org.genepattern.io.expr.cls
Class ClsWriter

java.lang.Object
  org.genepattern.io.expr.cls.ClsWriter

public class ClsWriter

extends java.lang.Object

Writer for cls files. CLS files are simple files created to load class information into GeneCluster. These files use spaces to separate the fields.

• The first line of a CLS file contains numbers indicating the number of samples and number of classes. The number of samples should correspond to the number of samples in the associated RES or GCT data file.
• Line format: (number of samples) (space) (number of classes) (space) 1
• For example: 58 2 1
• The second line in a CLS file contains names for the class numbers. The line should begin with a pound sign (#) followed by a space.
• Line format: # (space) (class 0 name) (space) (class 1 name)
• For example: # cured fatal/ref.
• The third line contains numeric class labels for each of the samples. The number of class labels should be the same as the number of samples specified in the first line.
• Line format: (sample 1 class) (space) (sample 2 class) (space) ... (sample N class)
• For example: 0 0 0 ... 1

Constructor Summary

ClsWriter()

Method Summary

java.lang.String	checkFileExtension(java.lang.String pathname)
void	write(ClassVector cv, java.io.OutputStream os) Writes an ClassVector instance to a file.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ClsWriter

public ClsWriter()

Method Detail

checkFileExtension

public java.lang.String checkFileExtension(java.lang.String pathname)

write

public void write(ClassVector cv,
                  java.io.OutputStream os)
           throws java.io.IOException

Writes an ClassVector instance to a file. The correct file extension will be added to the file name if it does not already exist.

Parameters:

cv - the class vector

os - the output stream

Throws:

java.io.IOException - if an I/O error occurs during writing