providers

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Revision 9266 - Directory Listing
Modified Sat Sep 24 22:35:58 2011 UTC (19 months, 3 weeks ago) by andreas

several improvements for better dealing with alignments of domains and fetching domain definitions from remote services.

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Revision 9265 - Directory Listing
Modified Thu Sep 22 22:06:24 2011 UTC (19 months, 3 weeks ago) by andreas

fixing problem when requesting PDP domains from cache

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Revision 9264 - Directory Listing
Modified Thu Sep 22 21:09:33 2011 UTC (19 months, 3 weeks ago) by andreas

making method that manipulates the alignment matrix with sequence conservation public accessible

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Revision 9262 - Directory Listing
Modified Wed Sep 21 22:24:25 2011 UTC (19 months, 3 weeks ago) by andreas

update to new package structure

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Revision 9260 - Directory Listing
Modified Wed Sep 21 21:31:43 2011 UTC (19 months, 3 weeks ago) by andreas

now with support for fetching PDP protein domain assignments.

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Revision 9259 - Directory Listing
Modified Wed Sep 21 21:29:39 2011 UTC (19 months, 3 weeks ago) by andreas

new support for fetching PDP domains via remote web services calls

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Revision 9250 - Directory Listing
Modified Wed Sep 21 21:05:39 2011 UTC (19 months, 3 weeks ago) by andreas

check alignment length, to avoid division by 0 

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Revision 9249 - Directory Listing
Modified Wed Sep 21 21:04:51 2011 UTC (19 months, 3 weeks ago) by andreas

now write % sequence ID to DB search results.

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Revision 9248 - Directory Listing
Modified Wed Sep 21 21:03:44 2011 UTC (19 months, 3 weeks ago) by andreas

new CE parameter: run Ce while slightly preferring the alignment of sequence conserved residues

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Revision 9247 - Directory Listing
Modified Wed Sep 21 21:02:51 2011 UTC (19 months, 3 weeks ago) by andreas

new CE parameter: run Ce while slightly preferring the alignment of sequence conserved residues

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Revision 9246 - Directory Listing
Modified Wed Sep 21 21:01:23 2011 UTC (19 months, 3 weeks ago) by andreas

From now on we use remote scop calls to fetch the data. No need to waste local memory. Only drawback: port 80 needs to be open.

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Revision 9245 - Directory Listing
Modified Wed Sep 21 03:58:05 2011 UTC (19 months, 3 weeks ago) by andreas

fixing typo

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Revision 9244 - Directory Listing
Modified Wed Sep 21 03:57:23 2011 UTC (19 months, 3 weeks ago) by andreas

updating tests to stringmanipulationtesthelper class

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Revision 9241 - Directory Listing
Modified Tue Sep 20 23:03:08 2011 UTC (19 months, 3 weeks ago) by blivens

Minor doc update

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Revision 9240 - Directory Listing
Modified Mon Sep 19 11:59:34 2011 UTC (19 months, 4 weeks ago) by aalhossary

moving StringManipulationTestsHelper to org.biojava3.core.util

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Revision 9239 - Directory Listing
Modified Fri Sep 16 23:18:57 2011 UTC (20 months ago) by andreas

documenting why we use unix endline here

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Revision 9235 - Directory Listing
Modified Wed Sep 14 19:00:07 2011 UTC (20 months ago) by andreas

getSubranges now assigns a new new to a Structure object

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Revision 9233 - Directory Listing
Modified Wed Sep 14 14:31:53 2011 UTC (20 months ago) by aalhossary

just code template & class documentation

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Revision 9232 - Directory Listing
Modified Wed Sep 14 14:20:46 2011 UTC (20 months ago) by aalhossary

fixed different end line characters test failure; added String manipulation helper class (for further enhancements)

---

Revision 9230 - Directory Listing
Modified Tue Sep 13 23:40:38 2011 UTC (20 months ago) by andreas

new util method in StructureUtils, preparation for XML serialization of SCOP and a new SCOPInstallation that is powered by web service requests to require minimum memory.  Also a few other improvements

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Revision 9229 - Directory Listing
Modified Tue Sep 13 23:26:04 2011 UTC (20 months ago) by andreas

new utility method for duplicating and cloning a set of Calpha atoms.

---

Revision 9228 - Directory Listing
Modified Tue Sep 13 14:33:49 2011 UTC (20 months ago) by aalhossary

specifying all Date formats to Locale.US

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Revision 9227 - Directory Listing
Modified Tue Sep 13 00:38:43 2011 UTC (20 months ago) by blivens

Referred to some static variables by full name. This prevents confusion when subclasses define a variable with the same name.

---

Revision 9225 - Directory Listing
Modified Tue Sep 13 00:33:29 2011 UTC (20 months ago) by blivens

Added an OptimalCECPParameters class to control the OptimalCECPMain aligner. It currently has two parameters: tryAllCPs, and cpPoint.

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Revision 9223 - Directory Listing
Modified Mon Sep 12 23:04:25 2011 UTC (20 months ago) by blivens

Added another alignment algorithm for detecting circular permutations: OptimalCECPMain. It is extremely slow but thorough. This algorithm requires additional testing and may contain bugs.

---

Revision 9222 - Directory Listing
Modified Mon Sep 12 21:11:33 2011 UTC (20 months ago) by blivens

Minor changes in CeMain and CeCPMain, including additional comments, better debugging info, and a different distance matrix (no longer doubled). Renamed CeMainTest to CeCPMainTest to better reflect its contents.

---

Revision 9220 - Directory Listing
Modified Thu Sep 8 22:14:22 2011 UTC (20 months, 1 week ago) by andreas

making getAlgorithm more usable in multi threaded environment, to avoid two threads using the same CeCalculator.

---

Revision 9169 - Directory Listing
Modified Fri Sep 2 15:17:53 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 9167 - Directory Listing
Modified Fri Sep 2 15:17:45 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.2

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Revision 9166 - Directory Listing
Modified Thu Sep 1 00:43:19 2011 UTC (20 months, 2 weeks ago) by andreas

and also needed to fix an assertion...

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Revision 9165 - Directory Listing
Modified Thu Sep 1 00:10:38 2011 UTC (20 months, 2 weeks ago) by andreas

fixing index out of bounds error

---

Revision 9163 - Directory Listing
Modified Wed Aug 31 18:16:54 2011 UTC (20 months, 2 weeks ago) by andreas

moving alignment pre and post processing into public static methods

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Revision 9162 - Directory Listing
Modified Wed Aug 31 17:51:29 2011 UTC (20 months, 2 weeks ago) by andreas

bean-ifying access methods

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Revision 9161 - Directory Listing
Modified Wed Aug 31 17:39:23 2011 UTC (20 months, 2 weeks ago) by andreas

removing javadoc warning

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Revision 9160 - Directory Listing
Modified Wed Aug 31 17:38:25 2011 UTC (20 months, 2 weeks ago) by andreas

removing javadoc warning

---

Revision 9159 - Directory Listing
Modified Wed Aug 31 17:37:34 2011 UTC (20 months, 2 weeks ago) by andreas

removing javadoc warning

---

Revision 9158 - Directory Listing
Modified Wed Aug 31 17:36:00 2011 UTC (20 months, 2 weeks ago) by andreas

improving javadoc

---

Revision 9157 - Directory Listing
Modified Wed Aug 31 17:34:32 2011 UTC (20 months, 2 weeks ago) by andreas

bean-ifying access methods

---

Revision 9156 - Directory Listing
Modified Wed Aug 31 17:33:17 2011 UTC (20 months, 2 weeks ago) by andreas

bean-ifying access methods

---

Revision 9150 - Directory Listing
Modified Wed Aug 31 05:56:52 2011 UTC (20 months, 2 weeks ago) by andreas

fixing all javadoc warnings in biojava-structure

---

Revision 9149 - Directory Listing
Modified Wed Aug 31 05:49:29 2011 UTC (20 months, 2 weeks ago) by andreas

fixing all javadoc warnings in biojava-structure

---

Revision 9148 - Directory Listing
Modified Wed Aug 31 05:14:31 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9147 - Directory Listing
Modified Wed Aug 31 05:14:06 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9146 - Directory Listing
Modified Wed Aug 31 05:13:40 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9145 - Directory Listing
Modified Wed Aug 31 05:13:19 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9144 - Directory Listing
Modified Wed Aug 31 05:12:29 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9143 - Directory Listing
Modified Wed Aug 31 05:11:48 2011 UTC (20 months, 2 weeks ago) by blivens

Rolling back r9132 since we're officially using java 1.6

---

Revision 9142 - Directory Listing
Modified Wed Aug 31 05:11:32 2011 UTC (20 months, 2 weeks ago) by andreas

update for better parsing of new remediated files

---

Revision 9141 - Directory Listing
Modified Wed Aug 31 05:11:19 2011 UTC (20 months, 2 weeks ago) by andreas

update for better parsing of new remediated files

---

Revision 9140 - Directory Listing
Modified Wed Aug 31 05:01:57 2011 UTC (20 months, 2 weeks ago) by andreas

more cleanup

---

Revision 9139 - Directory Listing
Modified Wed Aug 31 05:00:58 2011 UTC (20 months, 2 weeks ago) by andreas

more cleanup

---

Revision 9138 - Directory Listing
Modified Wed Aug 31 05:00:27 2011 UTC (20 months, 2 weeks ago) by andreas

update to new AtomCache constructor

---

Revision 9137 - Directory Listing
Modified Wed Aug 31 04:48:06 2011 UTC (20 months, 2 weeks ago) by andreas

adding new cif field

---

Revision 9136 - Directory Listing
Modified Wed Aug 31 04:44:55 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9135 - Directory Listing
Modified Wed Aug 31 04:44:00 2011 UTC (20 months, 2 weeks ago) by andreas

removing javadoc warnings

---

Revision 9134 - Directory Listing
Modified Wed Aug 31 04:38:40 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warnings

---

Revision 9132 - Directory Listing
Modified Wed Aug 31 04:27:09 2011 UTC (20 months, 2 weeks ago) by blivens

Commented out @Overrides of interface methods for java 1.5

---

Revision 9130 - Directory Listing
Modified Wed Aug 31 04:22:13 2011 UTC (20 months, 2 weeks ago) by andreas

deleting files that should not be in svn

---

Revision 9129 - Directory Listing
Modified Wed Aug 31 04:16:13 2011 UTC (20 months, 2 weeks ago) by andreas

update to new AtomCache constructor

---

Revision 9126 - Directory Listing
Modified Wed Aug 31 04:04:31 2011 UTC (20 months, 2 weeks ago) by andreas

cleaning pom files, removing warnings.

---

Revision 9125 - Directory Listing
Modified Wed Aug 31 04:02:56 2011 UTC (20 months, 2 weeks ago) by blivens

Preserve more AFPChain information (such as PDB name) across structural operations and alignments. 

---

Revision 9124 - Directory Listing
Modified Wed Aug 31 04:02:19 2011 UTC (20 months, 2 weeks ago) by andreas

fixing broken junit test

---

Revision 9123 - Directory Listing
Modified Wed Aug 31 02:12:49 2011 UTC (20 months, 2 weeks ago) by blivens

Removed/suppressed some warnings

---

Revision 9122 - Directory Listing
Modified Wed Aug 31 02:08:52 2011 UTC (20 months, 2 weeks ago) by blivens

Refactored CeMain and CeCPMain to improve isolation of the circular permutation code. To check for CPs, use CeCPMain rather than setting a parameter to CeMain.

---

Revision 9121 - Directory Listing
Modified Tue Aug 30 23:55:14 2011 UTC (20 months, 2 weeks ago) by blivens

Removing CEHook classes in favor of a subclass pattern.

---

Revision 9120 - Directory Listing
Modified Tue Aug 30 23:54:22 2011 UTC (20 months, 2 weeks ago) by blivens

Adding CEHook classes for posterity

---

Revision 9119 - Directory Listing
Modified Tue Aug 30 23:42:06 2011 UTC (20 months, 2 weeks ago) by andreas

Adding a new version of a ScopDatabase, driven by a remote webservice calls, to avoid Memory overhead.

---

Revision 9118 - Directory Listing
Modified Tue Aug 30 23:41:19 2011 UTC (20 months, 2 weeks ago) by andreas

testing new ScopDatabase implementation for a version of Scop driven by remote webservice calls.

---

Revision 9113 - Directory Listing
Modified Tue Aug 30 09:44:31 2011 UTC (20 months, 2 weeks ago) by blivens

Added default constructors for AtomCache and SCOPInstallation with reasonable file paths.

---

Revision 9112 - Directory Listing
Modified Tue Aug 30 05:10:21 2011 UTC (20 months, 2 weeks ago) by andreas

fixing javadoc warning

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Revision 9111 - Directory Listing
Modified Tue Aug 30 03:25:02 2011 UTC (20 months, 2 weeks ago) by blivens

UserConfiguration checks the PDB_DIR environmental variable, as well as the system property

---

Revision 9110 - Directory Listing
Modified Mon Aug 29 22:45:44 2011 UTC (20 months, 2 weeks ago) by andreas

cleanup

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Revision 9109 - Directory Listing
Modified Mon Aug 29 22:39:25 2011 UTC (20 months, 2 weeks ago) by andreas

adding junit test for #3282

---

Revision 9108 - Directory Listing
Modified Mon Aug 29 22:10:30 2011 UTC (20 months, 2 weeks ago) by andreas

Now with a new flag: automatically replace local files with the latest remediated files from PDB (default: disabled)

---

Revision 9107 - Directory Listing
Modified Mon Aug 29 22:09:33 2011 UTC (20 months, 2 weeks ago) by andreas

Now with a new flag: automatically replace local files with the latest remediated files from PDB (default: disabled)

---

Revision 9106 - Directory Listing
Modified Mon Aug 29 16:41:16 2011 UTC (20 months, 2 weeks ago) by andreas

less verbose

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Revision 9105 - Directory Listing
Modified Fri Aug 26 21:56:26 2011 UTC (20 months, 3 weeks ago) by andreas

further refinement of regexp

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Revision 9104 - Directory Listing
Modified Fri Aug 26 21:56:05 2011 UTC (20 months, 3 weeks ago) by andreas

further refinement of regexp

---

Revision 9103 - Directory Listing
Modified Fri Aug 26 19:53:57 2011 UTC (20 months, 3 weeks ago) by andreas

extending AtomCache to new convention, which is more friendly to be used in file names

---

Revision 9102 - Directory Listing
Modified Fri Aug 26 19:53:48 2011 UTC (20 months, 3 weeks ago) by andreas

extending AtomCache to new convention, which is more friendly to be used in file names

---

Revision 9101 - Directory Listing
Modified Fri Aug 26 19:53:38 2011 UTC (20 months, 3 weeks ago) by andreas

extending AtomCache to new convention, which is more friendly to be used in file names

---

Revision 9098 - Directory Listing
Modified Thu Aug 25 23:29:03 2011 UTC (20 months, 3 weeks ago) by andreas

fixing warnings

---

Revision 9097 - Directory Listing
Modified Thu Aug 25 22:36:13 2011 UTC (20 months, 3 weeks ago) by andreas

new test to make sure loading structures from a URL works ok.

---

Revision 9096 - Directory Listing
Modified Thu Aug 25 18:10:18 2011 UTC (20 months, 3 weeks ago) by andreas

making ChemComp comparable

---

Revision 9095 - Directory Listing
Modified Wed Aug 24 19:37:31 2011 UTC (20 months, 3 weeks ago) by andreas

new StructureProvider that works off a different directory structure

---

Revision 9094 - Directory Listing
Modified Wed Aug 24 19:25:08 2011 UTC (20 months, 3 weeks ago) by andreas

deprecating most of the org.biojava.bio.structure.server package. Better to use the AtomCache

---

Revision 9093 - Directory Listing
Modified Wed Aug 24 19:23:13 2011 UTC (20 months, 3 weeks ago) by andreas

fixing a problem when working with altLocs

---

Revision 9092 - Directory Listing
Modified Wed Aug 24 19:22:23 2011 UTC (20 months, 3 weeks ago) by andreas

now with version nr

---

Revision 9091 - Directory Listing
Modified Wed Aug 24 19:21:58 2011 UTC (20 months, 3 weeks ago) by andreas

now with version nr

---

Revision 9090 - Directory Listing
Modified Wed Aug 24 19:21:25 2011 UTC (20 months, 3 weeks ago) by andreas

better javadoc

---

Revision 9089 - Directory Listing
Modified Wed Aug 24 19:17:48 2011 UTC (20 months, 3 weeks ago) by andreas

now also throws structureexception

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Revision 9088 - Directory Listing
Modified Wed Aug 24 19:16:45 2011 UTC (20 months, 3 weeks ago) by andreas

new error if biol unit can't be downloaded

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Revision 9087 - Directory Listing
Modified Wed Aug 24 19:15:21 2011 UTC (20 months, 3 weeks ago) by andreas

now comparable, serializable

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Revision 9086 - Directory Listing
Modified Wed Aug 24 19:14:59 2011 UTC (20 months, 3 weeks ago) by andreas

now comparable, serializable

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Revision 9085 - Directory Listing
Modified Wed Aug 24 19:14:22 2011 UTC (20 months, 3 weeks ago) by andreas

synchronizing toXML access

---

Revision 9084 - Directory Listing
Modified Wed Aug 24 19:13:42 2011 UTC (20 months, 3 weeks ago) by andreas

update to new Scop interfaces and fixing a windows specific bug

---

Revision 9083 - Directory Listing
Modified Wed Aug 24 19:11:44 2011 UTC (20 months, 3 weeks ago) by andreas

improved handling of SCOP domains, ids and ranges

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Revision 9082 - Directory Listing
Modified Wed Aug 24 19:10:06 2011 UTC (20 months, 3 weeks ago) by andreas

making some strings static properties

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Revision 9081 - Directory Listing
Modified Wed Aug 24 19:09:27 2011 UTC (20 months, 3 weeks ago) by andreas

more exception handling

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Revision 9080 - Directory Listing
Modified Wed Aug 24 19:08:27 2011 UTC (20 months, 3 weeks ago) by andreas

now allows specification of sequence weight

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Revision 9070 - Directory Listing
Modified Wed Aug 17 00:09:08 2011 UTC (21 months ago) by andreas

parser now less verbose. Moving many warnings to logger.fine level.

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Revision 9069 - Directory Listing
Modified Wed Aug 17 00:08:43 2011 UTC (21 months ago) by andreas

less verbose

---

Revision 9068 - Directory Listing
Modified Wed Aug 17 00:05:09 2011 UTC (21 months ago) by blivens

Fixed equals/hashCode methods of ResidueNumber to handle Null properly.

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Revision 9067 - Directory Listing
Modified Wed Aug 17 00:04:00 2011 UTC (21 months ago) by blivens

Improved documentation (and testing) of getting a structure by range.

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Revision 9054 - Directory Listing
Modified Thu Aug 4 16:19:34 2011 UTC (21 months, 2 weeks ago) by andreas

less verbose

---

Revision 9053 - Directory Listing
Modified Thu Aug 4 15:00:07 2011 UTC (21 months, 2 weeks ago) by andreas

updating test to new remediated version

---

Revision 9026 - Directory Listing
Modified Wed Jun 29 18:47:49 2011 UTC (22 months, 2 weeks ago) by andreas

adding check if no domains can be found for a PDB id to avoid nullpointerexception

---

Revision 9018 - Directory Listing
Modified Sat Jun 25 00:32:11 2011 UTC (22 months, 3 weeks ago) by andreas

some more refinements

---

Revision 9017 - Directory Listing
Modified Sat Jun 25 00:01:24 2011 UTC (22 months, 3 weeks ago) by andreas

some more refinements

---

Revision 9016 - Directory Listing
Modified Fri Jun 24 22:59:10 2011 UTC (22 months, 3 weeks ago) by andreas

more display options

---

Revision 9014 - Directory Listing
Modified Fri Jun 24 22:17:22 2011 UTC (22 months, 3 weeks ago) by andreas

moved a utility method from DisplayAFP to AFPAlignmentDisplay

---

Revision 9013 - Directory Listing
Modified Fri Jun 24 21:47:32 2011 UTC (22 months, 3 weeks ago) by andreas

nicer website display and fixing an issue where the PDB residue ranges were one line off

---

Revision 9008 - Directory Listing
Modified Wed Jun 22 22:31:33 2011 UTC (22 months, 3 weeks ago) by andreas

better javadoc

---

Revision 9007 - Directory Listing
Modified Tue Jun 21 17:03:46 2011 UTC (22 months, 3 weeks ago) by andreas

fixing typo in method name

---

Revision 9005 - Directory Listing
Modified Mon Jun 20 23:37:01 2011 UTC (22 months, 4 weeks ago) by Peter Rose

Fixed storeUnAlignedSeqRes so it works for biological assemblies (need to loop over all models, rather than just use first model).

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Revision 9003 - Directory Listing
Modified Mon Jun 20 02:18:20 2011 UTC (22 months, 4 weeks ago) by andreas

giving precise CE version number and reference

---

Revision 9002 - Directory Listing
Modified Mon Jun 20 02:17:38 2011 UTC (22 months, 4 weeks ago) by andreas

giving precise CE version number and reference

---

Revision 9001 - Directory Listing
Modified Thu Jun 16 23:39:42 2011 UTC (23 months ago) by andreas

ignoring missing chain ids

---

Revision 9000 - Directory Listing
Modified Thu Jun 16 23:22:23 2011 UTC (23 months ago) by andreas

making access public

---

Revision 8999 - Directory Listing
Modified Thu Jun 16 23:02:03 2011 UTC (23 months ago) by andreas

now can store SEQRES without aligning them

---

Revision 8998 - Directory Listing
Modified Thu Jun 16 23:01:54 2011 UTC (23 months ago) by andreas

now can store SEQRES without aligning them

---

Revision 8989 - Directory Listing
Modified Fri Jun 10 20:45:31 2011 UTC (23 months, 1 week ago) by Peter Rose

Updated javadoc for isBiologicalAssembly()

---

Revision 8984 - Directory Listing
Modified Wed Jun 8 19:15:40 2011 UTC (23 months, 1 week ago) by andreas

beans are now serializable

---

Revision 8983 - Directory Listing
Modified Wed Jun 8 19:14:34 2011 UTC (23 months, 1 week ago) by andreas

now serializable

---

Revision 8982 - Directory Listing
Modified Wed Jun 8 18:51:19 2011 UTC (23 months, 1 week ago) by andreas

providing an interface and factory on top of a SCOP installation, so we can also plug in database-backed installations.

---

Revision 8976 - Directory Listing
Modified Thu Jun 2 06:20:40 2011 UTC (23 months, 2 weeks ago) by andreas

new filterByClassificationId method

---

Revision 8969 - Directory Listing
Modified Wed May 25 00:21:48 2011 UTC (23 months, 3 weeks ago) by Peter Rose

Set flag in structure that indicates if structure was loaded from a biological assembly file (i.e. *.pdb1.gz).

---

Revision 8968 - Directory Listing
Modified Wed May 25 00:19:48 2011 UTC (23 months, 3 weeks ago) by Peter Rose

Added biologicalAssembly flag that indicates if this structure was loaded from a biological assembly file (i.e. *.pdb.gz).

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Revision 8967 - Directory Listing
Modified Wed May 25 00:19:33 2011 UTC (23 months, 3 weeks ago) by Peter Rose

Added biologicalAssembly flag that indicates if this structure was loaded from a biological assembly file (i.e. *.pdb.gz).

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Revision 8965 - Directory Listing
Modified Tue May 24 23:36:24 2011 UTC (23 months, 3 weeks ago) by Peter Rose

Removed commented out code.

---

Revision 8964 - Directory Listing
Modified Tue May 24 22:43:36 2011 UTC (23 months, 3 weeks ago) by Peter Rose

Added methods to download biological assembly files.

---

Revision 8963 - Directory Listing
Modified Tue May 24 22:42:41 2011 UTC (23 months, 3 weeks ago) by Peter Rose

Added method to load biological assembly by pdbId and bioAssemblyId.

---

Revision 8961 - Directory Listing
Modified Mon May 23 22:28:25 2011 UTC (23 months, 3 weeks ago) by andreas

adding MODEL as a status

---

Revision 8959 - Directory Listing
Modified Wed May 18 23:24:20 2011 UTC (2 years ago) by andreas

refinement - now only ignoring hetatom groups

---

Revision 8958 - Directory Listing
Modified Wed May 18 23:21:23 2011 UTC (2 years ago) by andreas

less verbose

---

Revision 8957 - Directory Listing
Modified Wed May 18 23:12:04 2011 UTC (2 years ago) by andreas

adding another check for things that can go wrong with seqres mapping

---

Revision 8956 - Directory Listing
Modified Wed May 18 18:54:34 2011 UTC (2 years ago) by andreas

fixing an endless loop that can happen with v. long headers

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Revision 8955 - Directory Listing
Modified Wed May 18 18:53:54 2011 UTC (2 years ago) by andreas

testing for a possible endless loop in long headers

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Revision 8953 - Directory Listing
Modified Tue May 17 22:44:29 2011 UTC (2 years ago) by andreas

now correctly using the global PDB path

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Revision 8952 - Directory Listing
Modified Tue May 17 22:41:51 2011 UTC (2 years ago) by andreas

now propagating fileParsingparameters

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Revision 8940 - Directory Listing
Modified Mon May 16 21:44:27 2011 UTC (2 years ago) by andreas

now can deal with custom user provided PDB files (and chain Id) via URLs

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Revision 8936 - Directory Listing
Modified Mon May 16 17:21:36 2011 UTC (2 years ago) by andreas

downloading a file again if something is wrong with it. 

---

Revision 8930 - Directory Listing
Modified Tue May 10 15:36:39 2011 UTC (2 years ago) by blivens

Added methods to StructureAlignmentFactory to allow removing algorithms at runtime.

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Revision 8926 - Directory Listing
Modified Tue May 10 02:40:23 2011 UTC (2 years ago) by andreas

toPDB method now also prints altLocs

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Revision 8925 - Directory Listing
Modified Tue May 10 02:31:29 2011 UTC (2 years ago) by andreas

javadoc improvement

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Revision 8922 - Directory Listing
Modified Tue May 10 02:26:28 2011 UTC (2 years ago) by andreas

setting chain for alternate groups

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Revision 8920 - Directory Listing
Modified Mon May 9 22:05:11 2011 UTC (2 years ago) by andreas

small cleanup

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Revision 8919 - Directory Listing
Modified Mon May 9 22:03:10 2011 UTC (2 years ago) by andreas

fix: Now getAtoms also checks alternate location, if the atom could not be found in the primary group.

---

Revision 8918 - Directory Listing
Modified Mon May 9 21:58:57 2011 UTC (2 years ago) by andreas

new unit test to make sure we check also altLocs if atoms are requested. some Atoms are only provided with altLoc flags...

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Revision 8916 - Directory Listing
Modified Sat May 7 00:24:05 2011 UTC (2 years ago) by blivens

Added method to StructureAlignmentFactory allowing algorithms to be added at runtime.

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Revision 8915 - Directory Listing
Modified Thu May 5 22:54:03 2011 UTC (2 years ago) by andreas

return statement at wrong location

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Revision 8914 - Directory Listing
Modified Thu May 5 22:50:20 2011 UTC (2 years ago) by andreas

fixing more index boundary issues

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Revision 8913 - Directory Listing
Modified Thu May 5 22:15:21 2011 UTC (2 years ago) by andreas

adding a length check for the alignment formatting

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Revision 8912 - Directory Listing
Modified Thu May 5 22:05:07 2011 UTC (2 years ago) by andreas

now trimming to match nucleotides

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Revision 8911 - Directory Listing
Modified Thu May 5 21:47:49 2011 UTC (2 years ago) by andreas

now trying a quick matching of SEQRES and ATOM records first, before falling back to aligning them.

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Revision 8906 - Directory Listing
Modified Wed May 4 21:24:42 2011 UTC (2 years ago) by andreas

adding check for null value

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Revision 8905 - Directory Listing
Modified Wed May 4 21:08:39 2011 UTC (2 years ago) by andreas

adding check for null value

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Revision 8904 - Directory Listing
Modified Wed May 4 21:07:58 2011 UTC (2 years ago) by andreas

adding check for null value

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Revision 8903 - Directory Listing
Modified Wed May 4 21:06:49 2011 UTC (2 years ago) by andreas

checking for null value

---

Revision 8898 - Directory Listing
Modified Wed Apr 27 01:48:06 2011 UTC (2 years ago) by blivens

Merging modifications by Amr Al-Hossary to allow fetching obsolete PDB IDs from AtomCache and PDBFileReader.

Changes covered by TestAtomCache and TestPDBStatus.

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Revision 8897 - Directory Listing
Modified Tue Apr 26 22:26:39 2011 UTC (2 years ago) by blivens

Modified PDBStatus for more robust support for obsolete files, including multiple current versions of obsolete IDs. Compatible with the 4/26/2011 release of the PDB website.

---

Revision 8892 - Directory Listing
Modified Mon Apr 25 18:01:58 2011 UTC (2 years ago) by blivens

Changed PDBStatus.

 * Changed signature to getReplaces methods to allow multiple values to be returned.
 * Fixed an internal bug involving object reuse that might have been a problem in the future.
 * Updated test cases.

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Revision 8891 - Directory Listing
Modified Sun Apr 24 17:23:58 2011 UTC (2 years ago) by andreas

adding new parameter

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Revision 8890 - Directory Listing
Modified Sun Apr 24 17:14:50 2011 UTC (2 years ago) by andreas

adding a couple of new ways to interact with the internals from the outside, also some code cleanup

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Revision 8889 - Directory Listing
Modified Sun Apr 24 17:12:39 2011 UTC (2 years ago) by andreas

adding new event listener class

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Revision 8888 - Directory Listing
Modified Fri Apr 22 21:29:43 2011 UTC (2 years ago) by blivens

Fixed exception in PDBStatus that occured when a ID was made obsolete but not replaced.

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Revision 8887 - Directory Listing
Modified Fri Apr 22 01:37:04 2011 UTC (2 years ago) by blivens

Added bio.structure.PDBStatus class, which provides utility methods for handling obsolete PDB IDs.

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Revision 8885 - Directory Listing
Modified Thu Apr 21 18:43:40 2011 UTC (2 years ago) by andreas

preventing a nullpointer exception from being thrown here.

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Revision 8878 - Directory Listing
Modified Thu Apr 7 20:07:17 2011 UTC (2 years, 1 month ago) by blivens

Improved ScopDescription.

Added equals/hashcode methods.
Added method to get Class, Fold, etc. for a particular ScopDescription.
Added Unit Tests.

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Revision 8877 - Directory Listing
Modified Thu Apr 7 00:30:22 2011 UTC (2 years, 1 month ago) by andreas

making sure that TMscore gets communicated when filterDuplicateAFPs

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Revision 8875 - Directory Listing
Modified Tue Apr 5 21:58:50 2011 UTC (2 years, 1 month ago) by blivens

Changed the parameter order of the Structure.getChain(int,int) method to
match that actually used by StructureImpl.

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Revision 8865 - Directory Listing
Modified Wed Mar 30 20:43:05 2011 UTC (2 years, 1 month ago) by andreas

making sure the parser does not change the global Calpha parsing flag, only local change, if a particular PDB ID is very large.

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Revision 8854 - Directory Listing
Modified Thu Mar 17 23:40:55 2011 UTC (2 years, 2 months ago) by andreas

use the new method that checks the correct order of the pair in the afpChain

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Revision 8853 - Directory Listing
Modified Thu Mar 17 23:40:23 2011 UTC (2 years, 2 months ago) by andreas

new methods that checks for the correct order of the pair in the afpChain

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Revision 8851 - Directory Listing
Modified Tue Mar 15 23:47:19 2011 UTC (2 years, 2 months ago) by andreas

making sure we can lookup in allElements in O(1);

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Revision 8850 - Directory Listing
Modified Tue Mar 15 23:31:47 2011 UTC (2 years, 2 months ago) by andreas

disabling Hill order for now, since it seems wrong.

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Revision 8849 - Directory Listing
Modified Tue Mar 15 23:09:55 2011 UTC (2 years, 2 months ago) by andreas

small speedup in Element class

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Revision 8847 - Directory Listing
Modified Tue Mar 15 00:53:25 2011 UTC (2 years, 2 months ago) by andreas

ignoring if a group can't be found...

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Revision 8846 - Directory Listing
Modified Mon Mar 14 19:07:59 2011 UTC (2 years, 2 months ago) by andreas

adding check to make sure that map of sites is not null

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Revision 8845 - Directory Listing
Modified Mon Mar 14 19:03:36 2011 UTC (2 years, 2 months ago) by andreas

catching linking of SITE records to groups

---

Revision 8842 - Directory Listing
Modified Mon Mar 14 04:40:22 2011 UTC (2 years, 2 months ago) by andreas

if a line causes a crash, print that line now.

---

Revision 8836 - Directory Listing
Modified Wed Mar 9 22:57:59 2011 UTC (2 years, 2 months ago) by andreas

new utility method that allows to access all atoms in all models

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Revision 8835 - Directory Listing
Modified Wed Mar 9 22:50:19 2011 UTC (2 years, 2 months ago) by andreas

fixing some minor issues and docu improvements for biological units.

---

Revision 8834 - Directory Listing
Modified Wed Mar 9 22:48:59 2011 UTC (2 years, 2 months ago) by blivens

Fixed a few warnings (deprecation, improper use of generics).
Improved reporting when guessing scop domains.

---

Revision 8833 - Directory Listing
Modified Wed Mar 9 20:17:57 2011 UTC (2 years, 2 months ago) by andreas

setting path now system wide

---

Revision 8832 - Directory Listing
Modified Wed Mar 9 20:07:33 2011 UTC (2 years, 2 months ago) by andreas

AtomCache can now fetch Biological unit files and cache them locally.

---

Revision 8830 - Directory Listing
Modified Tue Mar 8 22:40:57 2011 UTC (2 years, 2 months ago) by andreas

beginning to break out caching functionality from pdbfilereader

---

Revision 8829 - Directory Listing
Modified Tue Mar 8 22:39:32 2011 UTC (2 years, 2 months ago) by andreas

now with a debug flag

---

Revision 8827 - Directory Listing
Modified Sun Mar 6 22:32:18 2011 UTC (2 years, 2 months ago) by blivens

Removed unused imports

---

Revision 8826 - Directory Listing
Modified Sun Mar 6 22:27:25 2011 UTC (2 years, 2 months ago) by blivens

Removing the test package org/biojava/bio/structure/align/benchmark.

This doesn't test CE very well, and the resource files slow down SVN checkouts. Contact Spencer Bliven if you still need access to any of this code.

---

Revision 8825 - Directory Listing
Modified Sun Mar 6 22:24:14 2011 UTC (2 years, 2 months ago) by blivens

Added additional flexibility to fetching SCOP domains from an AtomCache.

Default behavior is unchanged. However, if the new setStrictSCOP(false) is called, the AtomCache will do its best to give a reasonable result even if the scop domain is not found. For instance, the structure of d1gbga_ would be returned for the usually invalid identifier 'd1gbg__'.
See getStructure(String) and guessScopDomain(String) for details.

---

Revision 8824 - Directory Listing
Modified Sun Mar 6 22:13:26 2011 UTC (2 years, 2 months ago) by blivens

Added tests for StructureTools.getSubRanges(String) for tough cases like insertion codes and negative residues, then fixed StructureTools so it passes.

getSubRanges now uses a regular expression parser for subranges rather than the simple substring parser previously used.

Note that when running StructureToolsTest, setup() produces some parse errors for 1a4w (due to a bug handling SITE lines). However, all tests pass.

---

Revision 8819 - Directory Listing
Modified Fri Mar 4 21:35:11 2011 UTC (2 years, 2 months ago) by andreas

adding center of mass calculation

---

Revision 8818 - Directory Listing
Modified Fri Mar 4 21:34:31 2011 UTC (2 years, 2 months ago) by andreas

adding center of mass calculation

---

Revision 8816 - Directory Listing
Modified Wed Mar 2 14:06:02 2011 UTC (2 years, 2 months ago) by jacobsen

Implemented fast distance method for speed improvements when calculating thousands plus distances.
Tweaked StructureTools to give better H-Bonding results - this is now comparable to HBPlus/LigPlot/LPC
Added a couple of more bond types to Bond.
Corrected spelling mistake in ChemCompDescriptor toString() (wow serious stuff!)  

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Revision 8810 - Directory Listing
Modified Fri Feb 25 17:47:52 2011 UTC (2 years, 2 months ago) by jacobsen

Continued minor improvements on bond type detection in StructureTools. Added modified residues to parser.

---

Revision 8809 - Directory Listing
Modified Thu Feb 24 18:04:56 2011 UTC (2 years, 2 months ago) by jacobsen

Minor improvements on bond type detection in StructureTools

---

Revision 8807 - Directory Listing
Modified Wed Feb 23 04:59:23 2011 UTC (2 years, 2 months ago) by andreas

adding noargs constructure

---

Revision 8806 - Directory Listing
Modified Wed Feb 23 02:49:22 2011 UTC (2 years, 2 months ago) by andreas

now also printing Z-score if algo = CE

---

Revision 8805 - Directory Listing
Modified Wed Feb 23 02:48:06 2011 UTC (2 years, 2 months ago) by andreas

cleanup 

---

Revision 8804 - Directory Listing
Modified Wed Feb 23 02:46:40 2011 UTC (2 years, 2 months ago) by andreas

adding biojava copyright

---

Revision 8803 - Directory Listing
Modified Wed Feb 23 02:45:57 2011 UTC (2 years, 2 months ago) by andreas

adding @since annotation

---

Revision 8802 - Directory Listing
Modified Wed Feb 23 02:44:27 2011 UTC (2 years, 2 months ago) by andreas

Adding new ChemCompDescriptor to ChemComps

---

Revision 8801 - Directory Listing
Modified Wed Feb 23 02:44:06 2011 UTC (2 years, 2 months ago) by andreas

Adding new ChemCompDescriptor to ChemComps

---

Revision 8799 - Directory Listing
Modified Tue Feb 22 23:47:46 2011 UTC (2 years, 2 months ago) by andreas

cleanup and fixing wrong imports

---

Revision 8798 - Directory Listing
Modified Tue Feb 22 23:45:09 2011 UTC (2 years, 2 months ago) by andreas

exposing more internals of CE. Can be used to modify how CE works.

---

Revision 8795 - Directory Listing
Modified Tue Feb 22 18:02:58 2011 UTC (2 years, 2 months ago) by jacobsen

Added functionality for selecting a set of Groups in a Structure within a given radius of a given Group.

---

Revision 8791 - Directory Listing
Modified Sat Feb 19 08:01:10 2011 UTC (2 years, 2 months ago) by andreas

new setter method that allows to manipulate internal alignment matrix from outside

---

Revision 8780 - Directory Listing
Modified Tue Feb 15 23:51:26 2011 UTC (2 years, 3 months ago) by andreas

fixing a problem when reconstructing old XML serializations of structure alignments

---

Revision 8779 - Directory Listing
Modified Tue Feb 15 16:40:54 2011 UTC (2 years, 3 months ago) by andreas

adding a demo for how to split domains with PDP

---

Revision 8772 - Directory Listing
Modified Tue Feb 15 03:51:52 2011 UTC (2 years, 3 months ago) by andreas

new flag for verbosity level

---

Revision 8771 - Directory Listing
Modified Tue Feb 15 03:51:39 2011 UTC (2 years, 3 months ago) by andreas

new flag for verbosity level

---

Revision 8770 - Directory Listing
Modified Tue Feb 15 03:37:43 2011 UTC (2 years, 3 months ago) by andreas

now all systematic calculations will also calculate the tmScore

---

Revision 8769 - Directory Listing
Modified Tue Feb 15 03:36:14 2011 UTC (2 years, 3 months ago) by andreas

removing warnings

---

Revision 8768 - Directory Listing
Modified Tue Feb 15 03:33:26 2011 UTC (2 years, 3 months ago) by andreas

less verbose

---

Revision 8767 - Directory Listing
Modified Tue Feb 15 03:32:30 2011 UTC (2 years, 3 months ago) by andreas

speed up of junit tests

---

Revision 8766 - Directory Listing
Modified Tue Feb 15 03:30:21 2011 UTC (2 years, 3 months ago) by andreas

speed up of junit tests

---

Revision 8765 - Directory Listing
Modified Tue Feb 15 03:29:38 2011 UTC (2 years, 3 months ago) by andreas

speed up of junit tests

---

Revision 8764 - Directory Listing
Modified Tue Feb 15 03:28:46 2011 UTC (2 years, 3 months ago) by andreas

speed up of junit tests

---

Revision 8763 - Directory Listing
Modified Tue Feb 15 03:23:40 2011 UTC (2 years, 3 months ago) by andreas

speed up of junit tests

---

Revision 8762 - Directory Listing
Modified Tue Feb 15 03:15:37 2011 UTC (2 years, 3 months ago) by andreas

test flipping and serilisation of TMscores

---

Revision 8761 - Directory Listing
Modified Tue Feb 15 03:14:31 2011 UTC (2 years, 3 months ago) by andreas

no more random system.out

---

Revision 8760 - Directory Listing
Modified Tue Feb 15 03:13:20 2011 UTC (2 years, 3 months ago) by andreas

fixing javadoc warnings

---

Revision 8759 - Directory Listing
Modified Tue Feb 15 03:10:40 2011 UTC (2 years, 3 months ago) by andreas

now also using TM scores

---

Revision 8758 - Directory Listing
Modified Tue Feb 15 02:57:07 2011 UTC (2 years, 3 months ago) by andreas

new, reads Tmscore, if available

---

Revision 8757 - Directory Listing
Modified Tue Feb 15 02:54:10 2011 UTC (2 years, 3 months ago) by andreas

new, also write tmScore, if available

---

Revision 8756 - Directory Listing
Modified Tue Feb 15 02:49:50 2011 UTC (2 years, 3 months ago) by andreas

new toString, now also prints tmScore if available.

---

Revision 8752 - Directory Listing
Modified Mon Feb 14 04:49:52 2011 UTC (2 years, 3 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

---

Revision 8750 - Directory Listing
Modified Mon Feb 14 04:49:40 2011 UTC (2 years, 3 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.1

---

Revision 8743 - Directory Listing
Modified Wed Feb 9 09:13:50 2011 UTC (2 years, 3 months ago) by jacobsen

Went one step better and checked that the REF line was actually of the expected length before parsing it in case people have badly formatted home-brew PDB files or something. Will now log a warning and and back an empty ref section.

---

Revision 8742 - Directory Listing
Modified Wed Feb 9 08:54:55 2011 UTC (2 years, 3 months ago) by jacobsen

Added exception handling for when the JournalParser tries to convert a date in the PDB JRNL REF subsection from a string to an int. This will now warn the user that there is an incorrect datatype instead of falling over. 

---

Revision 8738 - Directory Listing
Modified Wed Feb 9 02:27:05 2011 UTC (2 years, 3 months ago) by andreas

making Sites comparable

---

Revision 8734 - Directory Listing
Modified Tue Feb 8 15:39:01 2011 UTC (2 years, 3 months ago) by jacobsen

Fix for http://bugzilla.open-bio.org/show_bug.cgi?id=3174

Multi-line REF sub-sections in the JRNL section are now correctly parsed to extract the full date, volume, etc and include the full-length journal name.

---

Revision 8733 - Directory Listing
Modified Tue Feb 8 02:44:34 2011 UTC (2 years, 3 months ago) by andreas

now also setting SITE records in reduced Structures

---

Revision 8730 - Directory Listing
Modified Mon Feb 7 02:58:14 2011 UTC (2 years, 3 months ago) by andreas

now allowing to call scaleablematrixpanel for debugging

---

Revision 8727 - Directory Listing
Modified Sat Feb 5 22:12:20 2011 UTC (2 years, 3 months ago) by andreas

catching some inconsistencies with some custom site records

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Revision 8714 - Directory Listing
Modified Thu Feb 3 06:05:52 2011 UTC (2 years, 3 months ago) by andreas

adding check for max-size

---

Revision 8710 - Directory Listing
Modified Wed Feb 2 17:41:47 2011 UTC (2 years, 3 months ago) by jacobsen

Added fix for rare cases when there are more than 18 chains in a COMPND and chains after 72 character limit are omitted form the structure. Entries such as 3mk3 will no longer throw a StructureException due to being unable to find a chain when  LinkChains2Compound() calls StructureImpl.findChain(). Test and test file included in commit.

---

Revision 8709 - Directory Listing
Modified Wed Feb 2 00:48:09 2011 UTC (2 years, 3 months ago) by andreas

fixing typo

---

Revision 8707 - Directory Listing
Modified Fri Jan 28 02:20:56 2011 UTC (2 years, 3 months ago) by andreas

making sure correct ChemCompProvider is being used.

---

Revision 8706 - Directory Listing
Modified Fri Jan 28 01:41:10 2011 UTC (2 years, 3 months ago) by andreas

adding check for problems during the alignment

---

Revision 8705 - Directory Listing
Modified Fri Jan 28 01:14:47 2011 UTC (2 years, 3 months ago) by andreas

now with test for amino acids that don;t have a one_letter code

---

Revision 8704 - Directory Listing
Modified Fri Jan 28 01:13:46 2011 UTC (2 years, 3 months ago) by andreas

mini fix

---

Revision 8703 - Directory Listing
Modified Fri Jan 28 00:28:26 2011 UTC (2 years, 3 months ago) by andreas

mini fix

---

Revision 8702 - Directory Listing
Modified Fri Jan 28 00:25:29 2011 UTC (2 years, 3 months ago) by andreas

security check to make sure field is not null

---

Revision 8697 - Directory Listing
Modified Thu Jan 27 21:33:09 2011 UTC (2 years, 3 months ago) by andreas

adding check that the PDB_DIR path ends with at / character.

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Revision 8692 - Directory Listing
Modified Thu Jan 27 01:37:14 2011 UTC (2 years, 3 months ago) by andreas

TITLE records can now go up to 80 chars.

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Revision 8689 - Directory Listing
Modified Tue Jan 25 16:50:27 2011 UTC (2 years, 3 months ago) by andreas

setting the path in system property so it gets propagatedcorrecty to all classes that are using it

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Revision 8688 - Directory Listing
Modified Tue Jan 25 16:47:00 2011 UTC (2 years, 3 months ago) by andreas

how to fetch all chem comps and install locally

---

Revision 8683 - Directory Listing
Modified Tue Jan 25 05:51:46 2011 UTC (2 years, 3 months ago) by andreas

updating according to feedback from Steve 

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Revision 8681 - Directory Listing
Modified Tue Jan 25 01:17:56 2011 UTC (2 years, 3 months ago) by andreas

test protected IDs on windows systems.

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Revision 8680 - Directory Listing
Modified Tue Jan 25 01:17:46 2011 UTC (2 years, 3 months ago) by andreas

test protected IDs on windows systems.

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Revision 8675 - Directory Listing
Modified Wed Jan 19 23:56:25 2011 UTC (2 years, 3 months ago) by andreas

only using model 0 for NMRs...

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Revision 8674 - Directory Listing
Modified Wed Jan 19 23:51:41 2011 UTC (2 years, 3 months ago) by andreas

only using model 0 for NMRs...

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Revision 8673 - Directory Listing
Modified Wed Jan 19 23:48:11 2011 UTC (2 years, 3 months ago) by andreas

javadoc cleanup, removed some warnings

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Revision 8672 - Directory Listing
Modified Wed Jan 19 23:12:12 2011 UTC (2 years, 3 months ago) by andreas

make sure we only use model 0 for multi-model structures.

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Revision 8669 - Directory Listing
Modified Mon Jan 17 07:39:12 2011 UTC (2 years, 4 months ago) by andreas

cleanup of api

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Revision 8665 - Directory Listing
Modified Sun Jan 16 18:45:44 2011 UTC (2 years, 4 months ago) by andreas

setting system parameter correctly now

---

Revision 8664 - Directory Listing
Modified Sun Jan 16 18:44:05 2011 UTC (2 years, 4 months ago) by andreas

First version of an implementation of PDP for automatically suggesting domains in structures

---

Revision 8661 - Directory Listing
Modified Sun Jan 9 20:07:25 2011 UTC (2 years, 4 months ago) by andreas

now the demo also prints more info about the various scores

---

Revision 8660 - Directory Listing
Modified Sun Jan 9 20:06:49 2011 UTC (2 years, 4 months ago) by andreas

better javadoc of scores

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Revision 8657 - Directory Listing
Modified Wed Jan 5 00:22:45 2011 UTC (2 years, 4 months ago) by andreas

ChemComp now serializable

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Revision 8656 - Directory Listing
Modified Tue Jan 4 23:28:49 2011 UTC (2 years, 4 months ago) by andreas

now with support for Atom.toPDB

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Revision 8655 - Directory Listing
Modified Tue Jan 4 23:28:39 2011 UTC (2 years, 4 months ago) by andreas

now with support for Atom.toPDB

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Revision 8654 - Directory Listing
Modified Tue Jan 4 23:28:24 2011 UTC (2 years, 4 months ago) by andreas

now with support for Atom.toPDB

---

Revision 8648 - Directory Listing
Modified Tue Dec 28 17:33:53 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

---

Revision 8646 - Directory Listing
Modified Tue Dec 28 17:33:41 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0

---

Revision 8645 - Directory Listing
Modified Sat Dec 25 08:54:54 2010 UTC (2 years, 4 months ago) by andreas

working around the no-download chem comp provider.

---

Revision 8644 - Directory Listing
Modified Fri Dec 24 13:07:04 2010 UTC (2 years, 4 months ago) by andreas

cleanup

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Revision 8643 - Directory Listing
Modified Fri Dec 24 08:26:14 2010 UTC (2 years, 4 months ago) by andreas

user now explicitely has to request download of big  file...

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Revision 8642 - Directory Listing
Modified Fri Dec 24 08:20:06 2010 UTC (2 years, 4 months ago) by andreas

new junit test for checking of correct loading of chem comps

---

Revision 8641 - Directory Listing
Modified Fri Dec 24 08:19:40 2010 UTC (2 years, 4 months ago) by andreas

fixing a problem with some chem comp definitions

---

Revision 8638 - Directory Listing
Modified Tue Dec 21 23:45:56 2010 UTC (2 years, 4 months ago) by andreas

fixing index offset issue

---

Revision 8637 - Directory Listing
Modified Tue Dec 21 23:44:21 2010 UTC (2 years, 4 months ago) by andreas

adding checkPath functionality

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Revision 8636 - Directory Listing
Modified Tue Dec 21 23:43:14 2010 UTC (2 years, 4 months ago) by andreas

cleanup warning

---

Revision 8635 - Directory Listing
Modified Tue Dec 21 23:42:54 2010 UTC (2 years, 4 months ago) by andreas

new demo for how to use alternate chem comp providers

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Revision 8634 - Directory Listing
Modified Tue Dec 21 23:42:27 2010 UTC (2 years, 4 months ago) by andreas

more javadoc

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Revision 8633 - Directory Listing
Modified Tue Dec 21 23:41:59 2010 UTC (2 years, 4 months ago) by andreas

more javadoc

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Revision 8632 - Directory Listing
Modified Tue Dec 21 23:41:42 2010 UTC (2 years, 4 months ago) by andreas

more javadoc

---

Revision 8631 - Directory Listing
Modified Tue Dec 21 23:41:29 2010 UTC (2 years, 4 months ago) by andreas

new provider for caching all components in memory

---

Revision 8630 - Directory Listing
Modified Tue Dec 21 23:40:58 2010 UTC (2 years, 4 months ago) by andreas

now with support for download all of the chem comp definitions

---

Revision 8627 - Directory Listing
Modified Sun Dec 19 10:37:20 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

---

Revision 8625 - Directory Listing
Modified Sun Dec 19 10:37:07 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta4

---

Revision 8615 - Directory Listing
Modified Sun Dec 19 08:14:57 2010 UTC (2 years, 4 months ago) by andreas

changing internal ArrayList to TreeSet

---

Revision 8614 - Directory Listing
Modified Sun Dec 19 07:59:03 2010 UTC (2 years, 4 months ago) by andreas

more javadoc

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Revision 8613 - Directory Listing
Modified Sat Dec 18 13:41:08 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

---

Revision 8612 - Directory Listing
Modified Sat Dec 18 13:40:56 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

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Revision 8611 - Directory Listing
Modified Sat Dec 18 13:39:25 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

---

Revision 8610 - Directory Listing
Modified Sat Dec 18 13:38:13 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

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Revision 8609 - Directory Listing
Modified Sat Dec 18 13:37:26 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warnings

---

Revision 8608 - Directory Listing
Modified Sat Dec 18 13:35:51 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

---

Revision 8607 - Directory Listing
Modified Sat Dec 18 13:34:34 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

---

Revision 8599 - Directory Listing
Modified Sat Dec 18 13:04:07 2010 UTC (2 years, 4 months ago) by andreas

fixing javadoc warning

---

Revision 8598 - Directory Listing
Modified Sat Dec 18 10:08:23 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

---

Revision 8597 - Directory Listing
Modified Sat Dec 18 10:07:23 2010 UTC (2 years, 5 months ago) by andreas

more javadoc

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Revision 8596 - Directory Listing
Modified Sat Dec 18 10:03:46 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

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Revision 8595 - Directory Listing
Modified Sat Dec 18 10:02:43 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warning

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Revision 8594 - Directory Listing
Modified Sat Dec 18 10:01:22 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warnings

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Revision 8593 - Directory Listing
Modified Sat Dec 18 09:58:30 2010 UTC (2 years, 5 months ago) by andreas

fixing javadoc warnings

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Revision 8589 - Directory Listing
Modified Fri Dec 17 12:12:02 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 8587 - Directory Listing
Modified Fri Dec 17 12:11:49 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta3

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Revision 8586 - Directory Listing
Modified Fri Dec 17 11:09:10 2010 UTC (2 years, 5 months ago) by andreas

Providing different types of Chemical Component providers, that can either fetch ChemComps from the RCSB site or from a reduced set of local files, if people dont want to have external access.

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Revision 8585 - Directory Listing
Modified Fri Dec 17 11:07:37 2010 UTC (2 years, 5 months ago) by andreas

fixing a problem that resulted in prints that some synonyms for GOL/Glycerol could not be set.

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Revision 8582 - Directory Listing
Modified Wed Dec 1 18:41:45 2010 UTC (2 years, 5 months ago) by andreas

color coding flexible alignments according to structural equivalence

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Revision 8581 - Directory Listing
Modified Wed Dec 1 00:04:03 2010 UTC (2 years, 5 months ago) by andreas

now with color coding for flexible FATCAT results

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Revision 8579 - Directory Listing
Modified Mon Nov 29 00:45:32 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8578 - Directory Listing
Modified Mon Nov 29 00:42:56 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8575 - Directory Listing
Modified Sun Nov 28 21:41:32 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8574 - Directory Listing
Modified Sun Nov 28 21:40:56 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8573 - Directory Listing
Modified Sun Nov 28 21:40:25 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8572 - Directory Listing
Modified Sun Nov 28 21:39:26 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8571 - Directory Listing
Modified Sun Nov 28 21:38:35 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8570 - Directory Listing
Modified Sun Nov 28 21:37:08 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8569 - Directory Listing
Modified Sun Nov 28 21:25:55 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8568 - Directory Listing
Modified Sun Nov 28 20:28:36 2010 UTC (2 years, 5 months ago) by andreas

improving javadoc

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Revision 8500 - Directory Listing
Modified Wed Nov 24 01:51:29 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 8498 - Directory Listing
Modified Wed Nov 24 01:51:21 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta1

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Revision 8495 - Directory Listing
Modified Wed Nov 24 01:45:19 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] rollback the release of biojava-3.0-beta1

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Revision 8494 - Directory Listing
Modified Wed Nov 24 01:32:29 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

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Revision 8492 - Directory Listing
Modified Wed Nov 24 01:32:21 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta1

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Revision 8489 - Directory Listing
Modified Wed Nov 24 01:26:58 2010 UTC (2 years, 5 months ago) by andreas

setting correct project version

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Revision 8470 - Directory Listing
Modified Mon Nov 22 18:34:57 2010 UTC (2 years, 5 months ago) by andreas
Copied from: biojava-live/trunk/structure revision 8469

proper biojava3 namespace now

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Revision 8450 - Directory Listing
Modified Mon Nov 22 17:38:51 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

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Revision 8448 - Directory Listing
Modified Mon Nov 22 17:38:42 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha6

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Revision 8446 - Directory Listing
Modified Fri Nov 19 23:28:57 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

small formatting change

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Revision 8442 - Directory Listing
Modified Fri Nov 19 22:06:12 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

tagging current status

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Revision 8434 - Directory Listing
Modified Fri Nov 19 02:26:30 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

small fix

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Revision 8433 - Directory Listing
Modified Fri Nov 19 02:25:53 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

cleanup

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Revision 8432 - Directory Listing
Modified Fri Nov 19 02:25:41 2010 UTC (2 years, 5 months ago) by andreas
Original Path: biojava-live/trunk/structure

nicer web site display... now in color

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Revision 8425 - Directory Listing
Modified Wed Nov 17 07:09:27 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

adding a demo for how to use AtomCache

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Revision 8418 - Directory Listing
Modified Sat Nov 13 18:47:35 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

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Revision 8416 - Directory Listing
Modified Sat Nov 13 18:47:27 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha5

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Revision 8388 - Directory Listing
Modified Sat Oct 30 10:46:37 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

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Revision 8386 - Directory Listing
Modified Sat Oct 30 10:46:28 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha4

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Revision 8383 - Directory Listing
Modified Fri Oct 29 22:23:15 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

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Revision 8381 - Directory Listing
Modified Fri Oct 29 22:23:07 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha3

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Revision 8379 - Directory Listing
Modified Thu Oct 28 17:42:56 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

code cleanup, removing warnings

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Revision 8367 - Directory Listing
Modified Tue Oct 26 21:06:38 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

updating dependencies

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Revision 8353 - Directory Listing
Modified Fri Oct 22 17:35:31 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

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Revision 8351 - Directory Listing
Modified Fri Oct 22 17:35:22 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha2

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Revision 8348 - Directory Listing
Modified Thu Oct 21 22:53:49 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

some minor improvement for SITE parsing..

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Revision 8338 - Directory Listing
Modified Thu Oct 21 22:11:14 2010 UTC (2 years, 6 months ago) by andreas
Original Path: biojava-live/trunk/structure

now with correct artifact version nr

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Revision 8314 - Directory Listing
Modified Sat Oct 16 02:44:51 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

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Revision 8312 - Directory Listing
Modified Sat Oct 16 02:44:43 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha1

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Revision 8310 - Directory Listing
Modified Sat Oct 16 02:37:32 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] rollback the release of biojava-3.0-alpha1

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Revision 8308 - Directory Listing
Modified Sat Oct 16 02:07:11 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha1

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Revision 8307 - Directory Listing
Modified Sat Oct 16 01:44:19 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

---

Revision 8304 - Directory Listing
Modified Sat Oct 16 00:49:02 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] rollback the release of biojava-3.0-alpha1

---

Revision 8303 - Directory Listing
Modified Sat Oct 16 00:11:55 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare for next development iteration

---

Revision 8293 - Directory Listing
Modified Fri Oct 15 22:51:13 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

[maven-release-plugin] prepare release biojava-3.0-alpha1

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Revision 8280 - Directory Listing
Modified Wed Oct 13 06:15:53 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

updating new Atom nr. to match results after altLocs are being parsed.

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Revision 8279 - Directory Listing
Modified Wed Oct 13 06:05:36 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

making parsing less verbose

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Revision 8278 - Directory Listing
Modified Wed Oct 13 05:39:39 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

major API update. Renaming getParent methods and better handling of residue numbers, insCodes and altLocs.

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Revision 8276 - Directory Listing
Modified Wed Oct 6 22:49:50 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

adding method to reverse the pair

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Revision 8275 - Directory Listing
Modified Wed Oct 6 13:30:05 2010 UTC (2 years, 7 months ago) by jacobsen
Original Path: biojava-live/trunk/structure

Refactored Group interface and HetAtomImpl to use ResidueNumber as a replacement for the get/setPDBCode.

Site parsing and implementation is now compliant and reliant on this.

Changed Group.get/setParent() to Group.get/setChain() for clearer feedback about what sort of return type to expect.

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Revision 8274 - Directory Listing
Modified Wed Oct 6 13:27:23 2010 UTC (2 years, 7 months ago) by jacobsen
Original Path: biojava-live/trunk/structure

Refactored Group interface and HetAtomImpl to use ResidueNumber as a replacement for the get/setPDBCode.

Site parsing and implementation is now compliant and reliant on this.

Changed Group.get/setParent() to Group.get/setChain() for clearer feedback about what sort of return type to expect.

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Revision 8252 - Directory Listing
Modified Thu Sep 23 23:02:00 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

and disabling debug mode...

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Revision 8251 - Directory Listing
Modified Thu Sep 23 23:00:19 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

using local alignment rather than global alignment, to avoid end gap issues.

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Revision 8247 - Directory Listing
Modified Mon Sep 20 02:39:35 2010 UTC (2 years, 7 months ago) by andreas
Original Path: biojava-live/trunk/structure

disabling debug mode

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Revision 8244 - Directory Listing
Modified Fri Sep 17 21:13:19 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

new seqres2atom aligner, based on biojava3-alignment code

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Revision 8243 - Directory Listing
Modified Fri Sep 17 20:50:45 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

more inline docu

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Revision 8238 - Directory Listing
Modified Thu Sep 9 18:09:02 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadocs

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Revision 8237 - Directory Listing
Modified Thu Sep 9 18:07:02 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadocs

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Revision 8234 - Directory Listing
Modified Thu Sep 9 17:58:48 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

version upgrade

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Revision 8233 - Directory Listing
Modified Thu Sep 9 17:58:16 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

mini code cleanup

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Revision 8232 - Directory Listing
Modified Thu Sep 9 17:57:36 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

removing Override statements to make sure we can still compile with Java 1.5

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Revision 8231 - Directory Listing
Modified Thu Sep 9 17:57:06 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadocs and @Override statements

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Revision 8230 - Directory Listing
Modified Thu Sep 9 17:56:17 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadocs

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Revision 8229 - Directory Listing
Modified Thu Sep 9 17:55:46 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

new command line arguments to write to file system

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Revision 8226 - Directory Listing
Modified Thu Sep 9 17:49:25 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

adding link to JAMA

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Revision 8225 - Directory Listing
Modified Thu Sep 9 17:39:00 2010 UTC (2 years, 8 months ago) by andreas
Original Path: biojava-live/trunk/structure

small fix for a javadoc warning

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Revision 8223 - Directory Listing
Modified Fri Sep 3 10:41:52 2010 UTC (2 years, 8 months ago) by jacobsen
Original Path: biojava-live/trunk/structure

Updated SiteTest and PDBFileParserTest to include REMARK 800 parsing and functionality - new methods added to Site to get/set and print  its related REMARK 800 section.

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Revision 8222 - Directory Listing
Modified Fri Sep 3 08:46:45 2010 UTC (2 years, 8 months ago) by jacobsen
Original Path: biojava-live/trunk/structure

Updated SiteTest to have the correct tests! 

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Revision 8221 - Directory Listing
Modified Thu Sep 2 17:11:55 2010 UTC (2 years, 8 months ago) by jacobsen
Original Path: biojava-live/trunk/structure

Added new SITE parser, class and tests. Still work in progress, but works fine. REMARK 800 coming next. 

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Revision 8207 - Directory Listing
Modified Sat Aug 14 01:22:40 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

replacing core dependency with new biojava3-core and biojava3-alignment dependencies

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Revision 8206 - Directory Listing
Modified Sat Aug 14 01:21:49 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

replacing core dependency with new biojava3-core and biojava3-alignment dependencies

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Revision 8185 - Directory Listing
Modified Wed Aug 11 01:50:34 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

removing warning

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Revision 8184 - Directory Listing
Modified Wed Aug 11 01:49:24 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

better multi-threaded execution of structure alignments triggered via the User Interface

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Revision 8183 - Directory Listing
Modified Wed Aug 11 01:46:23 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

performance improvement when run in multi-threaded environments

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Revision 8182 - Directory Listing
Modified Mon Aug 9 23:34:01 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

reducing time spent on test

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Revision 8181 - Directory Listing
Modified Mon Aug 9 23:29:45 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

reducing time spent on test

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Revision 8180 - Directory Listing
Modified Mon Aug 9 23:03:33 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

reducing time spent on test

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Revision 8179 - Directory Listing
Modified Mon Aug 9 21:44:32 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

reducing time spent on test

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Revision 8178 - Directory Listing
Modified Mon Aug 9 19:34:47 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing hard coded /tmp directory

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Revision 8165 - Directory Listing
Modified Fri Jul 30 22:54:43 2010 UTC (2 years, 9 months ago) by jgao
Original Path: biojava-live/trunk/structure

structure: add equals and hashCode to PDBResidueNumber; convert PDBResidueNumber back to Group in StructureTools

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Revision 8162 - Directory Listing
Modified Fri Jul 30 00:34:56 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

instead of throwing exception, print a warning now.

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Revision 8161 - Directory Listing
Modified Thu Jul 29 21:29:43 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

only considers certain types now for the alignment

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Revision 8155 - Directory Listing
Modified Wed Jul 28 19:08:54 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

now serializable

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Revision 8154 - Directory Listing
Modified Wed Jul 28 18:32:18 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

Metal hetero groups don't need to be aligned with SEQRES residues...

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Revision 8149 - Directory Listing
Modified Tue Jul 27 21:23:21 2010 UTC (2 years, 9 months ago) by pwrose
Original Path: biojava-live/trunk/structure

Tests for Element class.

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Revision 8148 - Directory Listing
Modified Tue Jul 27 21:22:35 2010 UTC (2 years, 9 months ago) by pwrose
Original Path: biojava-live/trunk/structure

Added ElementType to each element, and several associated methods isMetal, isMetalloid, isNonMetal, getElementType. Also added missing element Tl and updated the Hg values.

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Revision 8147 - Directory Listing
Modified Tue Jul 27 21:20:38 2010 UTC (2 years, 9 months ago) by pwrose
Original Path: biojava-live/trunk/structure

New enumeration which is used by the Element class to classify elements.

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Revision 8142 - Directory Listing
Modified Sat Jul 24 08:27:49 2010 UTC (2 years, 9 months ago) by Mark Chapman
Original Path: biojava-live/trunk/structure

disabled test to allow a successful build

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Revision 8133 - Directory Listing
Modified Thu Jul 22 03:08:15 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing a problem with Double as argument

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Revision 8132 - Directory Listing
Modified Thu Jul 22 03:02:24 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadoc warning

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Revision 8131 - Directory Listing
Modified Thu Jul 22 02:59:49 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadoc warning

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Revision 8130 - Directory Listing
Modified Thu Jul 22 02:58:46 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

fixing javadoc warning

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Revision 8129 - Directory Listing
Modified Thu Jul 22 02:57:57 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

removing slow pair to speed up

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Revision 8128 - Directory Listing
Modified Thu Jul 22 02:57:30 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

less verbose

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Revision 8127 - Directory Listing
Modified Thu Jul 22 02:57:00 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

less verbose

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Revision 8126 - Directory Listing
Modified Thu Jul 22 02:52:40 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

more log if something goes wrong...

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Revision 8125 - Directory Listing
Modified Thu Jul 22 02:50:22 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

setting default value for maxOptRMSD

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Revision 8124 - Directory Listing
Modified Thu Jul 22 02:48:49 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

prevent maxOptRMSD from getting set to null

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Revision 8123 - Directory Listing
Modified Thu Jul 22 02:22:20 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

diabling test for now

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Revision 8122 - Directory Listing
Modified Thu Jul 22 02:12:37 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

new public parameters

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Revision 8121 - Directory Listing
Modified Thu Jul 22 02:12:28 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

new public parameters

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Revision 8120 - Directory Listing
Modified Thu Jul 22 02:11:15 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

version upgrade due to new public parameters

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Revision 8116 - Directory Listing
Modified Wed Jul 21 04:50:47 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

javadoc update

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Revision 8115 - Directory Listing
Modified Wed Jul 21 04:49:51 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

exposing maxOptRMSD parameter

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Revision 8114 - Directory Listing
Modified Wed Jul 21 04:49:41 2010 UTC (2 years, 9 months ago) by andreas
Original Path: biojava-live/trunk/structure

exposing maxOptRMSD parameter