Bio::SearchIO::axt - a parser for axt format reports

  use Bio::SearchIO;
  my $parser = Bio::SearchIO->new(-format => 'axt',
                                 -file   => 't/data/report.blastz');
  while( my $result = $parser->next_result ) {
    while( my $hit = $result->next_hit ) {
      while( my $hsp = $hit->next_hsp ) {
      }
    }
  }

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  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://redmine.open-bio.org/projects/bioperl/

 Title   : new
 Usage   : my $obj = Bio::SearchIO::axt->new();
 Function: Builds a new Bio::SearchIO::axt object 
 Returns : an instance of Bio::SearchIO::axt
 Args    :

 Title   : next_result
 Usage   : my $hit = $searchio->next_result;
 Function: Returns the next Result from a search
 Returns : Bio::Search::Result::ResultI object
 Args    : none

 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

 Title   : start_element
 Usage   : $eventgenerator->end_element
 Function: Handles an end element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'

 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string

 Title   : _mode
 Usage   : $obj->_mode($newval)
 Function: 
 Example : 
 Returns : value of _mode
 Args    : newvalue (optional)

 Title   : within_element
 Usage   : if( $eventgenerator->within_element($element) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name 

 Title   : in_element
 Usage   : if( $eventgenerator->in_element($element) ) {}
 Function: Test if we are in a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name 

 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handles a start document event
 Returns : none
 Args    : none

 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none

 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none

#
# BioPerl module for Bio::SearchIO::axt
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

# Let the code begin...


package Bio::SearchIO::axt;
use vars qw(%MODEMAP %MAPPING @STATES $GAPCHAR);
use strict;

use Bio::Search::Result::ResultFactory;
use Bio::Search::HSP::HSPFactory;
use base qw(Bio::SearchIO);

use POSIX;

BEGIN { 
    # mapping of NCBI Blast terms to Bioperl hash keys
    %MODEMAP = ('AXTOutput'   => 'result',
		'Hit'         => 'hit',
		'Hsp'         => 'hsp'
		);
    $GAPCHAR = '-';
    %MAPPING = 
	( 
	  'Hsp_score'      => 'HSP-score',
          'Hsp_query-from' => 'HSP-query_start',
          'Hsp_query-to'   => 'HSP-query_end',
          'Hsp_hit-from'   => 'HSP-hit_start',
          'Hsp_hit-to'     => 'HSP-hit_end',
	  'Hsp_positive'   => 'HSP-conserved',
          'Hsp_identity'   => 'HSP-identical',
          'Hsp_gaps'       => 'HSP-hsp_gaps',
          'Hsp_hitgaps'    => 'HSP-hit_gaps',
          'Hsp_querygaps'  => 'HSP-query_gaps',
          'Hsp_qseq'       => 'HSP-query_seq',
          'Hsp_hseq'       => 'HSP-hit_seq',
          'Hsp_midline'    => 'HSP-homology_seq', # ignoring this for now
          'Hsp_align-len'  => 'HSP-hsp_length',
	  
	  'Hit_id'        => 'HIT-name',	  
	  'AXTOutput_query-def'=> 'RESULT-query_name',	  
	  );
}

sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  return $self;
}

sub next_result{
    my ($self) = @_;
    local $/ = "\n";
    local $_;

    my ($curquery,$curhit);
    $self->start_document();
    my @hit_signifs;
    while( defined ($_ = $self->_readline )) { 
	next if (/^\s+$/);
	if( m/^(\d+)\s+      # alignment number - we'll throw this away anyways
	    	    (\S+)\s+         # Query name      
	    	    (\d+)\s+(\d+)\s+ # Query start Query end (always + strand, 0 based)
	    	    (\S+)\s+         # Hit name
	    	    (\d+)\s+(\d+)\s+ # Hit start Hit end (0 based)
	    	    ([\-\+])\s+      # Hit strand
	    	    ([\d\.\-]+)\s+   # Score
	    	    /ox ) {
	    my ($alnnum, $qname,$qstart,$qend, $hname,
		$hstart,$hend,$hstrand, $score) = ($1,$2,$3,$4,$5,
						   $6,$7,$8,$9);
	    $self->{'_reporttype'} = 'AXT';
	    # Jim's code is 0 based
        # yes, but axt format is one-based, see bug 3145 - cjfields 10-11-10
	    #$qstart++;  $qend++; $hstart++; $hend++;
	    if( defined $curquery &&  $curquery ne $qname ) { 
            $self->end_element({'Name' => 'Hit'});
            $self->_pushback($_);
            $self->end_element({'Name' => 'AXTOutput'});
            return $self->end_document();
	    }
	    
	    if( defined $curhit &&
		$curhit ne $hname) {
		# slight duplication here -- keep these in SYNC
		$self->end_element({'Name' => 'Hit'});
		$self->start_element({'Name' => 'Hit'});
		$self->element({'Name' => 'Hit_id',
				'Data' => $hname});
	    } elsif ( ! defined $curquery ) { 
		$self->start_element({'Name' => 'AXTOutput'});
		$self->{'_result_count'}++;
		$self->element({'Name' => 'AXTOutput_query-def',
				'Data' => $qname });
		
		$self->start_element({'Name' => 'Hit'});
		$self->element({'Name' => 'Hit_id',
				'Data' => $hname});
	    }
	    $self->start_element({'Name' => 'Hsp'});
	    my $queryalign = $self->_readline;
	    my $hitalign   = $self->_readline;
	    chomp($queryalign);
	    chomp($hitalign);
	    my $alnlen = length($queryalign);
	    my $qgapnum = ( $queryalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); 
	    my $hgapnum = ( $hitalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); 
	    my $totalgaps = ($qgapnum + $hgapnum);
	    
	    if( $hstrand eq '-' ) { # strand gets inferred by start/end
		($hstart,$hend) = ($hend,$hstart);
	    }
	    $self->element({'Name' => 'Hsp_score',
			    'Data' => $score});
	    $self->element({'Name' => 'Hsp_query-from',
			    'Data' => $qstart});
	    $self->element({'Name' => 'Hsp_query-to',
			    'Data' => $qend});
	    $self->element({'Name' => 'Hsp_hit-from',
			    'Data' => $hstart});
	    $self->element({'Name' => 'Hsp_hit-to',
			    'Data' => $hend});
	    $self->element({'Name' => 'Hsp_gaps',
			    'Data' => $qgapnum + $hgapnum});
	    $self->element({'Name' => 'Hsp_querygaps',
			    'Data' => $qgapnum});
	    $self->element({'Name' => 'Hsp_hitgaps',
			    'Data' => $hgapnum});
	    
	    $self->element({'Name' => 'Hsp_identity',
			    'Data' => $alnlen - $totalgaps});
	    $self->element({'Name' => 'Hsp_positive',
			    'Data' => $alnlen - $totalgaps});
	    $self->element({'Name' => 'Hsp_qseq',
			    'Data' => $queryalign});
	    $self->element({'Name' => 'Hsp_hseq',
			    'Data' => $hitalign});
	    
	    $self->end_element({'Name' => 'Hsp'});	    
	    $curquery = $qname;
	    $curhit   = $hname;	   
	}
    }
    # fence post
    if( defined $curquery  ) {
	$self->end_element({'Name' => 'Hit'});
	$self->end_element({'Name' => 'AXTOutput'});
	return $self->end_document();
    }
    return;
}

sub _initialize {
    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult'));

    $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::GenericHSP'));
}

sub start_element{
   my ($self,$data) = @_;
    # we currently don't care about attributes
    my $nm = $data->{'Name'};    
   if( my $type = $MODEMAP{$nm} ) {
	$self->_mode($type);
	if( $self->_eventHandler->will_handle($type) ) {
	    my $func = sprintf("start_%s",lc $type);
	    $self->_eventHandler->$func($data->{'Attributes'});
	}						 
	unshift @{$self->{'_elements'}}, $type;
    }
    if($nm eq 'AXTOutput') {
	$self->{'_values'} = {};
	$self->{'_result'}= undef;
	$self->{'_mode'} = '';
    }

}

sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $rc;
    # Hsp are sort of weird, in that they end when another
    # object begins so have to detect this in end_element for now
        
    if( my $type = $MODEMAP{$nm} ) {
	if( $self->_eventHandler->will_handle($type) ) {
	    my $func = sprintf("end_%s",lc $type);
	    $rc = $self->_eventHandler->$func($self->{'_reporttype'},
					      $self->{'_values'});	    
	}
	shift @{$self->{'_elements'}};

    } elsif( $MAPPING{$nm} ) { 	
	if ( ref($MAPPING{$nm}) =~ /hash/i ) {
	    my $key = (keys %{$MAPPING{$nm}})[0];	    
	    $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
	} else {
	    $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
	}
    } else { 
	$self->warn( "unknown nm $nm ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
				# end of an element
    $self->{'_result'} = $rc if( $nm eq 'AXTOutput' );
    return $rc;

}

sub element{
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}

sub characters{
   my ($self,$data) = @_;   

   return unless ( defined $data->{'Data'} );
   if( $data->{'Data'} =~ /^\s+$/ ) {
       return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
   }

   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
       
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  
   
   $self->{'_last_data'} = $data->{'Data'}; 
}

sub _mode{
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_mode'} = $value;
    }
    return $self->{'_mode'};
}

sub within_element{
   my ($self,$name) = @_;  
   return 0 if ( ! defined $name &&
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
	   return 1;
       } 
   }
   return 0;
}

sub in_element{
   my ($self,$name) = @_;  
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}

sub start_document{
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_mode'} = '';
    $self->{'_elements'} = [];
}

sub end_document{
   my ($self,@args) = @_;
   return $self->{'_result'};
}

sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}

sub report_count { shift->result_count }



1;