smile.data.parser.microarray

Class TXTParser

java.lang.Object

smile.data.parser.microarray.TXTParser

public class TXTParser
extends Object

TXT gene expression file parser. The TXT format is a tab delimited file format that describes an expression dataset. It is organized as follows:

The first line contains the labels Name and Description followed by the identifiers for each sample in the dataset. The Description is optional.

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 file contains data for each of the genes. There is one line for each gene. Each line contains the gene name, gene description, and a value for each sample in the dataset. If the first line contains the Description label, include a description for each gene. If the first line does not contain the Description label, do not include descriptions for any gene. Gene names and descriptions can contain spaces since fields are separated by tabs.

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
TXTParser() Constructor.

Method Summary

Methods

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

Methods inherited from class java.lang.Object

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

Constructor Detail

TXTParser

public TXTParser()

Constructor.

Method Detail

parse

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

Parse a TXT dataset from given URI.

Throws:

FileNotFoundException

IOException

ParseException

parse

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

Parse a TXT 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 TXT dataset from given file.

Throws:

FileNotFoundException

IOException

ParseException

parse

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

Parse a TXT 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 TXT dataset from given file.

Throws:

FileNotFoundException

IOException

ParseException

parse

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

Parse a TXT 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 TXT dataset from an input stream.

Parameters:

name - the name of dataset.

stream - the input stream of data.

Throws:

FileNotFoundException

IOException

ParseException