public class NeighborJoinAlgorithm extends ClusteringAlgorithm
| Constructor and Description |
|---|
NeighborJoinAlgorithm() |
NeighborJoinAlgorithm(double[][] distances,
String[] names) |
NeighborJoinAlgorithm(double[][] distances,
TupleND<IFileFragment> fragments,
PairwiseFeatureSequenceSimilarity ld) |
| Modifier and Type | Method and Description |
|---|---|
void |
calcR(int numclust) |
double[] |
dmat(int i,
int j,
int k) |
void |
findBestD(int numclust) |
void |
init(double[][] distances,
String[] names,
TupleND<IFileFragment> fragments) |
void |
joinIJtoK(int i,
int j,
int k,
double[] dist) |
static void |
main(String[] args) |
void |
printRMatrix() |
addNodeK, apply, configure, d, getChromatogramDistanceFunction, getChromatogramWarpCommand, getCluster, getCluster, getClusterNames, getClusters, getConsensus, getDescription, getDist, getFragments, getInputFiles, getL, getMinimizingArrayCompVariableName, getNames, getPairwiseDistanceMatrixVariableName, getPairwiseDistanceNamesVariableName, getUsedIndices, getWorkflowSlot, handleFileFragments, init, isMinimizeDist, isMinimizing, iterator, merge, printCluster, printDistanceToNewCluster, printDistMatrix, printNamesMatrix, putCluster, setChromatogramDistanceFunction, setChromatogramWarpCommand, setCluster, setClusterNames, setConsensus, setd, setDist, setFragments, setInputFiles, setL, setLDF, setMinimizeDist, setMinimizingArrayCompVariableName, setNames, setPairwiseDistanceMatrixVariableName, setPairwiseDistanceNamesVariableName, toGraphML, toStringaddListener, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResults, addWorkflowResults, appendXML, canEqual, createBlockingCompletionService, createCompletionService, createNonBlockingCompletionService, createWorkFragment, createWorkFragments, equals, fireEvent, getCvResolver, getProgress, getWorkflow, hashCode, initProgress, initSubCommand, mapToInput, mapToInputUri, postProcess, postProcessUri, removeListener, resolve, save, setCvResolver, setProgress, setWorkflowpublic NeighborJoinAlgorithm()
public NeighborJoinAlgorithm(double[][] distances,
String[] names)
public NeighborJoinAlgorithm(double[][] distances,
TupleND<IFileFragment> fragments,
PairwiseFeatureSequenceSimilarity ld)
public static void main(String[] args)
public void calcR(int numclust)
public double[] dmat(int i,
int j,
int k)
dmat in class ClusteringAlgorithmpublic void findBestD(int numclust)
findBestD in class ClusteringAlgorithmpublic void init(double[][] distances,
String[] names,
TupleND<IFileFragment> fragments)
init in class ClusteringAlgorithmpublic void joinIJtoK(int i,
int j,
int k,
double[] dist)
joinIJtoK in class ClusteringAlgorithmpublic void printRMatrix()
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