biyelunwen/99.scripts/trinity_utils/PerlLib/Overlap_piler.pm

package main;
our $SEE = 0;

## taken from CDNA::Overlap_assembler.pm
## really should be a more general purpose class as written here.


package Overlap_piler;


use strict;
use warnings;
use Carp;

sub new {
    my $packagename = shift;
    my $self = {
        node_list => []
        };
    bless ($self, $packagename);
    return ($self);
}


#### Static method!!!
sub simple_coordsets_collapser {
    my @coordsets = @_; ## list of coordinates [a, b], [c, d], ...
    
    my $counter = 0;
    
    my $piler = new Overlap_piler();

    my %coords_mapping;
    foreach my $coordset (@coordsets) {
        $counter++;
        $coords_mapping{$counter} = [@$coordset];
        
        my ($lend, $rend) = @$coordset;
        if ($lend !~ /\d/ || $rend !~ /\d/) {
            confess "Error, coordinates [ $lend, $rend ] include a non-number";
        }

        $piler->add_coordSet($counter, @$coordset);
    }

    my @clusters = $piler->build_clusters();
    
    my @coord_spans;
    foreach my $cluster (@clusters) {
        my @eles = @$cluster;
        my @coords;
        foreach my $ele (@eles) {
            push (@coords, @{$coords_mapping{$ele}});
        }

        @coords = sort {$a<=>$b} @coords;
        
        my $min_coord = shift @coords;
        my $max_coord = pop @coords;

        push (@coord_spans, [$min_coord, $max_coord]);
    }

    return (@coord_spans);
    
}



####
sub add_coordSet {
    my $self = shift;
    my ($acc, $end5, $end3) = @_;
    my ($lend, $rend) = sort {$a<=>$b} ($end5, $end3);
    my $node = CoordSet_node->new($acc, $lend, $rend);
    push (@{$self->{node_list}}, $node);
}




####
sub build_clusters {
    my $self = shift;
    my $node_list_aref = $self->{node_list};
    @{$node_list_aref} = sort {$a->{lend}<=>$b->{lend}} @{$node_list_aref}; #sort by lend coord.
    ## set indices
    for (my $i = 0; $i <= $#{$node_list_aref}; $i++) {
        $node_list_aref->[$i]->{myIndex} = $i;
    }
    
    my @clusters;
    my $first_node = $node_list_aref->[0];
    my $start_pos = 0;
    my ($exp_left, $exp_right) = ($first_node->{lend}, $first_node->{rend});
    print $first_node->{acc} . " ($exp_left, $exp_right)\n" if $SEE;
    for (my $i = 1; $i <= $#{$node_list_aref}; $i++) {
        my $curr_node = $node_list_aref->[$i];
        my ($lend, $rend) = ($curr_node->{lend}, $curr_node->{rend});
        print $curr_node->{acc} . " ($lend, $rend)\n" if $SEE;
        if ($exp_left <= $rend && $exp_right >= $lend) { #overlap
            $exp_left = &min($exp_left, $lend);
            $exp_right = &max($exp_right, $rend);
            print "overlap. New expanded coords: ($exp_left, $exp_right)\n" if $SEE;
        } else {
            print "No overlap; Creating cluster: " if $SEE;
            my @cluster;
            for (my $j=$start_pos; $j < $i; $j++) {
                my $acc = $node_list_aref->[$j]->{acc};
                push (@cluster, $acc);
                print "$acc, " if $SEE;
            }
            push (@clusters, [@cluster]);
            $start_pos = $i;
            ($exp_left, $exp_right) = ($lend, $rend);
            print "\nResetting expanded coords: ($lend, $rend)\n" if $SEE;
        }
    }
    
    print "# Adding final cluster.\n" if $SEE;
    if ($start_pos != $#{$node_list_aref}) {
        print "final cluster: " if $SEE;
        my @cluster;
        for (my $j = $start_pos; $j <= $#{$node_list_aref}; $j++) {
            my $acc = $node_list_aref->[$j]->{acc};
            print "$acc, " if $SEE;
            push (@cluster, $acc);
        }
        push (@clusters, [@cluster]);
        print "\n" if $SEE;
    } else {
        my $acc = $node_list_aref->[$start_pos]->{acc};
        push (@clusters, [$acc]);
        print "adding final $acc.\n" if $SEE;
    }
    return (@clusters);
}

sub min {
    my (@x) = @_;
    @x = sort {$a<=>$b} @x;
    my $min = shift @x;
    return ($min);
}

sub max {
    my @x = @_;
    @x = sort {$a<=>$b} @x;
    my $max = pop @x;
    return ($max);
}

#################################################################
package CoordSet_node;
use strict;

sub new {
    my $packagename = shift;
    my ($acc, $lend, $rend) = @_;
    my $self = { acc=>$acc,
                 lend=>$lend,
                 rend=>$rend,
                 myIndex=>undef(),
                 overlapping_indices=>[]
                 };
    bless ($self, $packagename);
    return ($self);
}

1; #EOM