nct.graph
Interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>

All Superinterfaces:
java.lang.Cloneable, java.lang.Comparable<Graph<NodeType,WeightType>>, DistanceGraph<NodeType,WeightType>, Graph<NodeType,WeightType>
All Known Implementing Classes:
BlastGraph, FastaGraph, InteractionGraph

public interface SequenceGraph<NodeType extends java.lang.Comparable<? super NodeType>,WeightType extends java.lang.Comparable<? super WeightType>>
extends DistanceGraph<NodeType,WeightType>

An interface that describes accessing a sequence database associated with the graph.


Field Summary
static int BLAST
          A Blast database.
static int DUMMY
          A dummy (non-existant) database type.
static int FASTA
          A Fasta database, usually referring to a multiple fasta formatted file.
 
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 used.
 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 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

DUMMY

static final int DUMMY
A dummy (non-existant) database type.

See Also:
Constant Field Values

FASTA

static final int FASTA
A Fasta database, usually referring to a multiple fasta formatted file.

See Also:
Constant Field Values

BLAST

static final int BLAST
A Blast database.

See Also:
Constant Field Values
Method Detail

getDBName

java.lang.String getDBName()
Returns the name of the database used.

Returns:
The name of the database used.

getDBLocation

java.lang.String getDBLocation()
Returns the location of the database used.

Returns:
The location of the database used.

getDBType

int getDBType()
Returns an integer identifying the type of database used.

Returns:
An integer identifying the type of database used.

setDBName

void setDBName(java.lang.String name)
Sets the name of the database.

Parameters:
name - The new name of the sequence database.

setDBLocation

void setDBLocation(java.lang.String location)
Sets the location of the database.

Parameters:
location - The new location of the sequence database.

setDBType

void setDBType(int type)
Sets the type of the database.

Parameters:
type - The new type of the sequence database.