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revision 1.27, Wed Sep 14 12:56:13 2005 UTC revision 1.40, Wed Oct 12 03:12:24 2005 UTC
# Line 622  Line 622 
622          }          }
623          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
624          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
625            # Compute the initial base pair.
626            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
627          # Add the specifier to the list.          # Add the specifier to the list.
628          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
629      }      }
630      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
631      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 657  Line 659 
659      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
660      my ($location) = @_;      my ($location) = @_;
661      # Parse it into segments.      # Parse it into segments.
662      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
663      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
664      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
665      if ($dir eq "_") {      if ($dir eq "_") {
# Line 765  Line 767 
767          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
768          # before putting it in the return value.          # before putting it in the return value.
769          my ($start, $stop);          my ($start, $stop);
770            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
771          if ($dir eq "+") {          if ($dir eq "+") {
772              $start = $beg;              $start = $beg;
773              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
774          } else {          } else {
775              $start = $beg + $len + 1;              $start = $beg - $len + 1;
776              $stop = $beg;              $stop = $beg;
777          }          }
778            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
779          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
780              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
781              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 783  Line 787 
787                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
788                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
789              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
790                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
791              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
792              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
793              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
794                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
795              # Add the relevant data to the location data.              # Add the relevant data to the location data.
796              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
797          }          }
798          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
799          if ($dir eq '+') {          if ($dir eq '+') {
# Line 863  Line 869 
869      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
870      if ($sequence) {      if ($sequence) {
871          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
872          $retVal = $start + $len;          $retVal = $start + $len - 1;
873        }
874        # Return the result.
875        return $retVal;
876    }
877    
878    =head3 ClusterPEGs
879    
880    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
881    
882    Cluster the PEGs in a list according to the cluster coding scheme of the specified
883    subsystem. In order for this to work properly, the subsystem object must have
884    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
885    This causes the cluster numbers to be pulled into the subsystem's color hash.
886    If a PEG is not found in the color hash, it will not appear in the output
887    sequence.
888    
889    =over 4
890    
891    =item sub
892    
893    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
894    method.
895    
896    =item pegs
897    
898    Reference to the list of PEGs to be clustered.
899    
900    =item RETURN
901    
902    Returns a list of the PEGs, grouped into smaller lists by cluster number.
903    
904    =back
905    
906    =cut
907    #: Return Type $@@;
908    sub ClusterPEGs {
909        # Get the parameters.
910        my ($self, $sub, $pegs) = @_;
911        # Declare the return variable.
912        my $retVal = [];
913        # Loop through the PEGs, creating arrays for each cluster.
914        for my $pegID (@{$pegs}) {
915            my $clusterNumber = $sub->get_cluster_number($pegID);
916            # Only proceed if the PEG is in a cluster.
917            if ($clusterNumber >= 0) {
918                # Push this PEG onto the sub-list for the specified cluster number.
919                push @{$retVal->[$clusterNumber]}, $pegID;
920            }
921      }      }
922      # Return the result.      # Return the result.
923      return $retVal;      return $retVal;
# Line 1013  Line 1067 
1067    
1068  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1069    
1070  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1071    
1072  Return the annotations of a feature.  Return the annotations of a feature.
1073    
# Line 1023  Line 1077 
1077    
1078  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1079    
1080    =item rawFlag
1081    
1082    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1083    will be returned in human-readable form.
1084    
1085  =item RETURN  =item RETURN
1086    
1087  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1088    
1089  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1090    
1091  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1092    
1093  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1094    
# Line 1041  Line 1100 
1100  #: Return Type @%;  #: Return Type @%;
1101  sub FeatureAnnotations {  sub FeatureAnnotations {
1102      # Get the parameters.      # Get the parameters.
1103      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1104      # Create a query to get the feature's annotations and the associated users.      # Create a query to get the feature's annotations and the associated users.
1105      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1106                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1054  Line 1113 
1113              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1114                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1115                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1116            # Convert the time, if necessary.
1117            if (! $rawFlag) {
1118                $timeStamp = FriendlyTimestamp($timeStamp);
1119            }
1120          # Assemble them into a hash.          # Assemble them into a hash.
1121          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1122                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1123                                 user => $user, text => $text };                                 user => $user, text => $text };
1124          # Add it to the return list.          # Add it to the return list.
1125          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1260  Line 1323 
1323          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1324                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1325                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1326          # Look for the best hit.          # Peel off the BBHs found.
1327          my $bbh = $query->Fetch;          my @found = ();
1328          if ($bbh) {          while (my $bbh = $query->Fetch) {
1329              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1330          }          }
1331            $retVal{$featureID} = \@found;
1332      }      }
1333      # Return the mapping.      # Return the mapping.
1334      return \%retVal;      return \%retVal;
# Line 3148  Line 3211 
3211    
3212  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3213      my ($timeValue) = @_;      my ($timeValue) = @_;
3214      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3215      return $retVal;      return $retVal;
3216  }  }
3217    

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