bring objects up to API

svn path=/bioperl-pedigree/trunk/; revision=12107
bioperl · Jun 24, 2003 · feb2f3a · feb2f3a
1 parent bafb55c
commit feb2f3a
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Showing 3 changed files with 19 additions and 15 deletions.
diff --git a/Bio/Pedigree/Marker.pm b/Bio/Pedigree/Marker.pm
@@ -72,6 +72,7 @@ BEGIN {
  Returns : CHG::Lapis::Marker
  Args    : -name          => [string] marker name
            -description   => [string] marker description
+           -display_name  => [string] a display name for the marker (optional)
            -type          => [string] marker type
            -unique_id     => (optional) [string/int] unique id
            -allele_freq   => (optional) [hash ref] allele frequencies 
@@ -99,7 +100,14 @@ sub new {
     return $self;
 }
 
-sub _initialize {}
+sub _initialize {
+    my ($self,@args) = @_;    
+    my ($display,$dname) = $self->_rearrange([qw(DISPLAY 
+						 DISPLAY_NAME)], @args);
+    $display = $dname if( defined $dname );
+    defined $display && $self->display_name($display);
+    return;
+}
 
 =head2 name
 
@@ -169,12 +177,11 @@ sub description {
 
 =cut
 
-sub display_name{
-   my ($obj,$value) = @_;
-   if( defined $value) {
-      $obj->{'_display_name'} = $value;
-    }
-    return $obj->{'_display_name'};
+sub display_name {
+    my $self = shift;
+    $self->{'_display_name'} = shift if @_;
+    return $self->{'_display_name'};
+
 }
 
 =head2 type_code

diff --git a/Bio/Pedigree/Marker/disease.pm b/Bio/Pedigree/Marker/disease.pm
@@ -19,7 +19,7 @@ CHG::Lapis::Marker::disease - module for managing lapis DxMarker data
     use Bio::Pedigree::Marker;
     my $marker = new Bio::Pedigree::Marker::disease(-name       => $name,
 						    -type       => $type,
-						    -desc       => $desc,
+						    -description=> $desc,
 						    -liab_classes=>\%classes,
 						    -frequencies=>\@freqs);
 

diff --git a/Bio/Pedigree/Marker/variation.pm b/Bio/Pedigree/Marker/variation.pm
@@ -99,7 +99,7 @@ sub _initialize {
 
     $self->{'_alleles'} = {};
 
-    my ($alleles,$chrom, 
+    my ($alleles,$chrom,
 	$fwd,$rev) = $self->_rearrange([qw(ALLELES
 					   CHROM FWDFLANK
 					   REVFLANK)], @args);
@@ -112,8 +112,7 @@ sub _initialize {
     # optional fields
     $fwd     && $self->upstream_flanking_seq($fwd);
     $rev     && $self->dnstream_flanking_seq($rev);
-    $chrom   && $self->chromosome($chrom);
-
+    defined $chrom   && $self->chromosome($chrom);
     return;
 }
 
@@ -260,10 +259,8 @@ sub dnstream_flanking_seq{
 =cut
 
 sub chromosome {
-    my ($self, $value) = @_;
-    if( defined $value ) {
-	$self->{'_chrom'} = $value;
-    }
+    my $self = shift;
+    $self->{'_chrom'} = shift if @_;
     return $self->{'_chrom'};
 }