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Commits on Mar 16, 2012

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

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Commits on Mar 7, 2012

• Improved documentation

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• Added CECP test for short CECP alignments

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• Updating PDBFIleParser test to new Element symbol in toPDB method

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• converting ELement R to X

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

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• adding Element name toPDB method

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• parser now ignores empty lines

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Commits on Feb 28, 2012

• adding more details for SIFTs

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• fixing some details about sifts parsing

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Commits on Feb 27, 2012

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

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Commits on Feb 24, 2012

• better error catching for downloads

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Commits on Feb 23, 2012

• now uses the new FileDownload utility class

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• new utility class for downloading content from URLs to Files

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• less verbose

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Commits on Feb 10, 2012

• making sure the max thresholds are set before we start parsing

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• making sure the MAX parameters are set correctly

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Commits on Feb 8, 2012

• tiny cleanup

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• added a small note to javadoc

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• correct null check if file does not exist locally

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

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

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Commits on Feb 7, 2012

• much faster way of downloading biol. unit files

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Commits on Feb 5, 2012

• small code modification & comment

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• removing unnecessary .append("") statements

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Commits on Feb 3, 2012

• set structure names for user provided structures

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• just some cleanup

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• increasing version number

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• This change should be slightly more memory efficient

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• smarter caching of domain ranges

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

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• don't print ranges

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• doing things step by step for readability

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• track version of algorithm

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• track version of algorithm

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