ExonerateOutput.pir

#
# Output from Exonerate.
#

- PerlClass PirObject::ExonerateOutput
- InheritsFrom  PirObject
- FieldsTable

# Field name             Struct           Type            Comments
#---------------------- ---------------   --------------- -----------------------
command                 single            string          Command line
report                  array             <ExonerateReport>

- EndFieldsTable

- Methods

our $RCS_VERSION='$Id: ExonerateOutput.pir,v 1.2 2008/08/19 20:32:05 riouxp Exp $';
our ($VERSION) = ($RCS_VERSION =~ m#,v ([\w\.]+)#);

sub FillFeaturesFromTextOutput {
  my $self     = shift;
  my $tab      = shift;
  
  my $report = [];
  for (;;) {
    last if @$tab == 0;
    my @c4 = ();
    push(@c4,shift(@$tab)) while @$tab && $tab->[0] !~ m#^C4 Ali#;
    
    if ($c4[0] =~ /^Command line:\s*(.+)/){
    $self->set_command($1);
    }
    else {
    my $obj = new PirObject::ExonerateReport();
    $obj->FillFeaturesFromC4Report(\@c4);
    push(@$report,$obj);
    }
    shift(@$tab) if @$tab;
  }
  $self->set_report($report);
}