nct.graph
Class BlastGraph<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.BlastGraph<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 BlastGraph<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 SequenceGraph and contains a pointer to a Blast database.

Field Summary

protected java.lang.String	dbLocation This string is the location of the database files.
protected java.lang.String	dbName This string is the name of the database files.

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

BlastGraph(java.lang.String dbName, java.lang.String dbLocation)

Method Summary

java.lang.String	getDBLocation() Returns the location of the Blast database used.
java.lang.String	getDBName() Returns the name of the Blast database used.
int	getDBType() Returns an integer identifying the type of database as Blast.
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

dbName

protected java.lang.String dbName

This string is the name of the database files. In the Blast world, a single name identifies a "database" which consists of three files with the same prefix (the name), but with different suffixes.

dbLocation

protected java.lang.String dbLocation

This string is the location of the database files.

Constructor Detail

BlastGraph

public BlastGraph(java.lang.String dbName,
                  java.lang.String dbLocation)

Parameters:

dbName - The name of the database.

dbLocation - The location of the database.

Method Detail

getDBName

public java.lang.String getDBName()

Returns the name of the Blast database used. In the Blast world, this name identifies a "database" which consists of three files with the same prefix (the name), but with different suffixes.

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 Blast 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 Blast.

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 database as Blast.

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.