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revision 1.4, Mon Nov 28 22:52:11 2005 UTC revision 1.8, Sun Jun 18 05:50:10 2006 UTC
# Line 222  Line 222 
222      my ($self, $gidx) = @_;      my ($self, $gidx) = @_;
223      # Extract the variant code for the specified row index. It is the second      # Extract the variant code for the specified row index. It is the second
224      # element of the tuple from the "genomes" member.      # element of the tuple from the "genomes" member.
225      my $retVal = $self->{genomes}->{$gidx}->[1];      my $retVal = $self->{genomes}->[$gidx]->[1];
226      return $retVal;      return $retVal;
227  }  }
228    
# Line 533  Line 533 
533          }          }
534      }      }
535      # Construct the spreadsheet cell ID from the information we have.      # Construct the spreadsheet cell ID from the information we have.
536      my $cellID = $self->{name} . ":$genomeID:$colIdx";      my $cellID = $sprout->DigestKey($self->{name} . ":$genomeID:$colIdx");
537      # Get the list of PEG IDs and cluster numbers for the indicated cell.      # Get the list of PEG IDs and cluster numbers for the indicated cell.
538      my @pegList = $sprout->GetAll(['ContainsFeature'], 'ContainsFeature(from-link) = ?',      my @pegList = $sprout->GetAll(['ContainsFeature'], 'ContainsFeature(from-link) = ?',
539                                    [$cellID], ['ContainsFeature(to-link)',                                    [$cellID], ['ContainsFeature(to-link)',
# Line 550  Line 550 
550      return @retVal;      return @retVal;
551  }  }
552    
553    
554    
555  =head3 get_diagrams  =head3 get_diagrams
556    
557  C<< my @list = $sub->get_diagrams(); >>  C<< my @list = $sub->get_diagrams(); >>
# Line 590  Line 592 
592      my ($self) = @_;      my ($self) = @_;
593      # Find the subsystem directory.      # Find the subsystem directory.
594      my $subDir = Subsystem::get_dir_from_name($self->{name});      my $subDir = Subsystem::get_dir_from_name($self->{name});
595        Trace("Subsystem directory is $subDir.") if T(3);
596      # Get the diagram IDs.      # Get the diagram IDs.
597      my @diagramIDs = Subsystem::GetDiagramIDs($subDir);      my @diagramIDs = Subsystem::GetDiagramIDs($subDir);
598        Trace("Diagram IDs are " . join(", ", @diagramIDs)) if T(3);
599      # Create the return variable.      # Create the return variable.
600      my @retVal = ();      my @retVal = ();
601      # Loop through the diagram IDs.      # Loop through the diagram IDs.
602      for my $diagramID (@diagramIDs) {      for my $diagramID (@diagramIDs) {
603            Trace("Processing diagram $diagramID.") if T(3);
604          # Get the diagram name.          # Get the diagram name.
605          my $name = Subsystem::GetDiagramName($diagramID);          my $name = Subsystem::GetDiagramName($subDir, $diagramID);
606          # If a name was found, get the URLs.          Trace("Diagram name is $name.") if T(3);
607          if ($name) {          # Get the URLs.
608              my ($link, $imgLink) = Subsystem::ComputeDiagramURLs($self->{name},              my ($link, $imgLink) = Subsystem::ComputeDiagramURLs($self->{name},
609                                                                   $diagramID);                                                                   $diagramID);
610            Trace("Diagram URLs are \"$link\" and \"$imgLink\".") if T(3);
611              push @retVal, [$diagramID, $name, $link, $imgLink];              push @retVal, [$diagramID, $name, $link, $imgLink];
612          }          }
613      }      # Return the result.
614        return @retVal;
615  }  }
616    
617    

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