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)