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

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