edu.mssm.crover.tools.blast
Class ExtractAcIdentity

java.lang.Object
  |
  +--edu.mssm.crover.tools.blast.ExtractAcIdentity

public class ExtractAcIdentity

extends java.lang.Object

Extracts the accession numbers from the definition line of a BLAST output. Blast databases must be formatted with -s T -o T, to create search indices. Required to extract the accession number from the Hit_Id tag.

Constructor Summary

ExtractAcIdentity()

Method Summary

java.lang.String[]	convert(BlastResult br)
int	getDefaultMinLength()
double	getDefaultPercentIdentity()
int	getMinLength()
double	getPercentIdentity()
void	setMinLength(int minLength)
void	setPercentIdentity(double percentIdentity)

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtractAcIdentity

public ExtractAcIdentity()

Method Detail

getDefaultPercentIdentity

public double getDefaultPercentIdentity()

setPercentIdentity

public void setPercentIdentity(double percentIdentity)

getPercentIdentity

public double getPercentIdentity()

getDefaultMinLength

public int getDefaultMinLength()

setMinLength

public void setMinLength(int minLength)

getMinLength

public int getMinLength()

convert

public java.lang.String[] convert(BlastResult br)
                           throws XMLVersionNotSupportedException,
                                  java.lang.NumberFormatException

XMLVersionNotSupportedException

java.lang.NumberFormatException