 ../
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PdbaseInfo.java
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135
(17 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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AA.java
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135
(17 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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PdbaseInconsistencyError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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MsdsdInfo.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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MsdsdAcCodeNotFoundError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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GraphIdNotFoundError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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PdbaseAcCodeNotFoundError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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MsdsdInconsistentResidueNumbersError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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Pdb.java
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175
(17 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
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ContactList.java
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178
(17 years ago)
by duarte:
Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact
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EdgeNbh.java
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179
(17 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
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Graph.java
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179
(17 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
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NodeNbh.java
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182
(17 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
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NbhProbDistribution.java
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183
(17 years ago)
by duarte:
Fixed bug: calculateEntropy was wrong when a pi was 0
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GenericContact.java
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185
(17 years ago)
by duarte:
Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString
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Contact.java
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185
(17 years ago)
by duarte:
Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString
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