edu.mssm.crover.tools.blast
Class MegablastHSIterator

java.lang.Object
  |
  +--edu.mssm.crover.tools.blast.MegablastHSIterator
All Implemented Interfaces:
edu.mssm.crover.tools.blast.HitSummaryIterator

public class MegablastHSIterator
extends java.lang.Object
implements edu.mssm.crover.tools.blast.HitSummaryIterator

Iterates through a megablast -D 3 output file, returns HitSummaries.


Constructor Summary
MegablastHSIterator(java.io.File mbFile)
           
MegablastHSIterator(java.io.Reader r)
           
 
Method Summary
static java.lang.String getAC(java.lang.String defline)
          Method to parse the unique accession number from a gi identifier.
 boolean hasNext()
          Returns true if the iteration has more HitSummaries.
 HitSummary next()
          Returns the next HitSummary in the interation.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MegablastHSIterator

public MegablastHSIterator(java.io.File mbFile)
                    throws java.io.FileNotFoundException,
                           java.io.IOException,
                           WrongFileFormatException

MegablastHSIterator

public MegablastHSIterator(java.io.Reader r)
                    throws java.io.IOException,
                           WrongFileFormatException
Method Detail

getAC

public static java.lang.String getAC(java.lang.String defline)
Method to parse the unique accession number from a gi identifier.


hasNext

public boolean hasNext()
                throws java.io.IOException
Returns true if the iteration has more HitSummaries.

Specified by:
hasNext in interface edu.mssm.crover.tools.blast.HitSummaryIterator
java.io.IOException

next

public HitSummary next()
                throws CommandNotInstalled,
                       WrongFileFormatException,
                       java.io.IOException
Returns the next HitSummary in the interation.

Specified by:
next in interface edu.mssm.crover.tools.blast.HitSummaryIterator
CommandNotInstalled
WrongFileFormatException
java.io.IOException


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