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

java.lang.Object
  extended by nct.graph.basic.BasicGraph<NodeType,WeightType>
      extended by nct.graph.basic.BasicDistanceGraph<NodeType,WeightType>
          extended by nct.graph.basic.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.basic.BasicDistanceGraph
distMap
 
Fields inherited from class nct.graph.basic.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.basic.BasicDistanceGraph
getDistance
 
Methods inherited from class nct.graph.basic.BasicGraph
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
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, 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.