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


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.