| Removing Java 1.7-specific exception constructors |
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almost 12 years ago
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| Revert "Start of implementation to semiglobal alignment. (Any complaints/suggestions so far?)" |
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almost 12 years ago
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| Merge branch 'master' of github.com:biojava/biojava |
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almost 12 years ago
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| updating my code signing key |
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almost 12 years ago
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| Merge branch 'master' of github.com:biojava/biojava |
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almost 12 years ago
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| Start of implementation to semiglobal alignment. (Any complaints/suggestions so far?) |
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almost 12 years ago
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| Deleted the unused UriIdentifier. |
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almost 12 years ago
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| Just allow main() to throw Exception; there's no reason they need to be caught. |
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almost 12 years ago
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| Extracted length-related code from ResidueRange to its new subclass ResidueRangeAndLength. |
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almost 12 years ago
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| All minor changes: simplified code, removed commented-out code, and removed some deprecated methods. Some improved logging and exception handling. Changed lots of StringBuffers and StringWriters to StringBuilders, and for loops to foreach loops. Inlined a lot of local variable declarations. Also fixed severe spacing, indentation, and Javadoc issues. |
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almost 12 years ago
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| Small bug fix: need to force lower case in getLocalFile |
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almost 12 years ago
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| Fixed issue with pdb 1ao2, related to commit e9562781f23da0ebf3547146a307d7edd5741090 |
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almost 12 years ago
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| Better fix for chains having non-polymers only, relates to commit 9e7325909a2ad947eca48e37742f048c81be123e Now all chains that have purely non-polymer molecules will be discarded, be it water only chains or some other type of non-poly only. |
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almost 12 years ago
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| Fixing log |
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almost 12 years ago
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| Fixing issue with crystal building for entries with non-standard SG |
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almost 12 years ago
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| Fixed bug in mmCIF parser: null pointer for 3zyb with seqres align |
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almost 12 years ago
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| Now parsing biounits that have no oligomeric count (relates to #230) Entries like 3j26 are not consistent and have no oligomeric count for bioassemblies with numeric ids |
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almost 12 years ago
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| Fixing parsing issue: removing chains that are water-only, e.g. 3o6j. They don't comply with standard PDB practices and cause problems |
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almost 12 years ago
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| Fixed bug: escaping chains with null compounds in contact overlap calc |
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almost 12 years ago
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| Merge branch 'master' of github.com:biojava/biojava |
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almost 12 years ago
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| Adding some missing fields in EntitySrcGen, better warnings for empty data fields |
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almost 12 years ago
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| Fixed bug: was not sorting chainIds correctly when mixed cases |
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almost 12 years ago
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| Fixed bug: can't use nuc4.2 matrix when both sequences contain ambiguous nucleotides Fixed also some warnings and added some docs |
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almost 12 years ago
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| Issue #111 for SCOP, and a little of #155. Also simplified some code, made clone() call super.clone(), and switched from StringWriter and StringBuffer to the faster (asynchronous) StringBuilder. |
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almost 12 years ago
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| Fixed a NullPointerException in AbstractLocation. Also simplified Equals class. |
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almost 12 years ago
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| Merge remote-tracking branch 'upstream/master' |
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almost 12 years ago
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| Fixed bug in global alignment: opening gap penalty should not be applied to start of alignment |
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almost 12 years ago
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| Merge pull request #239 from sbliven/master |
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almost 12 years ago
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| Fix #231: Remove StructureProvider/StructureIOFile redundancy |
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almost 12 years ago
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| Making sure that loading is always flagged |
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almost 12 years ago
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