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java.lang.Objectnct.graph.BasicGraph<NodeType,WeightType>
nct.graph.BasicDistanceGraph<java.lang.String,java.lang.Double>
nct.networkblast.InteractionGraph
public class InteractionGraph
An implementation of a SequenceGraph that is specified by a SIF file.
Field Summary |
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Fields inherited from class nct.graph.BasicDistanceGraph |
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distMap |
Fields inherited from class nct.graph.BasicGraph |
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assumeGraphFinished, descMap, id, numEdges, score, weightMap |
Fields inherited from interface nct.graph.SequenceGraph |
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BLAST, DUMMY, FASTA |
Constructor Summary | |
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InteractionGraph()
Constructor. |
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InteractionGraph(java.lang.String fileName)
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Method Summary | |
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java.lang.String |
getDBLocation()
Dummy method needed to implement the SequenceGraph interface. |
java.lang.String |
getDBName()
Dummy method needed to implement the SequenceGraph interface. |
int |
getDBType()
Dummy method needed to implement the SequenceGraph interface. |
java.lang.Double |
getEdgeWeight(java.lang.String nodeA,
java.lang.String nodeB)
Instead of returning null when an edge doesn't exist, it returns -1. |
void |
setDBLocation(java.lang.String loc)
Dummy method needed to implement the SequenceGraph interface. |
void |
setDBName(java.lang.String name)
Dummy method needed to implement the SequenceGraph interface. |
void |
setDBType(int type)
Dummy method needed to implement the SequenceGraph interface. |
Methods inherited from class nct.graph.BasicDistanceGraph |
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getDistance |
Methods inherited from class nct.graph.BasicGraph |
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addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdgeList, getEdges, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface nct.graph.DistanceGraph |
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getDistance |
Methods inherited from interface nct.graph.Graph |
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addEdge, addEdge, addNode, clone, compareTo, degreeOfNode, getEdge, getEdgeDescription, getEdgeList, getEdges, getId, getNeighbors, getNodes, getScore, isEdge, isNode, numberOfEdges, numberOfNodes, removeEdge, removeNode, setEdgeDescription, setEdgeWeight, setScore, toString |
Constructor Detail |
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public InteractionGraph()
public InteractionGraph(java.lang.String fileName) throws java.io.FileNotFoundException, java.io.IOException
fileName
- The SIF input file containing the graph specification.
java.io.FileNotFoundException
java.io.IOException
Method Detail |
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public java.lang.Double getEdgeWeight(java.lang.String nodeA, java.lang.String nodeB)
getEdgeWeight
in interface Graph<java.lang.String,java.lang.Double>
getEdgeWeight
in class BasicGraph<java.lang.String,java.lang.Double>
nodeA
- The source node of the edge.nodeB
- The target node of the edge.
public java.lang.String getDBName()
getDBName
in interface SequenceGraph<java.lang.String,java.lang.Double>
public java.lang.String getDBLocation()
getDBLocation
in interface SequenceGraph<java.lang.String,java.lang.Double>
public int getDBType()
getDBType
in interface SequenceGraph<java.lang.String,java.lang.Double>
public void setDBType(int type)
setDBType
in interface SequenceGraph<java.lang.String,java.lang.Double>
type
- The new type of the sequence database.public void setDBLocation(java.lang.String loc)
setDBLocation
in interface SequenceGraph<java.lang.String,java.lang.Double>
loc
- The new location of the sequence database.public void setDBName(java.lang.String name)
setDBName
in interface SequenceGraph<java.lang.String,java.lang.Double>
name
- The new name of the sequence database.
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