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r183
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PdbaseInfo.java 135 (12 years ago) by duarte: NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd) Reading chain also in Pdb in read_pdb_data_from_file Not reading chain anymore in read_atomData of PdbaseInfo Added oneletter2threeletter and getoneletter2threeletter to AA class Changes in Graph: - added db static vars and getUserName method - new member variables graphid and sm_id - new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db - new method getgraphid New Exception class GraphIdNotFoundError
PdbaseInconsistencyError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
PdbaseAcCodeNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
Pdb.java 175 (12 years ago) by duarte: FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList NEW FUNCTIONALITY in Graph: -New member variable modified -New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy -Improved slightly the implementation of getEdgeNbh FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList New class ContactList NEW FUNCTIONALITY in Graph: -New member variable modified -New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy -Improved slightly the implementation of getEdgeNbh New method getRange in Contact
NodeNbh.java 182 (12 years ago) by duarte: FIXED BUG: the switch statement was missing the breaks This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow
NbhProbDistribution.java 183 (12 years ago) by duarte: Fixed bug: calculateEntropy was wrong when a pi was 0
MsdsdInfo.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
MsdsdInconsistentResidueNumbersError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
MsdsdAcCodeNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
Graph.java 179 (12 years ago) by duarte: FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh New method getResidueType
EdgeNbh.java 179 (12 years ago) by duarte: FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh New method getResidueType
ContactList.java 178 (12 years ago) by duarte: Fixed bug in getMaxRange method, was not assigning to the max variable Added toString method to Contact
Contact.java 178 (12 years ago) by duarte: Fixed bug in getMaxRange method, was not assigning to the max variable Added toString method to Contact
AA.java 135 (12 years ago) by duarte: NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd) Reading chain also in Pdb in read_pdb_data_from_file Not reading chain anymore in read_atomData of PdbaseInfo Added oneletter2threeletter and getoneletter2threeletter to AA class Changes in Graph: - added db static vars and getUserName method - new member variables graphid and sm_id - new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db - new method getgraphid New Exception class GraphIdNotFoundError
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