| C is the natural Generic type for compounds in BioJava not T |
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over 16 years ago
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| Relaxing requirements on Generic types which prevented writing something like Sequence<Compound> to a FASTA file. This is unacceptable and brought about because of an increase in strictness I thought would help the API. It does not. |
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over 16 years ago
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| RMSD metric now respects the AFPChain's RMSD, if set. |
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over 16 years ago
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| Added the ability to run the benchmark using different scoring strategies. |
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over 16 years ago
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| Adding the new scoring strategy to the alignment GUI |
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over 16 years ago
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| Added a new scoring strategy to CE, CA_AND_SIDE_CHAIN_ANGLE_SCORING, as well as fixing SIDE_CHAIN_ANGLE_SCORING. |
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over 16 years ago
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| now with antialiasing |
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over 16 years ago
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| nicer colors |
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over 16 years ago
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| nicer colors |
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over 16 years ago
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| now with timeout for server connection |
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over 16 years ago
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| try to load alignments from central server |
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over 16 years ago
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| adding view as FATCAT menu |
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over 16 years ago
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| now correct color display of alignments with multiple blocks |
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over 16 years ago
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| now correct color display of alignments with multiple blocks |
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over 16 years ago
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| now with pretty print of alignments |
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over 16 years ago
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| now correct color display of alignments with multiple blocks |
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over 16 years ago
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| now also shift ligands of 2nd structure, if alignment has more than 1 block. Rotation to be applied is the one of block 0... |
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over 16 years ago
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| Added BioJava3 license header. |
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over 16 years ago
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| making sure that the element parsing does not fail if fullname.length < 2 |
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over 16 years ago
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| Added test for checking element assignment. |
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over 16 years ago
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| Added parsing of element. |
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over 16 years ago
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| Added element to toString() method. |
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over 16 years ago
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| Added an assert statement for the new getElement method. |
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over 16 years ago
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| Added setElement and getElement methods. |
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over 16 years ago
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| Added setElement and getElement methods. |
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over 16 years ago
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| Added Element enumeration. |
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over 16 years ago
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| Added a test class for CeMain. Currently it only tests the filterDuplicateAFPs method, which is responsible for cleaning up alignments with circular permutations. |
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over 16 years ago
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| Improved the way CE determines where a circular permutation has occured, resolving situations where the initial alignment assigns a single residue to two aligned pairs. |
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over 16 years ago
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| Improved handling of AFPChains with null components. |
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over 16 years ago
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| removing AStex dependency |
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over 16 years ago
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