Subroutine store() formatted for readability.

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

@@ -138,89 +138,100 @@ sub _columns {
 =cut
 
 sub store {
-  my ($self, @feats) = @_;
+  my ( $self, @feats ) = @_;
 
-  throw("Must call store with features") if( scalar(@feats) == 0 );
+  throw("Must call store with features") if ( scalar(@feats) == 0 );
 
   my @tabs = $self->_tables;
-  my ($tablename) = @{$tabs[0]};
+  my ($tablename) = @{ $tabs[0] };
 
-  my $db = $self->db();
+  my $db               = $self->db();
   my $analysis_adaptor = $db->get_AnalysisAdaptor();
 
   my $sth = $self->prepare(
-     "INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
-                             seq_region_strand, hit_start, hit_end,
-                             hit_strand, hit_name, cigar_line,
-                             analysis_id, score, evalue, perc_ident, external_db_id, 
-                             hcoverage, pair_dna_align_feature_id)
-     VALUES (?,?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?, ?)");
-
- FEATURE: foreach my $feat ( @feats ) {
-    if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
+    "INSERT INTO $tablename (seq_region_id, seq_region_start,
+                             seq_region_end, seq_region_strand,
+                             hit_start, hit_end, hit_strand, hit_name,
+                             cigar_line, analysis_id, score, evalue,
+                             perc_ident, external_db_id, hcoverage,
+                             pair_dna_align_feature_id)
+     VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)"    # 16 arguments
+  );
+
+FEATURE:
+  foreach my $feat (@feats) {
+    if ( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") )
+    {
       throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature,"
-            . " not a [".ref($feat)."].");
+          . " not a ["
+          . ref($feat)
+          . "]." );
     }
 
-    if($feat->is_stored($db)) {
-      warning("DnaDnaAlignFeature [".$feat->dbID."] is already stored" .
-              " in this database.");
+    if ( $feat->is_stored($db) ) {
+      warning( "DnaDnaAlignFeature ["
+          . $feat->dbID()
+          . "] is already stored in this database." );
       next FEATURE;
     }
 
-    my $hstart = $feat->hstart();
-    my $hend   = $feat->hend();
+    my $hstart  = $feat->hstart();
+    my $hend    = $feat->hend();
     my $hstrand = $feat->hstrand();
-    $self->_check_start_end_strand($hstart,$hend, $hstrand);
+    $self->_check_start_end_strand( $hstart, $hend, $hstrand );
 
     my $cigar_string = $feat->cigar_string();
-    if(!$cigar_string) {
+    if ( !$cigar_string ) {
       $cigar_string = $feat->length() . 'M';
-      warning("DnaDnaAlignFeature does not define a cigar_string.\n" .
-              "Assuming ungapped block with cigar_line=$cigar_string .");
+      warning( "DnaDnaAlignFeature does not define a cigar_string.\n"
+          . "Assuming ungapped block with cigar_line=$cigar_string ." );
     }
 
     my $hseqname = $feat->hseqname();
-    if(!$hseqname) {
+    if ( !$hseqname ) {
       throw("DnaDnaAlignFeature must define an hseqname.");
     }
 
-    if(!defined($feat->analysis)) {
-      throw("An analysis must be attached to the features to be stored.");
+    if ( !defined( $feat->analysis ) ) {
+      throw(
+        "An analysis must be attached to the features to be stored.");
     }
 
     #store the analysis if it has not been stored yet
-    if(!$feat->analysis->is_stored($db)) {
-      $analysis_adaptor->store($feat->analysis());
+    if ( !$feat->analysis->is_stored($db) ) {
+      $analysis_adaptor->store( $feat->analysis() );
     }
 
     my $original = $feat;
     my $seq_region_id;
-    ($feat, $seq_region_id) = $self->_pre_store($feat);
-    $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
-    $sth->bind_param(2,$feat->start,SQL_INTEGER);
-    $sth->bind_param(3,$feat->end,SQL_INTEGER);
-    $sth->bind_param(4,$feat->strand,SQL_TINYINT);
-    $sth->bind_param(5,$hstart,SQL_INTEGER);
-    $sth->bind_param(6,$hend,SQL_INTEGER);
-    $sth->bind_param(7,$hstrand,SQL_TINYINT);
-    $sth->bind_param(8,$hseqname,SQL_VARCHAR);
-    $sth->bind_param(9,$cigar_string,SQL_LONGVARCHAR);
-    $sth->bind_param(10,$feat->analysis->dbID,SQL_INTEGER);
-    $sth->bind_param(11,$feat->score,SQL_DOUBLE);
-    $sth->bind_param(12,$feat->p_value,SQL_DOUBLE);
-    $sth->bind_param(13,$feat->percent_id,SQL_FLOAT);
-    $sth->bind_param(14,$feat->external_db_id,SQL_INTEGER);
-    $sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE);
-    $sth->bind_param(16,$feat->pair_dna_align_feature_id, SQL_INTEGER);
+    ( $feat, $seq_region_id ) = $self->_pre_store($feat);
+
+    $sth->bind_param( 1,  $seq_region_id,        SQL_INTEGER );
+    $sth->bind_param( 2,  $feat->start,          SQL_INTEGER );
+    $sth->bind_param( 3,  $feat->end,            SQL_INTEGER );
+    $sth->bind_param( 4,  $feat->strand,         SQL_TINYINT );
+    $sth->bind_param( 5,  $hstart,               SQL_INTEGER );
+    $sth->bind_param( 6,  $hend,                 SQL_INTEGER );
+    $sth->bind_param( 7,  $hstrand,              SQL_TINYINT );
+    $sth->bind_param( 8,  $hseqname,             SQL_VARCHAR );
+    $sth->bind_param( 9,  $cigar_string,         SQL_LONGVARCHAR );
+    $sth->bind_param( 10, $feat->analysis->dbID, SQL_INTEGER );
+    $sth->bind_param( 11, $feat->score,          SQL_DOUBLE );
+    $sth->bind_param( 12, $feat->p_value,        SQL_DOUBLE );
+    $sth->bind_param( 13, $feat->percent_id,     SQL_FLOAT );
+    $sth->bind_param( 14, $feat->external_db_id, SQL_INTEGER );
+    $sth->bind_param( 15, $feat->hcoverage,      SQL_DOUBLE );
+    $sth->bind_param( 16, $feat->pair_dna_align_feature_id,
+      SQL_INTEGER );
 
     $sth->execute();
-    $original->dbID($sth->{'mysql_insertid'});
+
+    $original->dbID( $sth->{'mysql_insertid'} );
     $original->adaptor($self);
-  }
+  } ## end foreach my $feat (@feats)
 
   $sth->finish();
-}
+} ## end sub store
 
 
 sub save {