mast documentation.

sub new {

    my($class, @args)=@_;
    my $self = $class->SUPER::new(@args);
    my (%instances,@header,$n);
    my ($file)=$self->_rearrange(['FILE'], @args);
    $self->{file} = $file;
    $self->{_factor}=1;
    $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now
    $self->{_end}=0;
    undef $self->{hid};
    return $self if ($file=~/^>/);#Just writing
    my $buf=$self->_readline;
	$self->throw('Cannot parse HTML format yet') if ($buf =~/^<HTML>/); 
    # this should probably be moved to its own function
    while ( defined($buf=$self->_readline)) {
	chomp($buf);
	if ($buf=~/DATABASE AND MOTIFS/) {
		while ($buf=$self->_readline) {
			if ($buf=~/DATABASE/) {
					$buf=~s/^[\s\t]+//;
					chomp $buf;
					($n,$self->{_dbname},$self->{_dbtype})=split(/\s/,$buf);
					$self->{_dbtype}=~s/[\(\)]//g;
			}
			if ($buf=~/MOTIFS/) {
					$buf=~s/^[\s\t]+//;
					chomp $buf;
					($n,$self->{_mrsc},$self->{_msrctype})=split(/\s/,$buf);
					$self->{_msrctype}=~s/[\(\)]//g;
					last;
			}
		}
		if ($self->{_msrctype} ne $self->{_dbtype}) {#Assume we have protein motifs, nuc DB (not handling opp.)
			$self->{_factor}=3;
			$self->{_mixquery}=1;
		}
	}
	if ($buf=~m/MOTIF WIDTH BEST POSSIBLE MATCH/) {
	    $self->_readline;
	    while (defined($buf=$self->_readline)) {
		last if ($buf!~/\w/);
		$buf=~s/\t+//g;
		$buf=~s/^\s+//g;
		my ($id,$width,$seq)=split(/\s+/,$buf);
		push @{$self->{hid}},$id;
		$self->{length}->{$id}=$width;
		$self->{seq}->{$id}=$seq;
	    }
	    next;
	}
	if ($buf=~m/section i:/i) {
	    $self->_readline;
	    $self->_readline;
	    $self->_readline;
	    %instances=_get_genes($self);
	    $self->{instances}=\%instances;
      	if (!(%instances)) {
        	$self->warn ("Your MAST analysis did not find any matches satisfying the current threshold.\nSee MAST documentation for more information.\n");
        	return $self; #The header might be useful so we return the object, not undef
      	}
	    next;
	}
	if ($buf=~m/section ii:/i) {
	    $self->_readline;
	    $self->_readline;
	    $self->_readline;
	    last;
	}
	$buf=~s/[\t+\s+]/ /g;
	push @header,$buf unless (($buf=~/\*{10,}/)||($buf!~/\w/));
    }
    $self->throw('Could not read Section I, probably wrong format, make sure it is not HTML, giving up...') if !(%instances);
    $self->warn( "This file might be an unreadable version, proceed with caution!\n") if (!grep(/\s+MAST\s+version\s+3/,@header));

    $self->{unstructured} =\@ header;
    $self->_initialize;
    return $self;

}

sub _get_genes {

	my $self=shift;
	my %llid;
	my $ok=0;
	my $i=0;
	my %instances;
	while (my $line=$self->_readline) {
		last if ($line=~/^[\s\t*]/); # Well, ids can be nearly anything...???
		chomp($line);
		$i++;
		next if ($line eq '');
		$line=~s/\s+/,/g;
		my ($id,$key,$eval,$len)=split(/,/,$line);
		unless ($len) {
			warn "Malformed data found: $line\n";
			next;
		}
		$instances{$id}=new Bio::Matrix::PSM::InstanceSite (-id=>$id,
																			  -desc=>$key,
																			  -score=>$eval, 
																			  -width=>$len,
																			  -seq=>'ACGT');
	}
	return %instances;

}

sub next_psm {

    my $self=shift;
    return if ($self->{_end}==1);
    my (@lmotifsm,%index,$eval,$scheme,$sid);
    %index= %{$self->{length}};
    my (@instances,%instances);
    my $line=$self->_readline;
    $line=~s/[\t\n]//;
    if ($line =~ /\*{10,}/) { #Endo of Section II if we do only section II
        $self->{_end}=1;
        return ;
    }
    do {
	if ($line!~/^\s/) {
	    ($sid,$eval,$scheme)=split(/\s+/,$line,3);
	}
	else
	{ $scheme .=$line; }
	$line=$self->_readline;
	$line=~s/[\t\n]//;
    } until ($line!~/^\s/);
    my $pos=1;
    $scheme=~s/\s+//g;
    $scheme=~s/\n//g;
    my @motifs=split(/_/,$scheme);
    while (@motifs) {
	my $next=shift(@motifs);
	if (!($next=~/\D/)) {
	    last if (!@motifs);
	    $pos+=$next;
	    next;
	}
        my $id=$next;
	my $score= $id=~m/\[/ ? 'strong' : 'weak' ;
	my $frame;
	my $strand = $id =~ m/\-\d/ ? -1 : 1 ;
	if ($self->{_mixquery}) {
		$frame = 0 if $id =~ m/\d+a/ ;
		$frame = 1 if $id =~ m/\d+b/ ;
		$frame = 2 if $id =~ m/\d+c/ ;
	}
	$id=~s/\D+//g;

	my @s;
	my $width=$index{$id};
    #We don't know the sequence, but we know the length
	my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq
	my $instance=new Bio::Matrix::PSM::InstanceSite 
	    ( -id=>"$id\@$sid", 
	      -mid=>$id, 
	      -accession_number=>$sid,
	      -desc=>"Motif $id occurrance in $sid",
	      -score=>$score, 
	      -seq=>$seq,
		  -alphabet => 'dna', 
	      -start=>$pos,
	      -strand=>$strand);
	  $instance->frame($frame) if ($self->{_mixquery});
	push @instances,$instance;
	$pos+=$index{$id}*$self->{_factor};
    }
    my $psm= new Bio::Matrix::PSM::Psm (-instances=>\@ instances, 
					-e_val    => $eval, 
					-id       => $sid);
    $self->_pushback($line);
    return $psm;

}

sub write_psm {

    my ($self,$matrix)=@_;
#    my $idline=">". $matrix->id . "\n";
    my $w=$matrix->width;
    my $header="ALPHABET= ACGT\nlog-odds matrix: alength= 4 w= $w\n";
    $self->_print($header);
    unless ($matrix->get_logs_array('A')) {
        warn "No log-odds data, available, using normal distribution to recalculate the PWM";
        $matrix->calc_weight({A=>0.25, C=>0.25, G=>0.25,T=>0.25});
    }
    while (my %h=$matrix->next_pos) {
	$self->_print (join("\t",$h{lA},$h{lC},$h{lG},$h{lT},"\n"));
    }

}

new	Description	Code
_get_genes	No description	Code
next_psm	Description	Code
write_psm	Description	Code