 ../
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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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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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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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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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Graph.java
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189
(17 years ago)
by duarte:
Added basic compare method to the Graph class and test class compareCMs
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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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MsdsdAcCodeNotFoundError.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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MsdsdInfo.java
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190
(17 years ago)
by duarte:
NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object
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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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NodeNbh.java
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186
(17 years ago)
by duarte:
FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning
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Pdb.java
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190
(17 years ago)
by duarte:
NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object
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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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PdbaseInconsistencyError.java
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172
(17 years ago)
by duarte:
Got rid of some unnecessary warnings
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PdbaseInfo.java
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190
(17 years ago)
by duarte:
NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object
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