smile.data.parser.microarray

Class PCLParser

java.lang.Object

smile.data.parser.microarray.PCLParser

public class PCLParser
extends java.lang.Object

Stanford cDNA file parser. The PCL file format is a tab delimited file format that describes a gene expression dataset. The first three columns are as follows:

Name

This column will contain a name ascribed to the entity on that row, such as ORF name, or CLONEID. The column itself can be named anything, but by convention is named YORF when it contains yeast ORF names, CLID when it contains clone IDs, and LUID when it contains LUIDs. This column MUST contain some text on every row.

Description

This column can contain descriptive information about the entity, e.g. process or function, or gene symbol. It too can be named anything. It can optionally be left blank, but the column itself must be present.

GWEIGHT

This column allows you to weight genes with different weights, for instance if a gene appears on an array twice, you may want to give them a weight of 0.5 each. For the most part people leave this column with a value of 1 for every gene. This column must be present, and each row must have an entry.

In addition the file must begin with the following two rows:

Row 1

This contains the column headers as described above for columns 1, 2 and 3, then contains the experiment names for all the data columns that exist in the file. Each data column must have a text entry as a name for that column.

Row 2

This is the EWEIGHT row. The entry in the first column for this row should say EWEIGHT, then for each experiment, there should be an EWEIGHT value. This will usually be 1, but if the same experiment is duplicated twice, you may want to give these repeats an EWEIGHT of 0.5.

The remaining cells in the file contain the actual data, such that the row and column specifies to which gene and which experiment a particular piece of data corresponds.

In general the PCL file will contain log-transformed data, which is needed for clustering to work properly.

Constructor Summary

Constructors

Constructor and Description
PCLParser() Constructor.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

PCLParser

public PCLParser()

Constructor.

Method Detail

parse

public AttributeDataset parse(java.net.URI uri)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from given URI.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.net.URI uri)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from given URI.

Parameters:

uri - the URI of data source.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String path)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from given file.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.lang.String path)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from given file.

Parameters:

path - the file path of data source.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.io.File file)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from given file.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.io.File file)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from given file.

Parameters:

file - the file of data source.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.io.InputStream stream)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a PCL dataset from an input stream.

Parameters:

name - the name of dataset.

stream - the input stream of data.

Throws:

java.io.IOException

java.text.ParseException