edu.mssm.crover.tools.blast
Class XMLBlastHSIterator

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

All Implemented Interfaces:

edu.mssm.crover.tools.blast.HitSummaryIterator

public class XMLBlastHSIterator

extends java.lang.Object

implements edu.mssm.crover.tools.blast.HitSummaryIterator

Iterates through an XML BLAST output file, returns HitSummaries.

Constructor Summary

XMLBlastHSIterator(java.io.File multipleFile)

XMLBlastHSIterator(java.io.Reader r)

Method Summary

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

XMLBlastHSIterator

public XMLBlastHSIterator(java.io.File multipleFile)
                   throws java.io.FileNotFoundException,
                          WrongFileFormatException

XMLBlastHSIterator

public XMLBlastHSIterator(java.io.Reader r)
                   throws WrongFileFormatException

Method Detail

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