org.genepattern.io.expr.cls
Class ClsParser
java.lang.Object
 org.genepattern.io.expr.cls.ClsParser
- public class ClsParser
- extends java.lang.Object
Class for reading cls files using callbacks.
The 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
| Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ClsParser
public ClsParser()
canDecode
public boolean canDecode(java.io.InputStream in)
parse
public void parse(java.io.InputStream is)
throws java.io.IOException,
ParseException
- Parses the
InputStream to create a ClassVector
instance
- Parameters:
is - The input stream
- Throws:
ParseException - If there is a problem with the data
java.io.IOException - if an I/O error occurs while reading the stream.
setHandler
public void setHandler(IClsHandler handler)
getFormatName
public java.lang.String getFormatName()
getFileSuffixes
public java.util.List getFileSuffixes()
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