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