smile.data.parser.microarray

Class GCTParser

java.lang.Object

smile.data.parser.microarray.GCTParser

public class GCTParser
extends Object

Gene Cluster Text file parser. The GCT format is a tab delimited file format that describes a gene expression dataset. It is organized as follows:

The first line contains the version string and is always the same for this file format. Therefore, the first line must be as follows:

#1.2

The second line contains numbers indicating the size of the data table that is contained in the remainder of the file. Note that the name and description columns are not included in the number of data columns.

Line format:

(# of data rows) (tab) (# of data columns)

Example:

7129 58

The third line contains a list of identifiers for the samples associated with each of the columns in the remainder of the file.

Line format:

Name(tab)Description(tab)(sample 1 name)(tab)(sample 2 name) (tab) ... (sample N name)

Example:

Name Description DLBC1_1 DLBC2_1 ... DLBC58_0

The remainder of the data file contains data for each of the genes. There is one row for each gene and one column for each of the samples. The number of rows and columns should agree with the number of rows and columns specified on line 2. Each row contains a name, a description, and an intensity value for each sample. Names and descriptions can contain spaces, but may not be empty. If no description is available, enter a text string such as NA or NULL. Intensity values may be missing. To specify a missing intensity value, leave the field empty: ...(tab)(tab)....

Line format:

(gene name) (tab) (gene description) (tab) (col 1 data) (tab) (col 2 data) (tab) ... (col N data)

Example:

AFFX-BioB-5_at AFFX-BioB-5_at (endogenous control) -104 -152 -158 ... -44

Author:

Haifeng Li

Constructor Summary

Constructors

Constructor and Description
GCTParser() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
AttributeDataset	parse(File file) Parse a GCT dataset from given file.
AttributeDataset	parse(String path) Parse a GCT dataset from given file.
AttributeDataset	parse(String name, File file) Parse a GCT dataset from given file.
AttributeDataset	parse(String name, InputStream stream) Parse a GCT dataset from an input stream.
AttributeDataset	parse(String name, String path) Parse a GCT dataset from given file.
AttributeDataset	parse(String name, URI uri) Parse a GCT dataset from given URI.
AttributeDataset	parse(URI uri) Parse a GCT dataset from given URI.

Methods inherited from class java.lang.Object

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

Constructor Detail

GCTParser

public GCTParser()

Constructor.

Method Detail

parse

public AttributeDataset parse(URI uri)
                       throws FileNotFoundException,
                              IOException,
                              ParseException

Parse a GCT dataset from given URI.

Throws:

FileNotFoundException

IOException

ParseException

parse

public AttributeDataset parse(String name,
                     URI uri)
                       throws FileNotFoundException,
                              IOException,
                              ParseException

Parse a GCT dataset from given URI.

Parameters:

uri - the URI of data source.

Throws:

FileNotFoundException

IOException

ParseException

parse

public AttributeDataset parse(String path)
                       throws FileNotFoundException,
                              IOException,
                              ParseException

Parse a GCT dataset from given file.

Throws:

FileNotFoundException

IOException

ParseException

parse

public AttributeDataset parse(String name,
                     String path)
                       throws FileNotFoundException,
                              IOException,
                              ParseException

Parse a GCT dataset from given file.

Parameters:

path - the file path of data source.

Throws:

FileNotFoundException

IOException

ParseException

parse

public AttributeDataset parse(File file)
                       throws FileNotFoundException,
                              IOException,
                              ParseException

Parse a GCT dataset from given file.

Throws:

FileNotFoundException

IOException

ParseException

parse

public AttributeDataset parse(String name,
                     File file)
                       throws FileNotFoundException,
                              IOException,
                              ParseException

Parse a GCT dataset from given file.

Parameters:

file - the file of data source.

Throws:

FileNotFoundException

IOException

ParseException

parse

public AttributeDataset parse(String name,
                     InputStream stream)
                       throws IOException,
                              ParseException

Parse a GCT dataset from an input stream.

Parameters:

name - the name of dataset.

stream - the input stream of data.

Throws:

FileNotFoundException

IOException

ParseException