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, getEdgeList, 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.