Added summary methods for use in Region Report

Minor POD corrections

modules/Bio/EnsEMBL/Feature.pm

@@ -1429,7 +1429,24 @@ sub get_nearest_Gene {
 
 }
 
+=head2 summary_as_hash
 
+  Example       : $feature_summary = $feature->summary_as_hash();
+  Description   : Retrieves a textual summary of this Feature.
+	              Should be overidden by subclasses for specific tweaking
+  Returns       : hashref of arrays of descriptive strings
+  Status        : Intended for internal use
+=cut
+
+sub summary_as_hash {
+  my $self = shift;
+  my %summary;
+  $summary{'ID'} = $self->display_id;
+  $summary{'start'} = $self->start;
+  $summary{'end'} = $self->end;
+  $summary{'strand'} = $self->strand;
+  return \%summary;
+}
 
 
 

modules/Bio/EnsEMBL/Gene.pm

@@ -1473,6 +1473,25 @@ sub is_reference{
   return $self->{'is_ref'};
 }
 
+=head2 summary_as_hash
+
+  Example       : $gene_summary = $gene->summary_as_hash();
+  Description   : Extends Feature::summary_as_hash
+                  Retrieves a summary of this Gene object.
+	                  
+  Returns       : hashref of arrays of descriptive strings
+  Status        : Intended for internal use
+=cut
+
+sub summary_as_hash {
+  my $self = shift;
+  my $summary_ref = $self->SUPER::summary_as_hash;
+  $summary_ref->{'description'} = $self->description;
+  $summary_ref->{'biotype'} = $self->biotype;
+  return $summary_ref;
+}
+
+
 ###########################
 # DEPRECATED METHODS FOLLOW
 ###########################

modules/Bio/EnsEMBL/Slice.pm

@@ -3447,6 +3447,25 @@ sub add_synonym{
   return;
 }
 
+=head2 summary_as_hash
+
+  Example       : $slice_summary = $slice->summary_as_hash();
+  Description   : Retrieves a textual summary of this slice.
+  Returns       : hashref of descriptive strings
+=cut
+
+sub summary_as_hash {
+  my $self = shift;
+  my %summary;
+  $summary{'display_id'} = $self->display_id;
+  $summary{'start'} = $self->start;
+  $summary{'end'} = $self->end;
+  $summary{'strand'} = $self->strand;
+  $summary{'Is_circular'} = $self->is_circular ? "true" : "false";
+  $summary{'region_name'} = $self->seq_region_name();
+  return \%summary;
+}
+
 #
 # Bioperl Bio::PrimarySeqI methods:
 #

modules/Bio/EnsEMBL/Transcript.pm

@@ -2650,6 +2650,25 @@ sub load {
 
 } ## end sub load
 
+=head2 summary_as_hash
+
+  Example       : $transcript_summary = $transcript->summary_as_hash();
+  Description   : Extends Feature::summary_as_hash
+                  Retrieves a summary of this Transcript.
+  Returns       : hashref of descriptive strings
+  Status        : Intended for internal use
+=cut
+
+sub summary_as_hash {
+  my $self = shift;
+  my $summary_ref = $self->SUPER::summary_as_hash;
+  $summary_ref->{'description'} = $self->description;
+  $summary_ref->{'biotype'} = $self->biotype;
+  my $parent_gene = $self->get_nearest_Gene;
+  $summary_ref->{'Parent'} = $parent_gene->display_id;
+  return $summary_ref;
+}
+
 ###########################
 # DEPRECATED METHODS FOLLOW
 ###########################

modules/Bio/EnsEMBL/Translation.pm

@@ -150,7 +150,7 @@ sub new_fast {
                   with this translation object.
   Exceptions    : Throws if there is no adaptor or no dbID defined for
                   the translation object.
-
+  Returntype    : Bio::EnsEMBL::Transcript
 =cut
 
 sub transcript {
@@ -170,7 +170,7 @@ sub transcript {
     my $adaptor = $self->adaptor;
     if ( !defined($adaptor) ) {
       throw(   "Adaptor is not set for translation, "
-             . "can not fecth its transcript." );
+             . "can not fetch its transcript." );
     }
 
     my $dbID = $self->{'dbID'};
@@ -1204,5 +1204,24 @@ sub get_all_DAS_Features{
   return $self->SUPER::get_all_DAS_Features($slice);
 }
 
+=head2 summary_as_hash
+
+  Example       : $translation_summary = $translation->summary_as_hash();
+  Description   : Retrieves a textual summary of this Translation.
+                  Not inherited from Feature.
+  Returns       : hashref of arrays of descriptive strings
+  Status        : Intended for internal use
+=cut
+
+sub summary_as_hash {
+  my $self = shift;
+  my %summary;
+  $summary{'display_id'} = $self->display_id;
+  $summary{'genomic_start'} = $self->genomic_start;
+  $summary{'genomic_end'} = $self->genomic_end;
+  my $transcript = $self->transcript;
+  $summary{'Parent'} = $transcript->display_id;
+  return \%summary;
+}
 
 1;

modules/Bio/EnsEMBL/Utils/Iterator.pm

@@ -135,7 +135,7 @@ sub new {
 
   Example    : $obj = $iterator->next
   Description: returns the next object from this iterator, or undef if the iterator is exhausted
-  Returntype : the return type will depend on what this iterator is iterating over
+  Returntype : Object type will depend on what this iterator is iterating over
   Exceptions : none
   Caller     : general
   Status     : Experimental
@@ -153,7 +153,7 @@ sub next {
 =head2 has_next
 
   Example    : if ($iterator->has_next) { my $obj = $iterator->next }
-  Description: returns true if this iterator has more elements to fetch, false when
+  Description: Boolean - true if this iterator has more elements to fetch, false when
                it is exhausted
   Returntype : boolean
   Exceptions : none
@@ -176,7 +176,7 @@ sub has_next {
   Description: returns the next object from this iterator, or undef if the iterator is exhausted,
                much like next but does not advance the iterator (so the same object will be 
                returned on the following call to next or peek)
-  Returntype : the return type will depend on what this iterator is iterating over
+  Returntype : Object type will depend on what this iterator is iterating over
   Exceptions : none
   Caller     : general
   Status     : Experimental
@@ -403,7 +403,7 @@ sub skip {
                first element in the set
   Argument[2]: (optional) an initial value to use for the accumulator instead 
                of the first value of the set
-  Returntype : the same as the return type of the coderef 
+  Returntype : returntype of the coderef 
   Exceptions : thrown if the argument is not a coderef
   Caller     : general
   Status     : Experimental