util.bio.parsers
Class MultiFastaParser

java.lang.Object
  util.bio.parsers.MultiFastaParser

public class MultiFastaParser

extends java.lang.Object

Extracts sequences and headers out of multi fasta files. Will read in combine fasta files, skips blank lines, does not filter actual seq parses off the > character. Seqs and names are index matched, ie seqs[3] and names[3] refer to the same thing.

Constructor Summary

MultiFastaParser()

MultiFastaParser(java.io.File file)

MultiFastaParser(java.lang.String file)

Method Summary

java.lang.String	getFileName()
java.lang.String[]	getNames()
int	getNumReads()
java.lang.String[]	getSeqs()
boolean	isFastaFound()
void	parseIt(java.io.File file)
void	printMFP()
void	printReport()
void	resetFields()

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiFastaParser

public MultiFastaParser(java.io.File file)

MultiFastaParser

public MultiFastaParser(java.lang.String file)

MultiFastaParser

public MultiFastaParser()

Method Detail

resetFields

public void resetFields()

parseIt

public void parseIt(java.io.File file)

printMFP

public void printMFP()

printReport

public void printReport()

getSeqs

public java.lang.String[] getSeqs()

getNames

public java.lang.String[] getNames()

getFileName

public java.lang.String getFileName()

getNumReads

public int getNumReads()

isFastaFound

public boolean isFastaFound()