NAME

GH::EditOp - A simple perl object (implemented in C) that represents various edit operations used in sequence alignments.

SYNOPSIS

  # this example (and this man page) may be out of date.  Think twice.

  use GH::EditOp;
  
  my $editop = new GH::EditOp;
  
  # make the op a "no-op", and see if it worked.
  $editop->setType(NOP);
  Not() if ($editop->getType() != NOP); Ok($i++);
  Not() if ($editop->getOpName() ne "nop"); Ok($i++);
  
  # make the op a "match op" and see if it worked.
  $editop->setType(MATCH);
  Not() if ($editop->getType() != MATCH); Ok($i++);
  Not() if ($editop->getOpName() ne "match"); Ok($i++);
  
  # make the op a "mismatch op" and 
  $editop->setType(MISMATCH);
  Not() if ($editop->getType() != MISMATCH); Ok($i++);
  Not() if ($editop->getOpName() ne "mismatch"); Ok($i++);
  
  $editop->setType(INSERT_S1);
  Not() if ($editop->getType() != INSERT_S1); Ok($i++);
  Not() if ($editop->getOpName() ne "insert_s1"); Ok($i++);
  
  $editop->setType(INSERT_S2);
  Not() if ($editop->getType() != INSERT_S2); Ok($i++);
  Not() if ($editop->getOpName() ne "insert_s2"); Ok($i++);
  
  $editop->setCount(0);
  Not() if ($editop->getCount() != 0); Ok($i++);
  
  $editop->setCount(2345);
  Not() if ($editop->getCount() != 2345); Ok($i++);
  
  print $op->getOpName, " ", $op->getCount;
  if ($op->getCount == 1) {
    print " base.\n";
  }
  else {
    print " bases.\n";
  }

DESCRIPTION

GH::EditOp provides an object that encapsulates an operation that might be used in a sequence alignment. Each object has a name and a count.

EXPORT

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).