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Chipchip JBrowse tracks #152

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Chipchip JBrowse tracks #152

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443a443
add subTrackAttr property to cature in injector
Jan 29, 2026
9d40929
fix addChipChipTracks
Jan 29, 2026
1238a5e
use of GFFStore and other fixes for ChipChip modules
bgajria Feb 2, 2026
e31f3fc
chipChip smooth track to use BigWigStore
bgajria Feb 12, 2026
03504e6
chipChip peak track to use BedStore
bgajria Feb 12, 2026
7089ffb
edit makeChipChipPeak for peak and smooth tracks
bgajria Feb 12, 2026
6b8cb16
numerous fixes for ChipChip peak and smoothed tracks
bgajria Feb 17, 2026
40418ff
minor changes, and debugging
bgajria Feb 19, 2026
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58 changes: 39 additions & 19 deletions Model/lib/perl/JBrowseTrackConfig/ChipChipPeakTrackConfig.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,16 @@ package ApiCommonModel::Model::JBrowseTrackConfig::ChipChipPeakTrackConfig;
use base qw(ApiCommonModel::Model::JBrowseTrackConfig::Segments);
use strict;
use warnings;
use Data::Dumper;

use ApiCommonModel::Model::JBrowseTrackConfig::RestStore;
use ApiCommonModel::Model::JBrowseTrackConfig::BedStore;

sub getGlyph {$_[0]->{glyph} }
sub setGlyph {$_[0]->{glyph} = $_[1]}

sub getUrl {$_[0]->{url} }
sub setUrl {$_[0]->{url} = $_[1]}

use JSON;

sub new {
my ($class, $args) = @_;
Expand All @@ -17,51 +23,65 @@ sub new {
$datasetConfig->setCategory("Epigenomics");
$datasetConfig->setSubcategory("ChIP chip");

$self->setId($args->{pan_name});
$self->setLabel($args->{pan_name});
$self->setId($args->{key});
$self->setLabel($args->{label});
$self->setGlyph($args->{glyph});

$self->setDisplayMode(undef);
$self->setGlyph(undef);
$self->setUrl($args->{relative_path_to_file});
my $uu = $self->getUrl();
#print Dumper "PEAK CCPT url = $uu";

# $self->setDisplayMode(undef);
# $self->setGlyph(undef);

my $store;

if($self->getApplicationType() eq 'jbrowse' || $self->getApplicationType() eq 'apollo') {
$store = ApiCommonModel::Model::JBrowseTrackConfig::RestStore->new($args);
$store->setQuery("ChIP:ChIPchip_peaksjbrowse");
$store->setQueryParamsHash($args->{query_params});
$store = ApiCommonModel::Model::JBrowseTrackConfig::BedStore->new($args);
}
else {
# TODO
$store = ApiCommonModel::Model::JBrowseTrackConfig::BedStore->new($args);
}

$self->setStore($store);

$self->setGlyph("JBrowse/View/FeatureGlyph/Segments") unless(defined $self->getGlyph());

my $detailsFunction = "{peakTitleChipSeqFxn}";
$self->setOnClickContent($detailsFunction);
$self->setViewDetailsContent($detailsFunction);


return $self;
}

sub getJBrowseStyle {
my $self = shift;

sub getMetadata {
my $self = shift;
my $metadata = $self->SUPER::getMetadata();
my $jbrowseStyle = $self->SUPER::getJBrowseStyle();

$metadata->{attribution} = undef;
return $metadata;
# $jbrowseStyle->{color} = "";
# $jbrowseStyle->{label} = "Sample,sample,name";
return $jbrowseStyle;
}


sub getJBrowseObject{
my $self = shift;

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


return $jbrowseObject;
}

# TODO:
sub getJBrowse2Object{
my $self = shift;
my $self = shift;

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


return $jbrowse2Object;
return $jbrowse2Object;
}


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61 changes: 27 additions & 34 deletions Model/lib/perl/JBrowseTrackConfig/ChipChipSmoothedTrackConfig.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,15 @@ package ApiCommonModel::Model::JBrowseTrackConfig::ChipChipSmoothedTrackConfig;
use base qw(ApiCommonModel::Model::JBrowseTrackConfig::CoverageTrackConfig);
use strict;
use warnings;
use Data::Dumper;

use ApiCommonModel::Model::JBrowseTrackConfig::RestStore;
use ApiCommonModel::Model::JBrowseTrackConfig::BigWigStore;

use JSON;
sub getGlyph {$_[0]->{glyph} }
sub setGlyph {$_[0]->{glyph} = $_[1]}

sub getPanName {$_[0]->{pan_name}}
sub setPanName {$_[0]->{pan_name} = $_[1]}

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


sub new {
Expand All @@ -22,27 +21,33 @@ sub new {
$datasetConfig->setCategory("Epigenomics");
$datasetConfig->setSubcategory("ChIP chip");

$self->setPanName($args->{pan_name});
my $panName = $self->getPanName();
$self->setId($panName);
$self->setLabel($panName);
$self->setCovMaxScoreDefault($args->{cov_max_score_default});
$self->setCovMinScoreDefault($args->{cov_min_score_default});
$self->setId($args->{key});
$self->setLabel($args->{label});
$self->setGlyph($args->{glyph});

$self->setUrl($args->{relative_path_to_file});
my $uu = $self->getUrl();
#print Dumper "SMOOTH CCST url = $uu";


# $self->setDisplayMode(undef);
# $self->setGlyph(undef);

$self->setCovMaxScoreDefault(defined $args->{cov_max_score_default} ? $args->{cov_max_score_default} : 1000);
$self->setCovMinScoreDefault(defined $args->{cov_min_score_default} ? $args->{cov_min_score_default} : 0);

#TODO
$self->setTrackTypeDisplay("XYPlot");
### $self->setDisplayType("JBrowse/View/Track/CanvasFeatures");
$self->setDisplayType("JBrowse/View/Track/CanvasFeatures");

my $store;

if($self->getApplicationType() eq 'jbrowse' || $self->getApplicationType() eq 'apollo') {
$store = ApiCommonModel::Model::JBrowseTrackConfig::RestStore->new($args);
$store->setQuery("ChIP:ChIPchip_smoothedjbrowse");
$store->setQueryParamsHash($args->{query_params});

$store = ApiCommonModel::Model::JBrowseTrackConfig::BigWigStore->new($args);
}
else {
# TODO
$store = ApiCommonModel::Model::JBrowseTrackConfig::BigWigStore->new($args);
}

$self->setStore($store);
Expand All @@ -53,7 +58,7 @@ sub new {
sub getJBrowseStyle {
my $self = shift;

my $jbrowseStyle = {};
my $jbrowseStyle = $self->SUPER::getJBrowseStyle();

$jbrowseStyle->{height} = 40;
$jbrowseStyle->{neg_color} = "{chipColor}";
Expand All @@ -62,17 +67,6 @@ sub getJBrowseStyle {
return $jbrowseStyle;
}

sub getMetadata {
my $self = shift;

my $metadata = $self->SUPER::getMetadata();

$metadata->{attribution} = undef;


return $metadata;
}


sub getJBrowseObject{
my $self = shift;
Expand All @@ -83,18 +77,17 @@ sub getJBrowseObject{
# $jbrowseObject->{scale} = undef;

return $jbrowseObject;

}


# TODO:
sub getJBrowse2Object{
my $self = shift;
my $self = shift;

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


return $jbrowse2Object;
return $jbrowse2Object;
}


Expand Down
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