@@ -79,6 +79,11 @@ my $labelSub = sub {
#return eval{$_[0]->primary_tag};
};
+my $idSub = sub {
+ return $_[0]->load_id if ($_[0]->can('load_id') && defined($_[0]->load_id));
+ return $_[0]->can('primary_id') ? $_[0]->primary_id : $_[0]->id;
+};
+
my $streaming = 0;
my ($db, $stream);
if ($gff) {
@@ -109,6 +114,7 @@ my %style = ("autocomplete" => $autocomplete,
"subfeatures" => $getSubs,
"class" => $cssClass,
"label" => $getLabel ? $labelSub : 0,
+ "idSub" => $idSub,
"key" => defined($key) ? $key : $trackLabel,
"urlTemplate" => $urlTemplate,
"arrowheadClass" => $arrowheadClass,
bin/flatfile-to-json.pl
@@ -78,7 +78,8 @@ FeatureTrack.prototype.loadSuccess = function(trackInfo) {
alert("clicked on feature\nstart: " + feat[fields["start"]] +
", end: " + feat[fields["end"]] +
", strand: " + feat[fields["strand"]] +
- ", ID: " + feat[fields["name"]]);
+ ", label: " + feat[fields["name"]] +
+ ", ID: " + feat[fields["id"]]);
};
}
js/FeatureTrack.js
@@ -19,17 +19,12 @@ my @featMap = (
sub {shift->start - 1},
sub {int(shift->end)},
sub {int(shift->strand)},
- \&featureIdSub,
);
-my @mapHeaders = ('start', 'end', 'strand', 'id');
+my @mapHeaders = ('start', 'end', 'strand');
#positions of "start" and "end" in @mapHeaders (for NCList)
my $startIndex = 0;
my $endIndex = 1;
-sub featureIdSub {
- return $_[0]->can('primary_id') ? $_[0]->primary_id : $_[0]->id;
-}
-
sub featureLabelSub {
return $_[0]->display_name if $_[0]->can('display_name');
return $_[0]->info if $_[0]->can('info'); # deprecated
@@ -137,8 +132,12 @@ sub new {
$self->{getLabel} = ($style{autocomplete} =~ /label|all/);
$self->{getAlias} = ($style{autocomplete} =~ /alias|all/);
- my @curFeatMap = (@featMap, @$extraMap);
- my @curMapHeaders = (@mapHeaders, @$extraHeaders);
+ my $idSub = $style{idSub} || sub {
+ return $_[0]->can('primary_id') ? $_[0]->primary_id : $_[0]->id;
+ };
+
+ my @curFeatMap = (@featMap, $idSub, @$extraMap);
+ my @curMapHeaders = (@mapHeaders, "id", @$extraHeaders);
if ($style{label}) {
push @curFeatMap, $style{label};
@@ -167,7 +166,9 @@ sub new {
my @allSubfeatures;
$self->{allSubfeatures} = \@allSubfeatures;
- my $subfeatId = \&featureIdSub;
+ my $subfeatId = $style{idSub} || sub {
+ return $_[0]->can('primary_id') ? $_[0]->primary_id : $_[0]->id;
+ };
if ($autoshareSubs) {
$subfeatId = sub {
my $feat = shift;
lib/JsonGenerator.pm
b54bf71be0a66b8b1b47fc037e2570d3be1da638
Mitch Skinner
mitch_skinner@berkeley.edu
http://github.com/jbrowse/jbrowse/commit/020db6dde76a7922eb8117addc481f46c1358bbc
020db6dde76a7922eb8117addc481f46c1358bbc
2009-10-20T18:21:26-07:00
2009-10-20T18:21:26-07:00
allow the ID callback to vary
add a special Bio::DB::SeqFeature::Store ID callback for use with GFFs
8ff7455ee17cc96ace8ea4578f287dd2b5edc933
Mitch Skinner
mitch_skinner@berkeley.edu