edu.mssm.crover.bturns
Class AlignSeqPos

java.lang.Object
  |
  +--edu.mssm.crover.bturns.AlignSeqPos

public class AlignSeqPos
extends java.lang.Object

Help do the conversion between the position in the sequence and the position in the alignment, and reciprocally.


Constructor Summary
AlignSeqPos(RandomAccessAlignment ralign)
           
 
Method Summary
 int getAlignPos(java.lang.String shortname, int seq_pos)
          Returns the position in the alignment, from the sequence shortname and position in the sequence.
static void main(java.lang.String[] args)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlignSeqPos

public AlignSeqPos(RandomAccessAlignment ralign)
Method Detail

getAlignPos

public int getAlignPos(java.lang.String shortname,
                       int seq_pos)
                throws RandomAccessAlignment.SequenceNotFoundInAlignment
Returns the position in the alignment, from the sequence shortname and position in the sequence. By convention, seq_pos and align_pos start at zero.

RandomAccessAlignment.SequenceNotFoundInAlignment

main

public static void main(java.lang.String[] args)


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