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revision 1.26, Mon Jan 30 21:57:02 2006 UTC revision 1.62, Sun Jul 30 05:44:57 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the usable subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for usability.
142                for my $sub (@subs) {
143                    if ($fig->usable_subsystem($sub)) {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 250  Line 261 
261              $loadGenome->Add("genomeIn");              $loadGenome->Add("genomeIn");
262              # The access code comes in via the genome hash.              # The access code comes in via the genome hash.
263              my $accessCode = $genomeHash->{$genomeID};              my $accessCode = $genomeHash->{$genomeID};
264              # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
             # the genome ID to the strain. In some cases this is the totality of the strain name.  
265              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266              my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
267              # Get the full taxonomy.              # Get the full taxonomy.
268              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
269              # Output the genome record.              # Output the genome record.
# Line 330  Line 340 
340      my $fig = $self->{fig};      my $fig = $self->{fig};
341      # Get the genome hash.      # Get the genome hash.
342      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
343      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
344      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
345      # Start the loads.      # Start the loads.
346      my $loadCoupling = $self->_TableLoader('Coupling');      my $loadCoupling = $self->_TableLoader('Coupling');
347      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
# Line 365  Line 375 
375                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
376                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
377                      # Compute the coupling ID.                      # Compute the coupling ID.
378                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
379                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
380                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
381                          # Here we have a new coupling to store in the load files.                          # Here we have a new coupling to store in the load files.
# Line 401  Line 411 
411                              }                              }
412                          }                          }
413                          for my $evidenceID (keys %evidenceMap) {                          for my $evidenceID (keys %evidenceMap) {
414                                # Get the ID for this evidence.
415                                $pchID++;
416                              # Create the evidence record.                              # Create the evidence record.
417                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
418                              $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
419                              # Connect it to the coupling.                              # Connect it to the coupling.
420                              $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
421                              # Connect it to the features.                              # Connect it to the features.
422                              $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
423                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
424                          }                          }
425                      }                      }
426                  }                  }
# Line 436  Line 448 
448      FeatureTranslation      FeatureTranslation
449      FeatureUpstream      FeatureUpstream
450      IsLocatedIn      IsLocatedIn
451        HasFeature
452    
453  =over 4  =over 4
454    
# Line 461  Line 474 
474      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
475      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
476      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
477        my $loadHasFeature = $self->_TableLoader('HasFeature');
478      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
479      # locations.      # locations.
480      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 474  Line 488 
488              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
489              # Get the feature list for this genome.              # Get the feature list for this genome.
490              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
491                # Sort and count the list.
492                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
493                my $count = scalar @featureTuples;
494                Trace("$count features found for genome $genomeID.") if T(3);
495                # Set up for our duplicate-feature check.
496                my $oldFeatureID = "";
497              # Loop through the features.              # Loop through the features.
498              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
499                  # Split the tuple.                  # Split the tuple.
500                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
501                    # Check for duplicates.
502                    if ($featureID eq $oldFeatureID) {
503                        Trace("Duplicate feature $featureID found.") if T(1);
504                    } else {
505                        $oldFeatureID = $featureID;
506                        # Count this feature.
507                        $loadFeature->Add("featureIn");
508                  # Create the feature record.                  # Create the feature record.
509                  $loadFeature->Put($featureID, 1, $type);                  $loadFeature->Put($featureID, 1, $type);
510                        # Link it to the parent genome.
511                        $loadHasFeature->Put($genomeID, $featureID, $type);
512                  # Create the aliases.                  # Create the aliases.
513                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
514                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
# Line 532  Line 560 
560              }              }
561          }          }
562      }      }
563        }
564      # Finish the loads.      # Finish the loads.
565      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
566      return $retVal;      return $retVal;
# Line 620  Line 649 
649  The following relations are loaded by this method.  The following relations are loaded by this method.
650    
651      Subsystem      Subsystem
652        SubsystemClass
653      Role      Role
654      RoleEC      RoleEC
655      SSCell      SSCell
# Line 682  Line 712 
712      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
713      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
714      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
715        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
716      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
717          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
718      } else {      } else {
# Line 697  Line 728 
728          my ($genomeID, $roleID);          my ($genomeID, $roleID);
729          my %roleData = ();          my %roleData = ();
730          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
731              # Get the subsystem object.              # Get the subsystem object.
732              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
733                # Only proceed if the subsystem has a spreadsheet.
734                if (! $sub->{empty_ss}) {
735                    Trace("Creating subsystem $subsysID.") if T(3);
736                    $loadSubsystem->Add("subsystemIn");
737              # Create the subsystem record.              # Create the subsystem record.
738              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
739              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
740              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
741                    my $class = $fig->subsystem_classification($subsysID);
742                    if ($class) {
743                        $loadSubsystemClass->Put($subsysID, $class);
744                    }
745              # Connect it to its roles. Each role is a column in the subsystem spreadsheet.              # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
746              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
747                  # Connect to this role.                  # Connect to this role.
# Line 748  Line 785 
785                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
786                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
787                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
788                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
789                          # Only proceed if features exist.                          # Only proceed if features exist.
790                          if (@pegs > 0) {                          if (@pegs > 0) {
791                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 769  Line 806 
806                      if ($pegCount > 0) {                      if ($pegCount > 0) {
807                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
808                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
809                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
810                          # We default to -1 for all of them.                          # We default to -1 for all of them.
811                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
812                                # Partition the PEGs found into clusters.
813                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
814                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
815                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
816                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 801  Line 838 
838                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
839                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
840                  # Connect the subset to its roles.                  # Connect the subset to its roles.
841                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
842                  for my $roleID (@roles) {                  for my $roleID (@roles) {
843                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
844                  }                  }
# Line 821  Line 858 
858                  }                  }
859              }              }
860          }          }
861            }
862          # Now we loop through the diagrams. We need to create the diagram records          # Now we loop through the diagrams. We need to create the diagram records
863          # and link each diagram to its roles. Note that only roles which occur          # and link each diagram to its roles. Note that only roles which occur
864          # in subsystems (and therefore appear in the %ecToRoles hash) are          # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 1015  Line 1053 
1053          # Loop through the genomes.          # Loop through the genomes.
1054          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1055              Trace("Processing $genomeID.") if T(3);              Trace("Processing $genomeID.") if T(3);
             # Get the genome's PEGs.  
             my @pegs = $fig->pegs_of($genomeID);  
             for my $peg (@pegs) {  
                 Trace("Processing $peg.") if T(4);  
1056                  # Create a hash of timestamps. We use this to prevent duplicate time stamps                  # Create a hash of timestamps. We use this to prevent duplicate time stamps
1057                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1058                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1059                  # Loop through the annotations.              # Get the genome's annotations.
1060                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1061                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1062                for my $tuple (@annotations) {
1063                    # Get the annotation tuple.
1064                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1065                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1066                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1067                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1068                      # stop the substitution search.                      # stop the substitution search.
1069                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1039  Line 1076 
1076                          # Here it's a number. We need to insure the one we use to form                          # Here it's a number. We need to insure the one we use to form
1077                          # the key is unique.                          # the key is unique.
1078                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1079                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1080                              $keyStamp++;                              $keyStamp++;
1081                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1082                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1083                        $seenTimestamps{$annotationID} = 1;
1084                          # Insure the user exists.                          # Insure the user exists.
1085                          if (! $users{$user}) {                          if (! $users{$user}) {
1086                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1061  Line 1098 
1098                  }                  }
1099              }              }
1100          }          }
     }  
1101      # Finish the load.      # Finish the load.
1102      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1103      return $retVal;      return $retVal;
# Line 1190  Line 1226 
1226      } else {      } else {
1227          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1228          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1229          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1230          my $orgLine;          my $orgLine;
1231          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1232              # Clean the input line.              # Clean the input line.
# Line 1202  Line 1238 
1238          close ORGS;          close ORGS;
1239          # Now the function file.          # Now the function file.
1240          my $funcLine;          my $funcLine;
1241          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1242          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1243              # Clean the line ending.              # Clean the line ending.
1244              chomp $funcLine;              chomp $funcLine;
# Line 1381  Line 1417 
1417      return $retVal;      return $retVal;
1418  }  }
1419    
1420    =head3 LoadSynonymData
1421    
1422    C<< my $stats = $spl->LoadSynonymData(); >>
1423    
1424    Load the synonym groups into Sprout.
1425    
1426    The following relations are loaded by this method.
1427    
1428        SynonymGroup
1429        IsSynonymGroupFor
1430    
1431    The source information for these relations is taken from the C<maps_to_id> method
1432    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1433    SQL against the FIG database.
1434    
1435    =over 4
1436    
1437    =item RETURNS
1438    
1439    Returns a statistics object for the loads.
1440    
1441    =back
1442    
1443    =cut
1444    #: Return Type $%;
1445    sub LoadSynonymData {
1446        # Get this object instance.
1447        my ($self) = @_;
1448        # Get the FIG object.
1449        my $fig = $self->{fig};
1450        # Get the genome hash.
1451        my $genomeHash = $self->{genomes};
1452        # Create a load object for the table we're loading.
1453        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1454        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1455        if ($self->{options}->{loadOnly}) {
1456            Trace("Loading from existing files.") if T(2);
1457        } else {
1458            Trace("Generating synonym group data.") if T(2);
1459            # Get the database handle.
1460            my $dbh = $fig->db_handle();
1461            # Ask for the synonyms.
1462            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1463            my $result = $sth->execute();
1464            if (! defined($result)) {
1465                Confess("Database error in Synonym load: " . $sth->errstr());
1466            } else {
1467                # Remember the current synonym.
1468                my $current_syn = "";
1469                # Count the features.
1470                my $featureCount = 0;
1471                # Loop through the synonym/peg pairs.
1472                while (my @row = $sth->fetchrow()) {
1473                    # Get the synonym ID and feature ID.
1474                    my ($syn_id, $peg) = @row;
1475                    # Insure it's for one of our genomes.
1476                    my $genomeID = FIG::genome_of($peg);
1477                    if (exists $genomeHash->{$genomeID}) {
1478                        # Verify the synonym.
1479                        if ($syn_id ne $current_syn) {
1480                            # It's new, so put it in the group table.
1481                            $loadSynonymGroup->Put($syn_id);
1482                            $current_syn = $syn_id;
1483                        }
1484                        # Connect the synonym to the peg.
1485                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1486                        # Count this feature.
1487                        $featureCount++;
1488                        if ($featureCount % 1000 == 0) {
1489                            Trace("$featureCount features processed.") if T(3);
1490                        }
1491                    }
1492                }
1493            }
1494        }
1495        # Finish the load.
1496        my $retVal = $self->_FinishAll();
1497        return $retVal;
1498    }
1499    
1500    =head3 LoadFamilyData
1501    
1502    C<< my $stats = $spl->LoadFamilyData(); >>
1503    
1504    Load the protein families into Sprout.
1505    
1506    The following relations are loaded by this method.
1507    
1508        Family
1509        ContainsFeature
1510    
1511    The source information for these relations is taken from the C<families_for_protein>,
1512    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1513    
1514    =over 4
1515    
1516    =item RETURNS
1517    
1518    Returns a statistics object for the loads.
1519    
1520    =back
1521    
1522    =cut
1523    #: Return Type $%;
1524    sub LoadFamilyData {
1525        # Get this object instance.
1526        my ($self) = @_;
1527        # Get the FIG object.
1528        my $fig = $self->{fig};
1529        # Get the genome hash.
1530        my $genomeHash = $self->{genomes};
1531        # Create load objects for the tables we're loading.
1532        my $loadFamily = $self->_TableLoader('Family');
1533        my $loadContainsFeature = $self->_TableLoader('ContainsFeature');
1534        if ($self->{options}->{loadOnly}) {
1535            Trace("Loading from existing files.") if T(2);
1536        } else {
1537            Trace("Generating family data.") if T(2);
1538            # Create a hash for the family IDs.
1539            my %familyHash = ();
1540            # Loop through the genomes.
1541            for my $genomeID (sort keys %{$genomeHash}) {
1542                Trace("Processing features for $genomeID.") if T(2);
1543                # Loop through this genome's PEGs.
1544                for my $fid ($fig->all_features($genomeID, "peg")) {
1545                    $loadContainsFeature->Add("features", 1);
1546                    # Get this feature's families.
1547                    my @families = $fig->families_for_protein($fid);
1548                    # Loop through the families, connecting them to the feature.
1549                    for my $family (@families) {
1550                        $loadContainsFeature->Put($family, $fid);
1551                        # If this is a new family, create a record for it.
1552                        if (! exists $familyHash{$family}) {
1553                            $familyHash{$family} = 1;
1554                            $loadFamily->Add("families", 1);
1555                            my $size = $fig->sz_family($family);
1556                            my $func = $fig->family_function($family);
1557                            $loadFamily->Put($family, $size, $func);
1558                        }
1559                    }
1560                }
1561            }
1562        }
1563        # Finish the load.
1564        my $retVal = $self->_FinishAll();
1565        return $retVal;
1566    }
1567    
1568  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1569    
1570  =head3 TableLoader  =head3 TableLoader
# Line 1448  Line 1632 
1632      my $retVal = Stats->new();      my $retVal = Stats->new();
1633      # Get the loader list.      # Get the loader list.
1634      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1635        # Create a hash to hold the statistics objects, keyed on relation name.
1636        my %loaderHash = ();
1637      # Loop through the list, finishing the loads. Note that if the finish fails, we die      # Loop through the list, finishing the loads. Note that if the finish fails, we die
1638      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads more restartable.
1639      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1640          # Get the relation name.          # Get the relation name.
1641          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1460  Line 1646 
1646              # Here we really need to finish.              # Here we really need to finish.
1647              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1648              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1649              if ($self->{options}->{dbLoad} && ! $loader->Ignore) {              $loaderHash{$relName} = $stats;
1650            }
1651        }
1652        # Now we loop through again, actually loading the tables. We want to finish before
1653        # loading so that if something goes wrong at this point, all the load files are usable
1654        # and we don't have to redo all that work.
1655        for my $relName (sort keys %loaderHash) {
1656            # Get the statistics for this relation.
1657            my $stats = $loaderHash{$relName};
1658            # Check for a database load.
1659            if ($self->{options}->{dbLoad}) {
1660                  # Here we want to use the load file just created to load the database.                  # Here we want to use the load file just created to load the database.
1661                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
1662                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
# Line 1470  Line 1666 
1666              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1667              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1668          }          }
     }  
1669      # Return the load statistics.      # Return the load statistics.
1670      return $retVal;      return $retVal;
1671  }  }
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