sample.session.client

Class DAVIDParser

java.lang.Object

sample.session.client.DAVIDParser

public class DAVIDParser
extends java.lang.Object

Class responsible to dump DAVID's different outputs to tab separated files. These includes: 1) ChartReport: 2) TableReport: 3) GeneClusterReport: 4) TermClusterReport: Fun 5) ListReport: Show Gene List associated data (id, gene name, organism)

Since:

2012-12-31

Version:

1.0

Author:

Modifications by Cristobal Fresno (cristobalATgmailDOTcom) to DAVID's JavaClient-1.1.zip

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	EOL The end of line separator token "\n".
static java.lang.String	SEP The column separation token "\t".

Constructor Summary

Constructors

Constructor and Description
DAVIDParser()

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args) The main method.
static void	writeChartReport(java.lang.String fileName, sample.session.service.xsd.SimpleChartRecord[] simpleChartRecords) Parse DAVID's ChartReport and write them to a file using a StringBuffer.
static void	writeGeneClusterReport(java.lang.String fileName, sample.session.service.xsd.SimpleGeneClusterRecord[] simpleGeneClusterRecords) Parse DAVID's ClusterReport and write them to a file using a StringBuffer.
static void	writeListReport(java.lang.String fileName, david.xsd.ListRecord[] listRecords, java.lang.String idType) Parse DAVID's ListReport and write them to a file using a StringBuffer.
static void	writeSummaryReport(java.lang.String fileName, david.xsd.MainSummaryRecord[] mainSummaryRecords) Parse DAVID's SummaryReport and write them to a file using a StringBuffer.
static void	writeTableReport(java.lang.String fileName, david.xsd.TableRecord[] tableRecords) Parse DAVID's TableReport and write them to a file using a StringBuffer.
static void	writeTermClusterReport(java.lang.String fileName, sample.session.service.xsd.SimpleTermClusterRecord[] simpleTermClusterRecords) Parse DAVID's TermClusterReport and write them to a file using a StringBuffer.

Methods inherited from class java.lang.Object

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

Field Detail

SEP

public static final java.lang.String SEP

The column separation token "\t".

See Also:

Constant Field Values

EOL

public static final java.lang.String EOL

The end of line separator token "\n".

See Also:

Constant Field Values

Constructor Detail

DAVIDParser

public DAVIDParser()

Method Detail

writeChartReport

public static void writeChartReport(java.lang.String fileName,
                    sample.session.service.xsd.SimpleChartRecord[] simpleChartRecords)

Parse DAVID's ChartReport and write them to a file using a StringBuffer.

Parameters:

fileName - String with the output file name.

simpleChartRecords - returned by DAVID's ChartReport output.

writeTableReport

public static void writeTableReport(java.lang.String fileName,
                    david.xsd.TableRecord[] tableRecords)

Parse DAVID's TableReport and write them to a file using a StringBuffer.

Parameters:

fileName - String with the output file name.

tableRecords - returned by DAVID's TableReport output.

writeGeneClusterReport

public static void writeGeneClusterReport(java.lang.String fileName,
                          sample.session.service.xsd.SimpleGeneClusterRecord[] simpleGeneClusterRecords)

Parse DAVID's ClusterReport and write them to a file using a StringBuffer.

Parameters:

fileName - String with the output file name.

simpleGeneClusterRecords - returned by DAVID's ClusterReport output.

writeTermClusterReport

public static void writeTermClusterReport(java.lang.String fileName,
                          sample.session.service.xsd.SimpleTermClusterRecord[] simpleTermClusterRecords)

Parse DAVID's TermClusterReport and write them to a file using a StringBuffer.

Parameters:

fileName - String with the output file name.

simpleTermClusterRecords - returned by DAVID's TermClusterReport output.

writeListReport

public static void writeListReport(java.lang.String fileName,
                   david.xsd.ListRecord[] listRecords,
                   java.lang.String idType)

Parse DAVID's ListReport and write them to a file using a StringBuffer.

Parameters:

fileName - String with the output file name.

listRecords - returned by DAVID's ListReport output.

idType - String with DAVID's used id type for the specified list.

writeSummaryReport

public static void writeSummaryReport(java.lang.String fileName,
                      david.xsd.MainSummaryRecord[] mainSummaryRecords)

Parse DAVID's SummaryReport and write them to a file using a StringBuffer.

Parameters:

fileName - String with the output file name.

mainSummaryRecords - returned by DAVID's SummaryReport output.

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

The main method. Basically runs testParse method to see if every writeXXReport works!!

Parameters:

args - the arguments (not used)

Throws:

java.lang.Exception - Signals that an I/O exception has occurred.