edu.mssm.crover.tools.tissue
Class ReportParser

java.lang.Object
  |
  +--edu.mssm.crover.tools.tissue.ReportParser

public class ReportParser

extends java.lang.Object

Parses report files from tiquery. For every accession number, outputs the report filename, the accession number, the point in that file where the report for that accession number starts and stops.

Constructor Summary

ReportParser()

Method Summary

static java.lang.String	getInputFile(java.lang.String[] args) Returns the name of the input file.
static java.lang.String	getOutputFile(java.lang.String[] args) Returns the name of the output file.
static java.lang.String	getPrefix(java.lang.String[] args) Returns the prefix which partitions the file.
static void	main(java.lang.String[] args)
void	parse(java.io.File reportFile, java.io.File outFile, java.lang.String prefix)
java.lang.String	read(java.io.File reportFile, long start, long stop)

Methods inherited from class java.lang.Object

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

Constructor Detail

ReportParser

public ReportParser()

Method Detail

parse

public void parse(java.io.File reportFile,
                  java.io.File outFile,
                  java.lang.String prefix)

read

public java.lang.String read(java.io.File reportFile,
                             long start,
                             long stop)

getInputFile

public static java.lang.String getInputFile(java.lang.String[] args)

Returns the name of the input file. Read from the command line, after "-i" flag. This is a necessary parameter.

getOutputFile

public static java.lang.String getOutputFile(java.lang.String[] args)

Returns the name of the output file. Read from the command line, after "-o" flag. If no name given, the default is called report.parsed.

getPrefix

public static java.lang.String getPrefix(java.lang.String[] args)

Returns the prefix which partitions the file. Read from the command line, after "-prefix" flag. If no name given, the default is ">".

main

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