nct.graph
Class FastaGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

java.lang.Object
  nct.graph.BasicGraph<NodeType,WeightType>
      nct.graph.BasicDistanceGraph<NodeType,WeightType>
          nct.graph.FastaGraph<NodeType,WeightType>

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable<Graph<NodeType,WeightType>>, DistanceGraph<NodeType,WeightType>, Graph<NodeType,WeightType>, SequenceGraph<NodeType,WeightType>

public class FastaGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
extends BasicDistanceGraph<NodeType,WeightType>
implements SequenceGraph<NodeType,WeightType>

An extension of BasicDistanceGraph that implements the SequenceGraph interface and contains a (pointer to a) fasta database.

Field Summary

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.BasicDistanceGraph

distMap

Fields inherited from class nct.graph.BasicGraph

assumeGraphFinished, descMap, id, numEdges, score, weightMap

Fields inherited from interface nct.graph.SequenceGraph

BLAST, DUMMY, FASTA

Constructor Summary

FastaGraph(org.biojava.bio.seq.db.SequenceDB sdb, java.lang.String destFileName, java.lang.String destFileLocation)

FastaGraph(java.lang.String fileName, java.lang.String fileLocation)

Method Summary

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.BasicDistanceGraph

getDistance

Methods inherited from class nct.graph.BasicGraph

addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdgeList, getEdges, getEdgeWeight, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface nct.graph.DistanceGraph

getDistance

Methods inherited from interface nct.graph.Graph

addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdgeList, getEdges, getEdgeWeight, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString

Field Detail

fileName

protected java.lang.String fileName

The name of the multiple fasta file

fileLocation

protected java.lang.String fileLocation

The location of the multiple fasta file

Constructor Detail

FastaGraph

public FastaGraph(java.lang.String fileName,
                  java.lang.String fileLocation)

Parameters:

fileName - The name of the mulitple Fasta file.

fileLocation - The location of the mulitple Fasta file.

FastaGraph

public FastaGraph(org.biojava.bio.seq.db.SequenceDB sdb,
                  java.lang.String destFileName,
                  java.lang.String destFileLocation)

Parameters:

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

getDBName

public java.lang.String getDBName()

Returns the name of the database used.

Specified by:

getDBName in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

Returns:

The name of the database used.

getDBLocation

public java.lang.String getDBLocation()

Returns the location of the database used.

Specified by:

getDBLocation in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

Returns:

The location of the database used.

getDBType

public int getDBType()

Returns an integer identifying the type of database as FASTA.

Specified by:

getDBType in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

Returns:

An integer identifying the type of databas as FASTA.

setDBName

public void setDBName(java.lang.String name)

Sets the name of the database.

Specified by:

setDBName in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

Parameters:

name - The new name of the sequence database.

setDBLocation

public void setDBLocation(java.lang.String location)

Sets the location of the database.

Specified by:

setDBLocation in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

Parameters:

location - The new location of the sequence database.

setDBType

public void setDBType(int type)

Sets the type of the database.

Specified by:

setDBType in interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

Parameters:

type - The new type of the sequence database.