 ../
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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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GraphIdNotFoundError.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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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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EdgeNbh.java
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196
(17 years ago)
by duarte:
Added toString and getMotifFullGaps missing in EdgeNbh
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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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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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PdbChainCodeNotFoundError.java
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215
(17 years ago)
by stehr:
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
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PdbCodeNotFoundError.java
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215
(17 years ago)
by stehr:
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
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Interval.java
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222
(17 years ago)
by duarte:
New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval
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AA.java
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229
(17 years ago)
by duarte:
Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases
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NodeSet.java
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230
(17 years ago)
by stehr:
added class NodeSet
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NodeNbh.java
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233
(17 years ago)
by duarte:
Added method getCopy
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DbGraph.java
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234
(17 years ago)
by duarte:
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
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FileGraph.java
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234
(17 years ago)
by duarte:
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
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EdgeSet.java
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234
(17 years ago)
by duarte:
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
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ConformationsNotSameSizeError.java
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237
(17 years ago)
by duarte:
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
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Edge.java
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238
(17 years ago)
by duarte:
Optimised slightly the compareTo method in Edge
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NbhProbDistribution.java
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242
(17 years ago)
by duarte:
Got rid of doneRes ArrayList in getRanks, was redundant
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Alignment.java
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248
(17 years ago)
by duarte:
Added method hasTag
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MsdsdPdb.java
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250
(17 years ago)
by stehr:
added application to count grid density, suppressed warning for secondary structure reassignment
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Box.java
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250
(17 years ago)
by stehr:
added application to count grid density, suppressed warning for secondary structure reassignment
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PdbasePdb.java
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250
(17 years ago)
by stehr:
added application to count grid density, suppressed warning for secondary structure reassignment
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Graph.java
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252
(17 years ago)
by duarte:
Made constructor public
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Pdb.java
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257
(17 years ago)
by stehr:
fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)
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PdbfilePdb.java
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258
(17 years ago)
by duarte:
Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size
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