Clustering

Object
- Clustering

Direct Known Subclasses:

CAST_Clustering, Hierarchical_Clustering, KMeans_Clustering
```
public class Clustering
extends Object
```
An instance of the Clustering class represents a clustering (i.e., grouping or partitioning) of a collection of genes.

Field Summary

Fields
Modifier and Type	Field and Description
`protected java.util.Vector<Cluster>`	`clusters` A collection of clusters
`protected java.util.Vector<String>`	`experiments` A collection of experiment names
`protected java.util.Vector<Gene>`	`genes` A collection of genes

Constructor Summary

Constructors
Constructor and Description

Clustering(String fileName)
Creates an initially empty Clustering.

Constructors
Constructor and Description
`Clustering(String fileName)` Creates an initially empty `Clustering`.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.util.Vector<String>`	`getExperimentNamesFromFile(String fileName)` Returns a collection of experiment names for which there is data in the specified file.
`java.util.Vector<Gene>`	`getGeneInformationFromFile(String fileName)` Returns a collection of `Genes` based on data in the specified file.
`int`	`getNumClusters()` Returns the number of clusters in this `Clustering`.
`int`	`getNumExperiments()` Returns the number of experiments in this `Clustering`.
`int`	`getNumGenes()` Returns the total number of genes in this `Clustering`.
`static void`	`main(String[] args)` The `main` method creates an initially empty `Clustering` from a tab-delimited text file of gene and experiment data.
`String`	`toString()` Returns a `String` representation of all `Clusters` in this `Clustering`.

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - experiments
```
protected java.util.Vector<String> experiments
```
    A collection of experiment names
  - genes
```
protected java.util.Vector<Gene> genes
```
    A collection of genes
  - clusters
```
protected java.util.Vector<Cluster> clusters
```
    A collection of clusters
- Constructor Detail
  - Clustering
```
public Clustering(String fileName)
```
    Creates an initially empty Clustering.
    A set of genes and experiments are determined from the specified String representing the name of a file. Genes and experiments are read-in from the tab-delimited file. Initially, the constructed Clustering is empty.
    
    Parameters:
    
    fileName - the name of a tab-delimited text file containing gene and experiment data
- Method Detail
  - getNumExperiments
```
public int getNumExperiments()
```
    Returns the number of experiments in this Clustering.
    
    Returns:
    
    an integer representing the number of experiments
  - getNumGenes
```
public int getNumGenes()
```
    Returns the total number of genes in this Clustering.
    
    Returns:
    
    an integer representing the number of genes
  - getNumClusters
```
public int getNumClusters()
```
    Returns the number of clusters in this Clustering.
    
    Returns:
    
    an integer representing the number of clusters
  - getExperimentNamesFromFile
```
public java.util.Vector<String> getExperimentNamesFromFile(String fileName)
```
    Returns a collection of experiment names for which there is data in the specified file.
    The method assumes that the first line of the specified file contains a tab-delimited list of experiment names. The first two tokens on the first line do not correspond to experiment names and are ignored. Thus, if the first line of the file contains "m+2" tab-delimited tokens, then the line contains "m" experiment names. A Vector containing the names of the experiments is returned.
    
    Parameters:
    
    fileName - the name of a tab-delimited text file with gene and experiment data
    
    Returns:
    
    a collection of experiment names as extracted from the specified file
  - getGeneInformationFromFile
```
public java.util.Vector<Gene> getGeneInformationFromFile(String fileName)
```
    Returns a collection of Genes based on data in the specified file.
    The method assumes that the specified file is tab-delimited. The method assumes that the first line of the specified file is a header line that does not contain any gene information. Starting with the second line of the file and continuing until the end of the file, the method assumes that each line is a tab-delimited collection of gene information, including the gene's name, function, and expression values. A Vector of Gene objects is returned.
    
    Parameters:
    
    fileName - the name of a tab-delimited text file with gene and experiment data
    
    Returns:
    
    a collection of Genes as extracted from the specified file
  - toString
```
public String toString()
```
    Returns a String representation of all Clusters in this Clustering.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    a String represenation of this Clustering
  - main
```
public static void main(String[] args)
```
    The main method creates an initially empty Clustering from a tab-delimited text file of gene and experiment data.
    
    Parameters:
    
    args - an array of Strings representing any command line arguments

Class Clustering

Field Summary

Constructor Summary

Method Summary

Methods inherited from class Object

Field Detail

experiments

genes

clusters

Constructor Detail

Clustering

Method Detail

getNumExperiments

getNumGenes

getNumClusters

getExperimentNamesFromFile

getGeneInformationFromFile

toString

main