AlignmentsTrackConfig.pm

package ApiCommonModel::Model::JBrowseTrackConfig::AlignmentsTrackConfig;
use base qw(ApiCommonModel::Model::JBrowseTrackConfig::TrackConfig);

use strict;
use warnings;

use ApiCommonModel::Model::JBrowseTrackConfig::BamStore;

sub getMin {$_[0]->{min}}
sub setMin {$_[0]->{min} = $_[1]}

sub getMax {$_[0]->{max}}
sub setMax {$_[0]->{max} = $_[1]}

sub getYScalePosition {$_[0]->{yscale_position}}
sub setYScalePosition {$_[0]->{yscale_position} = $_[1]}

sub getChunkSizeLimit {$_[0]->{chunk_size}}
sub setChunkSizeLimit {$_[0]->{chunk_size} = $_[1]}

sub getColorFwdStrand {$_[0]->{color_fwd_strand}}
sub setColorFwdStrand {$_[0]->{color_fwd_strand} = $_[1]}

sub getColorRevStrand {$_[0]->{color_rev_strand}}
sub setColorRevStrand {$_[0]->{color_rev_strand} = $_[1]}

sub getBorderColor {$_[0]->{border_color}}
sub setBorderColor {$_[0]->{border_color} = $_[1]}

sub skipHistograms {$_[0]->{_skip_histograms}}

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

    my $store = ApiCommonModel::Model::JBrowseTrackConfig::BamStore->new($args);
    $self->setStore($store);

    if($self->getApplicationType() eq 'jbrowse' || $self->getApplicationType() eq 'apollo') {
        $self->setDisplayType("JBrowse/View/Track/Alignments2");
        $self->setTrackTypeDisplay("Coverage (Read Alignments zoomed)");
    }
    else {
        $self->setTrackType("AlignmentsTrack");
        $self->setDisplayType("LinearAlignmentsDisplay");
        $self->setTrackTypeDisplay("Alignment");
    }

    #my $displayName = $self->getDisplayName();
    #my $datasetName = $self->getDatasetName();
    
    $self->setId($args->{key});
    #$self->setId("${datasetName}_${displayName}_Alignments");
    #$self->setColor("black");
    $self->setMin(0);
    $self->setMax(500);
    $self->setYScalePosition("left");
    $self->setChunkSizeLimit(50000000);

    if($args->{skip_histograms}) {
      $self->{_skip_histograms} = 1;
    }

    if(my $colorFwdStrand = $args->{color_fwd_strand}) {
    $self->setColorFwdStrand($colorFwdStrand);
	}
    if(my $colorRevStrand = $args->{color_rev_strand}) {
    $self->setColorRevStrand($colorRevStrand);
        }

    return $self;
}

sub getJBrowseStyle {
    my $self = shift;
    my $jbrowseStyle = $self->SUPER::getJBrowseStyle();
    
    if ($self->getColorFwdStrand && $self->getColorRevStrand){
	$jbrowseStyle->{color_fwd_strand}=$self->getColorFwdStrand;
        $jbrowseStyle->{color_rev_strand}=$self->getColorRevStrand;
	}

    return $jbrowseStyle;
}

sub getHistograms {
    my $self = shift;

    my $store = $self->getStore();

    my $bigwigUrl = $store->getBigwigUrl();
    $bigwigUrl = "/a/service/jbrowse/store?data=" . $bigwigUrl;


    my $histograms = {};
    #$histograms->{color} = $self->getColor();
    $histograms->{color} = "black";
    $histograms->{storeClass} = $store->getBigWigStoreType();
    $histograms->{min} = $self->getMin();
    $histograms->{urlTemplate} = $bigwigUrl;
    $histograms->{max} = $self->getMax();
    return $histograms;
}


sub getJBrowseObject{
    my $self = shift;

    my $jbrowseObject = $self->SUPER::getJBrowseObject();


    $jbrowseObject->{yScalePosition} = $self->getYScalePosition();
    $jbrowseObject->{chunkSizeLimit} = $self->getChunkSizeLimit();;

    $jbrowseObject->{urlTemplate}= $self->getStore()->getUrlTemplate();

    unless($self->skipHistograms()) {
      my $histograms = $self->getHistograms();
      $jbrowseObject->{histograms} = $histograms;
    }

    return $jbrowseObject;
}

sub getJBrowse2Object{
    my $self = shift;

    my $jbrowse2Object = $self->SUPER::getJBrowse2Object();

    my $indexLocation = $self->getStore()->getIndexUrlTemplate();

    $jbrowse2Object->{adapter}->{index}->{location}->{uri} = $indexLocation;
    $jbrowse2Object->{adapter}->{bamLocation} = {uri => $self->getStore()->getUrlTemplate(),locationType => "UriLocation"};

    $jbrowse2Object->{displays}->[0]->{displayId} = "bam_" . scalar($self);

    return $jbrowse2Object;
}



1;