| Fixing completely the int overflow bug in #202. Alignment was still not working properly for very large sequences: tested with sequence of PDB 2y9r (102 residues) against UniProt Q8WZ42 (34350 residues), a null pointer exception was happening The key in this patch is the modification in AbstractMatrixAligner: score has to be initialized to Integer.MIN_VALUE and not to Short.MIN_VALUE |
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almost 12 years ago
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| Fixed nasty bug: some chem compounds map to more than 1 standard amino |
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almost 12 years ago
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| Better logging |
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almost 12 years ago
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| Improving logging for compounds without chains |
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almost 12 years ago
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| Fixed bug: no clusters need be calculated if no interfaces in list |
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almost 12 years ago
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| Merge branch 'master' of https://github.com/biojava/biojava |
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almost 12 years ago
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| only create bonds if configured in fileparsingparameters. |
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almost 12 years ago
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| catching an endless loop if runtime exception is thrown. |
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almost 12 years ago
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| Merge pull request #235 from josemduarte/master |
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almost 12 years ago
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| Adding new FetchBehavior: FETCH_IF_OUTDATED, see #228 |
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almost 12 years ago
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| Adding test for raw phenix-produced mmCIF file |
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almost 12 years ago
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| Minor improvement in parser |
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almost 12 years ago
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| Solving issue #230, now bioassembly ids are strictly numerical |
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almost 12 years ago
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| Merge pull request #233 from josemduarte/master |
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almost 12 years ago
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| Defaulting to http for PDB downloads(structure and chem comp files) Now the PDB.FILE.SERVER system property needs to have the protocol prefixing it, if not there it's added and a warning logged Removed the deprecated (in Biojava 3) package org.biojava.bio.structure.server |
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almost 12 years ago
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| Add test to verify #67 |
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almost 12 years ago
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| Merge remote-tracking branch 'origin/master' |
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almost 12 years ago
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| Merge pull request #229 from josemduarte/master |
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almost 12 years ago
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| Merge pull request #32 from biojava/master |
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almost 12 years ago
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| Improvements in file downloading, trying to address #227 |
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almost 12 years ago
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| Improvements in file downloading, trying to address #227 |
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almost 12 years ago
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| Bug fix for TestAtomCache: was failing if old files were around Removed some deprecations and warnings |
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almost 12 years ago
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| Merge remote-tracking branch 'sbliven/master' |
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almost 12 years ago
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| Fix bug in fetching of structures |
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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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| Merge pull request #228 from sbliven/master |
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almost 12 years ago
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| Merge remote-tracking branch 'sbliven/master' |
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almost 12 years ago
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| Introduced BioAssemblyInfo to encapsulate transformations and mmSize now macromolecular size of assembly is also parsed |
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almost 12 years ago
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| Removing more deprecated uses |
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almost 12 years ago
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| Fixing FatCat CLI parameters |
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almost 12 years ago
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