NAME

GH::Msp - A simple perl object (implemented in C) that represents a maximal segment pair.

SYNOPSIS

  use GH::Msp;
  
  $msp->setPos1(10);
  $pos1 = $msp->getPos1();

  $msp->setPos2(23456);
  $pos2 = $msp->getPos2();

  $msp->setLen(98765);
  $len = $msp->getLen();

  $msp->setScore(10);
  $score = $msp->getScore();

DESCRIPTION

GH::Msp provides an object that encapsulates a maximal segment pair. The pos1 value is the start position in the first sequence, the pos2 value is the start position in the second sequence, and the len value is the length of the segment pair. Positions are offsets from the beginning of the sequence, the first base is at position 0. The score value contains the score of the msp. The particular value depends on the scoring scheme used to create the msp.

EXPORT

None.

EXPORT_OK

None.

BUGS

The scoring scheme should more explicit.

Positions should start at 1. Except that then there would need to be a bug about positions starting at 0.

AUTHOR

George Hartzell, hartzell@cs.berkeley.edu

SEE ALSO

GH::MspTools.

perl(1).