 ../
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AA.java
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200
(17 years ago)
by duarte:
New isValidCT methods in AA
New method get_resser_from_atomser in Pdb
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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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DbGraph.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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EdgeNbh.java
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196
(17 years ago)
by duarte:
Added toString and getMotifFullGaps missing in EdgeNbh
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FileGraph.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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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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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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GraphFileFormatError.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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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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MsdsdPdb.java
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207
(17 years ago)
by duarte:
Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs
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NbhProbDistribution.java
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199
(17 years ago)
by duarte:
Implemented getRanks()
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NodeNbh.java
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196
(17 years ago)
by duarte:
Added toString and getMotifFullGaps missing in EdgeNbh
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Pdb.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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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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PdbasePdb.java
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207
(17 years ago)
by duarte:
Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs
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PdbfileFormatError.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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PdbfilePdb.java
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208
(17 years ago)
by duarte:
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
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