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java.lang.Objectnct.graph.basic.BasicGraph<NodeType,WeightType>
nct.graph.basic.BasicDistanceGraph<NodeType,WeightType>
nct.graph.basic.FastaGraph<NodeType,WeightType>
public class FastaGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
An extension of BasicDistanceGraph that implements the SequenceGraph interface and contains a (pointer to a) fasta database.
Field Summary | |
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protected java.lang.String |
fileLocation
The location of the multiple fasta file |
protected java.lang.String |
fileName
The name of the multiple fasta file |
Fields inherited from class nct.graph.basic.BasicDistanceGraph |
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distMap |
Fields inherited from class nct.graph.basic.BasicGraph |
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assumeGraphFinished, descMap, id, numEdges, score, weightMap |
Fields inherited from interface nct.graph.SequenceGraph |
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BLAST, DUMMY, FASTA |
Constructor Summary | |
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FastaGraph(org.biojava.bio.seq.db.SequenceDB sdb,
java.lang.String destFileName,
java.lang.String destFileLocation)
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FastaGraph(java.lang.String fileName,
java.lang.String fileLocation)
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Method Summary | |
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java.lang.String |
getDBLocation()
Returns the location of the database used. |
java.lang.String |
getDBName()
Returns the name of the database used. |
int |
getDBType()
Returns an integer identifying the type of database as FASTA. |
void |
setDBLocation(java.lang.String location)
Sets the location of the database. |
void |
setDBName(java.lang.String name)
Sets the name of the database. |
void |
setDBType(int type)
Sets the type of the database. |
Methods inherited from class nct.graph.basic.BasicDistanceGraph |
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getDistance |
Methods inherited from class nct.graph.basic.BasicGraph |
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addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdges, getEdgeWeight, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface nct.graph.DistanceGraph |
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getDistance |
Methods inherited from interface nct.graph.Graph |
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addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdges, getEdgeWeight, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString |
Field Detail |
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protected java.lang.String fileName
protected java.lang.String fileLocation
Constructor Detail |
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public FastaGraph(java.lang.String fileName, java.lang.String fileLocation)
fileName
- The name of the mulitple Fasta file.fileLocation
- The location of the mulitple Fasta file.public FastaGraph(org.biojava.bio.seq.db.SequenceDB sdb, java.lang.String destFileName, java.lang.String destFileLocation)
sdb
- A BioJava SequenceDB object that contains the sequences in question.destFileName
- The name of the mulitple Fasta file where the sequences
should be written.destFileLocation
- The location of the mulitple Fasta file.Method Detail |
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public java.lang.String getDBName()
getDBName
in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
public java.lang.String getDBLocation()
getDBLocation
in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
public int getDBType()
getDBType
in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
public void setDBName(java.lang.String name)
setDBName
in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
name
- The new name of the sequence database.public void setDBLocation(java.lang.String location)
setDBLocation
in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
location
- The new location of the sequence database.public void setDBType(int type)
setDBType
in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
type
- The new type of the sequence database.
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