=head1 NAME

seqaligndisplay module - part of the Wise2 package

=head1 SYNOPSIS

This module contains helper functions for the Wise2 package

=head1 DESCRIPTION

=over

=item write_pretty_str_align

&Wise2::write_pretty_str_align(alb,qname,query,tname,target,name,main,ofp)

  This gives an interface into the alignment
  display using strings and files.



  Argument alb          [UNKN ] alignment structure [AlnBlock *]
  Argument qname        [UNKN ] name of first sequence [char *]
  Argument query        [UNKN ] first sequence [char *]
  Argument tname        [UNKN ] name of second sequence [char *]
  Argument target       [UNKN ] second sequence [char *]
  Argument name         [UNKN ] length of the name block [int]
  Argument main         [UNKN ] length of the main block [int]
  Argument ofp          [UNKN ] output file [FILE *]
  Return [UNKN ] Undocumented return value [boolean]


=item write_pretty_seq_align

&Wise2::write_pretty_seq_align(alb,q,t,name,main,ofp)

  This gives an interface into the alignment
  display using sequences and files. A more
  generic function is write_pretty_str_align



  Argument alb          [UNKN ] alignment structure [AlnBlock *]
  Argument q            [UNKN ] first sequence [Sequence *]
  Argument t            [UNKN ] second sequence  [Sequence *]
  Argument name         [UNKN ] length of the name block [int]
  Argument main         [UNKN ] length of the main block [int]
  Argument ofp          [UNKN ] output file [FILE *]
  Return [UNKN ] Undocumented return value [boolean]


=item write_pretty_Protein_align

&Wise2::write_pretty_Protein_align(alb,q,t,name,main,ofp)

  This gives an interface into the
  alignment display using Protein
  objects



  Argument alb          [UNKN ] alignment structure [AlnBlock *]
  Argument q            [UNKN ] first sequence [Protein *]
  Argument t            [UNKN ] second sequence  [Protein *]
  Argument name         [UNKN ] length of the name block [int]
  Argument main         [UNKN ] length of the main block [int]
  Argument ofp          [UNKN ] output file [FILE *]
  Return [UNKN ] Undocumented return value [boolean]


=back