| Improved ScopDescription. |
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over 15 years ago
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| making sure that TMscore gets communicated when filterDuplicateAFPs |
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over 15 years ago
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| Added eclipse hidden files to svn:ignore for subprojects |
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over 15 years ago
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| Changed the parameter order of the Structure.getChain(int,int) method to match that actually used by StructureImpl. |
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over 15 years ago
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| Put BufferedOutputStream at FastaWriterHelper and made FastaWriter generic. |
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over 15 years ago
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| Added handling of BufferedOutputStream in FastaWriter. If the outputstream passed in is not Buffered then create one use it and then flush. |
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over 15 years ago
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| 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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over 15 years ago
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| Added handling of BufferedOutputStream in FastaWriter. If the outputstream passed in is not Buffered then create one use it and the close it. |
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over 15 years ago
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| add some generics to biojavax |
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over 15 years ago
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| Added generic for biojavax Note |
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over 15 years ago
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| More fix with circularity |
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over 15 years ago
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| use the new method that checks the correct order of the pair in the afpChain |
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over 15 years ago
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| new methods that checks for the correct order of the pair in the afpChain |
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over 15 years ago
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| biojava3-protmod: fix bugs when the atom groups are not aligned with the sequence groups: add those atom groups that have amino atoms back |
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over 15 years ago
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| making sure we can lookup in allElements in O(1); |
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over 15 years ago
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| disabling Hill order for now, since it seems wrong. |
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over 15 years ago
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| small speedup in Element class |
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over 15 years ago
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| more transparent warning message |
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over 15 years ago
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| ignoring if a group can't be found... |
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over 15 years ago
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| adding check to make sure that map of sites is not null |
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over 15 years ago
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| catching linking of SITE records to groups |
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over 15 years ago
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| if a line causes a crash, print that line now. |
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over 15 years ago
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| this is now a Comparable class |
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over 15 years ago
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| small speedup |
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over 15 years ago
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| Equality now added to backing stores & compounds. SequenceMixin now has a method for assessing sequence equality |
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over 15 years ago
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| Bugzilla 3180 applied. Frame parameter was ignored by code |
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over 15 years ago
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| Bug fix for dealing with X amino acids during translation. Submitted by Brad Chapman. Patch available at https://gist.github.com/864088. Many thanks. |
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over 15 years ago
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| new utility method that allows to access all atoms in all models |
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over 15 years ago
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| fixing some minor issues and docu improvements for biological units. |
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over 15 years ago
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| Fixed a few warnings (deprecation, improper use of generics). Improved reporting when guessing scop domains. |
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over 15 years ago
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