[Bio] / Sprout / Sprout.pm Repository:
ViewVC logotype

Diff of /Sprout/Sprout.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.20, Wed Aug 24 19:31:20 2005 UTC revision 1.47, Thu Oct 20 12:02:43 2005 UTC
# Line 70  Line 70 
70    
71  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
72    
73    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
74    
75  =back  =back
76    
77  For example, the following constructor call specifies a database named I<Sprout> and a user name of  For example, the following constructor call specifies a database named I<Sprout> and a user name of
# Line 98  Line 100 
100                                                          # database connection port                                                          # database connection port
101                         maxSegmentLength => 4500,        # maximum feature segment length                         maxSegmentLength => 4500,        # maximum feature segment length
102                         maxSequenceLength => 8000,       # maximum contig sequence length                         maxSequenceLength => 8000,       # maximum contig sequence length
103                           noDBOpen     => 0,               # 1 to suppress the database open
104                        }, $options);                        }, $options);
105      # Get the data directory.      # Get the data directory.
106      my $dataDir = $optionTable->{dataDir};      my $dataDir = $optionTable->{dataDir};
# Line 105  Line 108 
108      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
109      my ($userName, $password) = ($1, $2);      my ($userName, $password) = ($1, $2);
110      # Connect to the database.      # Connect to the database.
111      my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
112        if (! $optionTable->{noDBOpen}) {
113            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
114                                    $password, $optionTable->{port});
115        }
116      # Create the ERDB object.      # Create the ERDB object.
117      my $xmlFileName = "$optionTable->{xmlFileName}";      my $xmlFileName = "$optionTable->{xmlFileName}";
118      my $erdb = ERDB->new($dbh, $xmlFileName);      my $erdb = ERDB->new($dbh, $xmlFileName);
# Line 382  Line 389 
389    
390  =head3 LoadUpdate  =head3 LoadUpdate
391    
392  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
393    
394  Load updates to one or more database tables. This method enables the client to make changes to one  Load updates to one or more database tables. This method enables the client to make changes to one
395  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 603  Line 610 
610          if ($prevContig eq $contigID && $dir eq $prevDir) {          if ($prevContig eq $contigID && $dir eq $prevDir) {
611              # Here the new segment is in the same direction on the same contig. Insure the              # Here the new segment is in the same direction on the same contig. Insure the
612              # new segment's beginning is next to the old segment's end.              # new segment's beginning is next to the old segment's end.
613              if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
614                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
615                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
616                  # to include both segments.                  $len += $prevLen;
617                    # Pop the old segment off. The new one will replace it later.
618                    pop @retVal;
619                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
620                    # Here we need to merge two forward blocks. Adjust the beginning and
621                    # length values to include both segments.
622                  $beg = $prevBeg;                  $beg = $prevBeg;
623                  $len += $prevLen;                  $len += $prevLen;
624                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 615  Line 627 
627          }          }
628          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
629          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
630            # Compute the initial base pair.
631            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
632          # Add the specifier to the list.          # Add the specifier to the list.
633          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
634      }      }
635      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
636      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 650  Line 664 
664      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
665      my ($location) = @_;      my ($location) = @_;
666      # Parse it into segments.      # Parse it into segments.
667      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
668      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
669      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
670      if ($dir eq "_") {      if ($dir eq "_") {
# Line 758  Line 772 
772          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
773          # before putting it in the return value.          # before putting it in the return value.
774          my ($start, $stop);          my ($start, $stop);
775            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
776          if ($dir eq "+") {          if ($dir eq "+") {
777              $start = $beg;              $start = $beg;
778              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
779          } else {          } else {
780              $start = $beg + $len + 1;              $start = $beg - $len + 1;
781              $stop = $beg;              $stop = $beg;
782          }          }
783            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
784          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
785              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
786              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 776  Line 792 
792                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
793                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
794              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
795                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
796              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
797              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
798              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
799                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
800              # Add the relevant data to the location data.              # Add the relevant data to the location data.
801              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
802          }          }
803          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
804          if ($dir eq '+') {          if ($dir eq '+') {
805              $retVal .= $locationDNA;              $retVal .= $locationDNA;
806          } else {          } else {
807              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
808          }          }
809      }      }
810      # Return the result.      # Return the result.
# Line 857  Line 874 
874      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
875      if ($sequence) {      if ($sequence) {
876          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
877          $retVal = $start + $len;          $retVal = $start + $len - 1;
878        }
879        # Return the result.
880        return $retVal;
881    }
882    
883    =head3 ClusterPEGs
884    
885    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
886    
887    Cluster the PEGs in a list according to the cluster coding scheme of the specified
888    subsystem. In order for this to work properly, the subsystem object must have
889    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
890    This causes the cluster numbers to be pulled into the subsystem's color hash.
891    If a PEG is not found in the color hash, it will not appear in the output
892    sequence.
893    
894    =over 4
895    
896    =item sub
897    
898    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
899    method.
900    
901    =item pegs
902    
903    Reference to the list of PEGs to be clustered.
904    
905    =item RETURN
906    
907    Returns a list of the PEGs, grouped into smaller lists by cluster number.
908    
909    =back
910    
911    =cut
912    #: Return Type $@@;
913    sub ClusterPEGs {
914        # Get the parameters.
915        my ($self, $sub, $pegs) = @_;
916        # Declare the return variable.
917        my $retVal = [];
918        # Loop through the PEGs, creating arrays for each cluster.
919        for my $pegID (@{$pegs}) {
920            my $clusterNumber = $sub->get_cluster_number($pegID);
921            # Only proceed if the PEG is in a cluster.
922            if ($clusterNumber >= 0) {
923                # Push this PEG onto the sub-list for the specified cluster number.
924                push @{$retVal->[$clusterNumber]}, $pegID;
925            }
926      }      }
927      # Return the result.      # Return the result.
928      return $retVal;      return $retVal;
# Line 1007  Line 1072 
1072    
1073  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1074    
1075  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1076    
1077  Return the annotations of a feature.  Return the annotations of a feature.
1078    
# Line 1017  Line 1082 
1082    
1083  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1084    
1085    =item rawFlag
1086    
1087    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1088    will be returned in human-readable form.
1089    
1090  =item RETURN  =item RETURN
1091    
1092  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1093    
1094  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1095    
1096  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1097    
1098  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1099    
# Line 1035  Line 1105 
1105  #: Return Type @%;  #: Return Type @%;
1106  sub FeatureAnnotations {  sub FeatureAnnotations {
1107      # Get the parameters.      # Get the parameters.
1108      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1109      # 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.
1110      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1111                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1048  Line 1118 
1118              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1119                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1120                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1121            # Convert the time, if necessary.
1122            if (! $rawFlag) {
1123                $timeStamp = FriendlyTimestamp($timeStamp);
1124            }
1125          # Assemble them into a hash.          # Assemble them into a hash.
1126          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1127                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1128                                 user => $user, text => $text };                                 user => $user, text => $text };
1129          # Add it to the return list.          # Add it to the return list.
1130          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1079  Line 1153 
1153    
1154  =item RETURN  =item RETURN
1155    
1156  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1157    
1158  =back  =back
1159    
# Line 1089  Line 1163 
1163      # Get the parameters.      # Get the parameters.
1164      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1165      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1166      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1167                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1168                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1169                                               'MadeAnnotation(from-link)']);
1170      # Declare the return hash.      # Declare the return hash.
1171      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1172      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1173      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1174      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1175      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1176          # Get the annotation fields.          # Get the annotation fields.
1177          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1178          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1179          my ($user, $function) = _ParseAssignment($text);          my ($type, $function) = _ParseAssignment($text);
1180          if ($user && ! exists $timeHash{$user}) {          if ($type && ! exists $retVal{$user}) {
1181              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1182              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1183              # return hash.              # return hash.
1184              $retVal{$function} = $user;              $retVal{$user} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1185          }          }
1186      }      }
1187      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1126  Line 1197 
1197  The functional assignment is handled differently depending on the type of feature. If  The functional assignment is handled differently depending on the type of feature. If
1198  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1199  assignment is a type of annotation. The format of an assignment is described in  assignment is a type of annotation. The format of an assignment is described in
1200  L</ParseLocation>. Its worth noting that we cannot filter on the content of the  L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1201  annotation itself because it's a text field; however, this is not a big problem because  annotation itself because it's a text field; however, this is not a big problem because
1202  most features only have a small number of annotations.  most features only have a small number of annotations.
1203    
# Line 1217  Line 1288 
1288      return $retVal;      return $retVal;
1289  }  }
1290    
1291    =head3 FunctionsOf
1292    
1293    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1294    
1295    Return the functional assignments of a particular feature.
1296    
1297    The functional assignment is handled differently depending on the type of feature. If
1298    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1299    assignment is a type of annotation. The format of an assignment is described in
1300    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1301    annotation itself because it's a text field; however, this is not a big problem because
1302    most features only have a small number of annotations.
1303    
1304    If the feature is B<not> identified by a FIG ID, then the functional assignment
1305    information is taken from the B<ExternalAliasFunc> table. If the table does
1306    not contain an entry for the feature, an empty list is returned.
1307    
1308    =over 4
1309    
1310    =item featureID
1311    
1312    ID of the feature whose functional assignments are desired.
1313    
1314    =item RETURN
1315    
1316    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1317    that user.
1318    
1319    =back
1320    
1321    =cut
1322    #: Return Type @@;
1323    sub FunctionsOf {
1324        # Get the parameters.
1325        my ($self, $featureID) = @_;
1326        # Declare the return value.
1327        my @retVal = ();
1328        # Determine the ID type.
1329        if ($featureID =~ m/^fig\|/) {
1330            # Here we have a FIG feature ID. We must build the list of trusted
1331            # users.
1332            my %trusteeTable = ();
1333            # Build a query for all of the feature's annotations, sorted by date.
1334            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],
1335                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1336                                   [$featureID]);
1337            my $timeSelected = 0;
1338            # Loop until we run out of annotations.
1339            while (my $annotation = $query->Fetch()) {
1340                # Get the annotation text.
1341                my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);
1342                # Check to see if this is a functional assignment for a trusted user.
1343                my ($user, $function) = _ParseAssignment($text);
1344                if ($user) {
1345                    # Here it is a functional assignment.
1346                    push @retVal, [$user, $function];
1347                }
1348            }
1349        } else {
1350            # Here we have a non-FIG feature ID. In this case the user ID does not
1351            # matter. We simply get the information from the External Alias Function
1352            # table.
1353            push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1354        }
1355        # Return the assignments found.
1356        return @retVal;
1357    }
1358    
1359  =head3 BBHList  =head3 BBHList
1360    
1361  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1254  Line 1393 
1393          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1394                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1395                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1396          # Look for the best hit.          # Peel off the BBHs found.
1397          my $bbh = $query->Fetch;          my @found = ();
1398          if ($bbh) {          while (my $bbh = $query->Fetch) {
1399              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1400          }          }
1401            $retVal{$featureID} = \@found;
1402      }      }
1403      # Return the mapping.      # Return the mapping.
1404      return \%retVal;      return \%retVal;
# Line 1521  Line 1660 
1660          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1661          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1662          # we want feature 1 before feature 2 (normal).          # we want feature 1 before feature 2 (normal).
1663            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1664          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1665          # Get the coupling evidence.          # Get the coupling evidence.
1666          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
# Line 1534  Line 1674 
1674          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1675              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1676              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1677                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1678              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1679          }          }
1680            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1681      }      }
1682      # Return the result.      # Return the result.
1683      return @retVal;      return @retVal;
# Line 1585  Line 1727 
1727                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1728      # Check to see if we found anything.      # Check to see if we found anything.
1729      if (!@pegs) {      if (!@pegs) {
1730            Trace("No coupling found.") if T(Coupling => 4);
1731          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1732          $retVal = undef;          $retVal = undef;
1733      } else {      } else {
1734          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1735          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1736          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1737            $inverted = ($firstFound ne $peg1);
1738            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1739      }      }
1740      # Return the result.      # Return the result.
1741      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1695  Line 1840 
1840          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1841              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1842              if ($id) {              if ($id) {
1843                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1844              }              }
1845              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1846              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1847          } else {          } else {
1848              # Here we have a data line, so we add it to the sequence accumulator.              # Here we have a data line, so we add it to the sequence accumulator.
1849              # First, we get the actual data out. Note that we normalize to upper              # First, we get the actual data out. Note that we normalize to lower
1850              # case.              # case.
1851              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1852              $sequence .= $1;              $sequence .= $1;
# Line 1709  Line 1854 
1854      }      }
1855      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1856      if ($sequence) {      if ($sequence) {
1857          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1858      }      }
1859      # Close the file.      # Close the file.
1860      close FASTAFILE;      close FASTAFILE;
# Line 2035  Line 2180 
2180      # Get the parameters.      # Get the parameters.
2181      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2182      # Check for the entity instance.      # Check for the entity instance.
2183        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2184      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2185      # Return an existence indicator.      # Return an existence indicator.
2186      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2528  Line 2674 
2674                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2675      # Create the return value.      # Create the return value.
2676      my %retVal = ();      my %retVal = ();
2677        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2678        # in two spreadsheet cells.
2679        my %dupHash = ();
2680      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2681      for my $record (@subsystems) {      for my $record (@subsystems) {
2682            # Get this subsystem and role.
2683          my ($subsys, $role) = @{$record};          my ($subsys, $role) = @{$record};
2684          if (exists $retVal{$subsys}) {          # Insure it's the first time for both.
2685            my $dupKey = "$subsys\n$role";
2686            if (! exists $dupHash{"$subsys\n$role"}) {
2687                $dupHash{$dupKey} = 1;
2688              push @{$retVal{$subsys}}, $role;              push @{$retVal{$subsys}}, $role;
         } else {  
             $retVal{$subsys} = [$role];  
2689          }          }
2690      }      }
2691      # Return the hash.      # Return the hash.
# Line 3103  Line 3254 
3254      # Declare the return value.      # Declare the return value.
3255      my @retVal = ();      my @retVal = ();
3256      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3257      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3258      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set ([^ ]+) function to$/i) {
3259          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here it is, so we return the user name (which is in $1), the functional role text,
3260          # and the assigning user.          # and the assigning user.
3261          @retVal = ($1, $function, $user);          @retVal = ($1, $function);
3262      }      }
3263      # Return the result list.      # Return the result list.
3264      return @retVal;      return @retVal;
# Line 3135  Line 3286 
3286    
3287  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3288      my ($timeValue) = @_;      my ($timeValue) = @_;
3289      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3290      return $retVal;      return $retVal;
3291  }  }
3292    

Legend:
Removed from v.1.20  
changed lines
  Added in v.1.47

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3