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revision 1.121, Wed Oct 15 11:46:22 2008 UTC revision 1.122, Mon Jan 19 21:46:21 2009 UTC
# Line 4  Line 4 
4      use strict;      use strict;
5      use DBKernel;      use DBKernel;
6      use XML::Simple;      use XML::Simple;
7      use DBQuery;      use ERDBQuery;
8      use ERDBObject;      use ERDBObject;
9      use Tracer;      use Tracer;
10      use FIGRules;      use FIGRules;
# Line 14  Line 14 
14      use BasicLocation;      use BasicLocation;
15      use CustomAttributes;      use CustomAttributes;
16      use RemoteCustomAttributes;      use RemoteCustomAttributes;
17      use CGI;      use CGI qw(-nosticky);
18      use WikiTools;      use WikiTools;
19      use BioWords;      use BioWords;
20      use base qw(ERDB);      use base qw(ERDB);
# Line 41  Line 41 
41    
42  =cut  =cut
43    
 #: Constructor SFXlate->new_sprout_only();  
   
44  =head2 Public Methods  =head2 Public Methods
45    
46  =head3 new  =head3 new
# Line 91  Line 89 
89    
90      my $sprout = Sprout->new('Sprout', { userData => 'fig/admin', dataDir => '/usr/fig/SproutData' });      my $sprout = Sprout->new('Sprout', { userData => 'fig/admin', dataDir => '/usr/fig/SproutData' });
91    
92    In order to work properly with [[ERDBGeneratorPl]], the constructor has an alternate
93    form.
94    
95        my $sprout = Sprout->new(dbd => $filename);
96    
97    Where I<$fileName> is the name of the DBD file. This enables us to specify an alternate
98    DBD for the loader, which is important when the database format changes.
99    
100  =cut  =cut
101    
102  sub new {  sub new {
103      # Get the parameters.      # Get the parameters.
104      my ($class, $dbName, $options) = @_;      my ($class, $dbName, $options) = @_;
105      # Default the database name if it is missing.      # Check for the alternate signature, and default the database name if it is missing.
106      if (! defined $dbName) {      if ($dbName eq 'dbd') {
107            $dbName = $FIG_Config::sproutDB;
108            $options = { xmlFileName => $options };
109        } elsif (! defined $dbName) {
110          $dbName = $FIG_Config::sproutDB;          $dbName = $FIG_Config::sproutDB;
111      } elsif (ref $dbName eq 'HASH') {      } elsif (ref $dbName eq 'HASH') {
112          $options = $dbName;          $options = $dbName;
# Line 145  Line 154 
154      $retVal->{_xmlName} = $xmlFileName;      $retVal->{_xmlName} = $xmlFileName;
155      # Set up space for the group file data.      # Set up space for the group file data.
156      $retVal->{groupHash} = undef;      $retVal->{groupHash} = undef;
157      # Set up space for the genome hash. We use this to identify NMPDR genomes.      # Set up space for the genome hash. We use this to identify NMPDR genomes
158      $retVal->{genomeHash} = undef;      # and remember genome data.
159        $retVal->{genomeHash} = {};
160        $retVal->{genomeHashFilled} = 0;
161      # Remember the data directory name.      # Remember the data directory name.
162      $retVal->{dataDir} = $dataDir;      $retVal->{dataDir} = $dataDir;
163      # Return it.      # Return it.
# Line 342  Line 353 
353  The files are loaded based on the presumption that each line of the file is a record in the  The files are loaded based on the presumption that each line of the file is a record in the
354  relation, and the individual fields are delimited by tabs. Tab and new-line characters inside  relation, and the individual fields are delimited by tabs. Tab and new-line characters inside
355  fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must  fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must
356  be presented in the order given in the relation tables produced by the L</ShowMetaData> method.  be presented in the order given in the relation tables produced by the database documentation.
357    
358  =over 4  =over 4
359    
# Line 531  Line 542 
542  =item filter  =item filter
543    
544  If specified, a filter for the list of genomes to display. The filter should be in the form of a  If specified, a filter for the list of genomes to display. The filter should be in the form of a
545  list reference. The first element of the list should be the filter string, and the remaining elements  list reference, a string, or a hash reference. If it is a list reference, the first element
546  the filter parameters.  of the list should be the filter string, and the remaining elements the filter parameters. If it is a
547    string, it will be split into a list at each included tab. If it is a hash reference, it should be
548    a hash that maps genomes which should be included to a TRUE value.
549    
550  =item multiSelect  =item multiSelect
551    
# Line 571  Line 584 
584      my $divID = "${menuID}_status";      my $divID = "${menuID}_status";
585      my $urlID = "${menuID}_url";      my $urlID = "${menuID}_url";
586      # Compute the code to show selected genomes in the status area.      # Compute the code to show selected genomes in the status area.
587      my $showSelect = "showSelected('$menuID', '$divID', '$urlID', 1000)";      my $showSelect = "showSelected('$menuID', '$divID', '$urlID', $FIG_Config::genome_control_cap)";
588      # Check for single-select or multi-select.      # Check for single-select or multi-select.
589      my $multiSelect = $options{multiSelect} || 0;      my $multiSelect = $options{multiSelect} || 0;
590      # Get the style data.      # Get the style data.
# Line 583  Line 596 
596      }      }
597      my %selected = map { $_ => 1 } @{$selections};      my %selected = map { $_ => 1 } @{$selections};
598      # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited      # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited
599      # string or a list reference.      # string, a hash reference, or a list reference.
600        my ($filterHash, $filterString);
601      my $filterParms = $options{filter} || "";      my $filterParms = $options{filter} || "";
602        if (ref $filterParms eq 'HASH') {
603            $filterHash = $filterParms;
604            $filterParms = [];
605            $filterString = "";
606        } else {
607      if (! ref $filterParms) {      if (! ref $filterParms) {
608          $filterParms = [split /\t|\\t/, $filterParms];          $filterParms = [split /\t|\\t/, $filterParms];
609      }      }
610      my $filterString = shift @{$filterParms};          $filterString = shift @{$filterParms};
611        }
612        # Check for possible subsystem filtering. If there is one, we will tack the
613        # relationship onto the object name list.
614        my @objectNames = qw(Genome);
615        if ($filterString =~ /ParticipatesIn\(/) {
616            push @objectNames, 'ParticipatesIn';
617        }
618      # Get a list of all the genomes in group order. In fact, we only need them ordered      # Get a list of all the genomes in group order. In fact, we only need them ordered
619      # by name (genus,species,strain), but putting primary-group in front enables us to      # by name (genus,species,strain), but putting primary-group in front enables us to
620      # take advantage of an existing index.      # take advantage of an existing index.
621      my @genomeList = $self->GetAll(['Genome'], "$filterString ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",      my @genomeList = $self->GetAll(\@objectNames, "$filterString ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",
622                                     $filterParms,                                     $filterParms,
623                                     [qw(Genome(primary-group) Genome(id) Genome(genus) Genome(species) Genome(unique-characterization) Genome(taxonomy) Genome(contigs))]);                                     [qw(Genome(primary-group) Genome(id) Genome(genus) Genome(species) Genome(unique-characterization) Genome(taxonomy) Genome(contigs))]);
624        # Apply the hash filter (if any).
625        if (defined $filterHash) {
626            @genomeList = grep { $filterHash->{$_->[1]} } @genomeList;
627        }
628      # Create a hash to organize the genomes by group. Each group will contain a list of      # Create a hash to organize the genomes by group. Each group will contain a list of
629      # 2-tuples, the first element being the genome ID and the second being the genome      # 2-tuples, the first element being the genome ID and the second being the genome
630      # name.      # name.
# Line 624  Line 654 
654      my @groups = map { $sortGroups{$_} } sort keys %sortGroups;      my @groups = map { $sortGroups{$_} } sort keys %sortGroups;
655      # Remember the number of NMPDR groups.      # Remember the number of NMPDR groups.
656      my $nmpdrGroupCount = scalar @groups;      my $nmpdrGroupCount = scalar @groups;
657        # Are there any supporting genomes?
658        if (exists $gHash{$FIG_Config::otherGroup}) {
659      # Loop through the supporting genomes, classifying them by domain. We'll also keep a list      # Loop through the supporting genomes, classifying them by domain. We'll also keep a list
660      # of the domains found.      # of the domains found.
661      my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};      my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};
# Line 642  Line 674 
674      push @groups, sort @domains;      push @groups, sort @domains;
675      # Delete the supporting group.      # Delete the supporting group.
676      delete $gHash{$FIG_Config::otherGroup};      delete $gHash{$FIG_Config::otherGroup};
677        }
678      # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage      # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
679      # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes      # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
680      # and use that to make the selections.      # and use that to make the selections.
# Line 813  Line 846 
846  sub GenusSpecies {  sub GenusSpecies {
847      # Get the parameters.      # Get the parameters.
848      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
849      # Get the data for the specified genome.      # Declare the return value.
850      my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',      my $retVal;
851                                                                'Genome(unique-characterization)']);      # Get the genome data.
852      # Format the result and return it.      my $genomeData = $self->_GenomeData($genomeID);
853      my $retVal = join(' ', @values);      # Only proceed if we found the genome.
854        if (defined $genomeData) {
855            $retVal = $genomeData->PrimaryValue('Genome(scientific-name)');
856        }
857        # Return it.
858      return $retVal;      return $retVal;
859  }  }
860    
# Line 1155  Line 1192 
1192      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
1193      # Declare the return variable.      # Declare the return variable.
1194      my $retVal = 0;      my $retVal = 0;
1195      # Get the genome's contig sequence lengths.      # Get the genome data.
1196      my @lens = $self->GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',      my $genomeData = $self->_GenomeData($genomeID);
1197                         [$genomeID], 'IsMadeUpOf(len)');      # Only proceed if it exists.
1198      # Sum the lengths.      if (defined $genomeData) {
1199      map { $retVal += $_ } @lens;          $retVal = $genomeData->PrimaryValue('Genome(dna-size)');
1200        }
1201      # Return the result.      # Return the result.
1202      return $retVal;      return $retVal;
1203  }  }
# Line 1826  Line 1864 
1864      # Loop through the incoming features.      # Loop through the incoming features.
1865      for my $featureID (@{$featureList}) {      for my $featureID (@{$featureList}) {
1866          # Ask the server for the feature's best hit.          # Ask the server for the feature's best hit.
1867          my @bbhData = FIGRules::BBHData($featureID);          my $bbhData = FIGRules::BBHData($featureID);
1868          # Peel off the BBHs found.          # Peel off the BBHs found.
1869          my @found = ();          my @found = ();
1870          for my $bbh (@bbhData) {          for my $bbh (@$bbhData) {
1871              my $fid = $bbh->[0];              my $fid = $bbh->[0];
1872              my $bbGenome = $self->GenomeOf($fid);              my $bbGenome = $self->GenomeOf($fid);
1873              if ($bbGenome eq $genomeID) {              if ($bbGenome eq $genomeID) {
# Line 1868  Line 1906 
1906      # Get the parameters.      # Get the parameters.
1907      my ($self, $featureID, $count) = @_;      my ($self, $featureID, $count) = @_;
1908      # Ask for the best hits.      # Ask for the best hits.
1909      my @lists = FIGRules::BBHData($featureID);      my $lists = FIGRules::BBHData($featureID);
1910      # Create the return value.      # Create the return value.
1911      my %retVal = ();      my %retVal = ();
1912      for my $tuple (@lists) {      for my $tuple (@$lists) {
1913          $retVal{$tuple->[0]} = $tuple->[1];          $retVal{$tuple->[0]} = $tuple->[1];
1914      }      }
1915      # Return the result.      # Return the result.
# Line 1905  Line 1943 
1943      # Declare the return variable.      # Declare the return variable.
1944      my $retVal;      my $retVal;
1945      # Get the genome's data.      # Get the genome's data.
1946      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->_GenomeData($genomeID);
1947      if ($genomeData) {      # Only proceed if it exists.
1948        if (defined $genomeData) {
1949          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1950          $retVal = $genomeData->PrimaryValue('Genome(complete)');          $retVal = $genomeData->PrimaryValue('Genome(complete)');
1951      }      }
# Line 2022  Line 2061 
2061              $retVal{$featureID2} = $score;              $retVal{$featureID2} = $score;
2062          }          }
2063      }      }
     # Functional coupling is reflexive. If we found at least one coupled feature, we must add  
     # the incoming feature as well.  
     if (keys %retVal) {  
         $retVal{$featureID} = 9999;  
     }  
2064      # Return the hash.      # Return the hash.
2065      return %retVal;      return %retVal;
2066  }  }
# Line 2383  Line 2417 
2417  sub GetGenomeNameData {  sub GetGenomeNameData {
2418      # Get the parameters.      # Get the parameters.
2419      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
2420        # Declare the return variables.
2421        my ($genus, $species, $strain);
2422        # Get the genome's data.
2423        my $genomeData = $self->_GenomeData($genomeID);
2424        # Only proceed if the genome exists.
2425        if (defined $genomeData) {
2426      # Get the desired values.      # Get the desired values.
2427      my ($genus, $species, $strain) = $self->GetEntityValues('Genome', $genomeID =>          ($genus, $species, $strain) = $genomeData->Values(['Genome(genus)',
2428                                                              [qw(Genome(genus) Genome(species) Genome(unique-characterization))]);                                                             'Genome(species)',
2429      # Throw an error if they were not found.                                                             'Genome(unique-characterization)']);
2430      if (! defined $genus) {      } else {
2431            # Throw an error because they were not found.
2432          Confess("Genome $genomeID not found in database.");          Confess("Genome $genomeID not found in database.");
2433      }      }
2434      # Return the results.      # Return the results.
# Line 2688  Line 2729 
2729  sub Taxonomy {  sub Taxonomy {
2730      # Get the parameters.      # Get the parameters.
2731      my ($self, $genome) = @_;      my ($self, $genome) = @_;
     # Find the specified genome's taxonomy string.  
     my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);  
2732      # Declare the return variable.      # Declare the return variable.
2733      my @retVal = ();      my @retVal = ();
2734      # If we found the genome, return its taxonomy string.      # Get the genome data.
2735      if ($list) {      my $genomeData = $self->_GenomeData($genome);
2736          @retVal = split /\s*;\s*/, $list;      # Only proceed if it exists.
2737        if (defined $genomeData) {
2738            # Create the taxonomy from the taxonomy string.
2739            @retVal = split /\s*;\s*/, $genomeData->PrimaryValue('Genome(taxonomy)');
2740      } else {      } else {
2741            # Genome doesn't exist, so emit a warning.
2742          Trace("Genome \"$genome\" does not have a taxonomy in the database.\n") if T(0);          Trace("Genome \"$genome\" does not have a taxonomy in the database.\n") if T(0);
2743      }      }
2744      # Return the value found.      # Return the value found.
# Line 2740  Line 2783 
2783      }      }
2784      my @taxA = $self->Taxonomy($genomeA);      my @taxA = $self->Taxonomy($genomeA);
2785      my @taxB = $self->Taxonomy($genomeB);      my @taxB = $self->Taxonomy($genomeB);
2786      # Initialize the distance to 1. We'll reduce it each time we find a match between the      # Compute the distance.
2787      # taxonomies.      my $retVal = FIGRules::CrudeDistanceFormula(\@taxA, \@taxB);
     my $retVal = 1.0;  
     # Initialize the subtraction amount. This amount determines the distance reduction caused  
     # by a mismatch at the current level.  
     my $v = 0.5;  
     # Loop through the taxonomies.  
     for (my $i = 0; ($i < @taxA) && ($i < @taxB) && ($taxA[$i] eq $taxB[$i]); $i++) {  
         $retVal -= $v;  
         $v /= 2;  
     }  
2788      return $retVal;      return $retVal;
2789  }  }
2790    
# Line 3215  Line 3249 
3249      # Get the parameters.      # Get the parameters.
3250      my ($self, $featureID, $function, $userID) = @_;      my ($self, $featureID, $function, $userID) = @_;
3251      # Get a list of the features that are BBHs of the incoming feature.      # Get a list of the features that are BBHs of the incoming feature.
3252      my @bbhFeatures = map { $_->[0] } FIGRules::BBHData($featureID);      my $bbhData = FIGRules::BBHData($featureID);
3253        my @bbhFeatures = map { $_->[0] } @$bbhData;
3254      # Now we loop through the features, pulling out the ones that have the correct      # Now we loop through the features, pulling out the ones that have the correct
3255      # functional assignment.      # functional assignment.
3256      my @retVal = ();      my @retVal = ();
# Line 3388  Line 3423 
3423    
3424  =head3 BBHMatrix  =head3 BBHMatrix
3425    
3426      my %bbhMap = $sprout->BBHMatrix($genomeID, $cutoff, @targets);      my $bbhMap = $sprout->BBHMatrix($genomeID, $cutoff, @targets);
3427    
3428  Find all the bidirectional best hits for the features of a genome in a  Find all the bidirectional best hits for the features of a genome in a
3429  specified list of target genomes. The return value will be a hash mapping  specified list of target genomes. The return value will be a hash mapping
# Line 3412  Line 3447 
3447    
3448  =item RETURN  =item RETURN
3449    
3450  Returns a hash mapping each feature in the original genome to a hash mapping its  Returns a reference to a hash mapping each feature in the original genome
3451  BBH pegs in the target genomes to their scores.  to a sub-hash mapping its BBH pegs in the target genomes to their scores.
3452    
3453  =back  =back
3454    
# Line 3426  Line 3461 
3461      my %retVal = ();      my %retVal = ();
3462      # Ask for the BBHs.      # Ask for the BBHs.
3463      my @bbhList = FIGRules::BatchBBHs("fig|$genomeID.%", $cutoff, @targets);      my @bbhList = FIGRules::BatchBBHs("fig|$genomeID.%", $cutoff, @targets);
3464        Trace("Retrieved " . scalar(@bbhList) . " BBH results.") if T(3);
3465      # We now have a set of 4-tuples that we need to convert into a hash of hashes.      # We now have a set of 4-tuples that we need to convert into a hash of hashes.
3466      for my $bbhData (@bbhList) {      for my $bbhData (@bbhList) {
3467          my ($peg1, $peg2, $score) = @{$bbhData};          my ($peg1, $peg2, $score) = @{$bbhData};
# Line 3436  Line 3472 
3472          }          }
3473      }      }
3474      # Return the result.      # Return the result.
3475      return %retVal;      return \%retVal;
3476  }  }
3477    
3478    
# Line 3542  Line 3578 
3578      # Create the return hash.      # Create the return hash.
3579      my %retVal = ();      my %retVal = ();
3580      # Query for the desired BBHs.      # Query for the desired BBHs.
3581      my @bbhList = FIGRules::BBHData($featureID, $cutoff);      my $bbhList = FIGRules::BBHData($featureID, $cutoff);
3582      # Form the results into the return hash.      # Form the results into the return hash.
3583      for my $pair (@bbhList) {      for my $pair (@$bbhList) {
3584          my $fid = $pair->[0];          my $fid = $pair->[0];
3585          if ($self->Exists('Feature', $fid)) {          if ($self->Exists('Feature', $fid)) {
3586              $retVal{$fid} = $pair->[1];              $retVal{$fid} = $pair->[1];
# Line 4027  Line 4063 
4063  =cut  =cut
4064    
4065  sub GetSourceObject {  sub GetSourceObject {
4066      # Get access to the FIG code.      # Get the parameters.
4067        my ($self) = @_;
4068        # Check to see if we already have a source object.
4069        my $retVal = $self->{_fig};
4070        if (! defined $retVal) {
4071            # No, so create one.
4072      require FIG;      require FIG;
4073      # Return a FIG object.          $retVal = FIG->new();
4074      return FIG->new();      }
4075        # Return the object.
4076        return $retVal;
4077  }  }
4078    
4079  =head3 SectionList  =head3 SectionList
4080    
4081      my @sections = $erdb->SectionList($source);      my @sections = $erdb->SectionList();
4082    
4083  Return a list of the names for the different data sections used when loading this database.  Return a list of the names for the different data sections used when loading this database.
4084  The default is an empty string, in which case there is only one section representing the  The default is a single string, in which case there is only one section representing the
4085  entire database.  entire database.
4086    
 =over 4  
   
 =item source  
   
 Source object used to access the data from which the database is loaded. This is the  
 same object returned by L</GetSourceObject>; however, we ask the caller to pass it  
 in as a parameter so that we don't end up creating multiple copies of a potentially  
 expensive data structure.  
   
 =item RETURN  
   
 Returns a list of section names.  
   
 =back  
   
4087  =cut  =cut
4088    
4089  sub SectionList {  sub SectionList {
# Line 4063  Line 4091 
4091      my ($self, $source) = @_;      my ($self, $source) = @_;
4092      # Ask the BaseSproutLoader for a section list.      # Ask the BaseSproutLoader for a section list.
4093      require BaseSproutLoader;      require BaseSproutLoader;
4094      my @retVal = BaseSproutLoader::GetSectionList($self, $source);      my @retVal = BaseSproutLoader::GetSectionList($self);
4095      # Return the list.      # Return the list.
4096      return @retVal;      return @retVal;
4097  }  }
4098    
4099  =head3 Loader  =head3 Loader
4100    
4101      my $groupLoader = $erdb->Loader($groupName, $source, $options);      my $groupLoader = $erdb->Loader($groupName, $options);
4102    
4103  Return an [[ERDBLoadGroupPm]] object for the specified load group. This method is used  Return an [[ERDBLoadGroupPm]] object for the specified load group. This method is used
4104  by [[ERDBGeneratorPl]] to create the load group objects. If you are not using  by [[ERDBGeneratorPl]] to create the load group objects. If you are not using
# Line 4083  Line 4111 
4111  Name of the load group whose object is to be returned. The group name is  Name of the load group whose object is to be returned. The group name is
4112  guaranteed to be a single word with only the first letter capitalized.  guaranteed to be a single word with only the first letter capitalized.
4113    
 =item source  
   
 The source object used to access the data from which the load file is derived. This  
 is the same object returned by L</GetSourceObject>; however, we ask the caller to pass  
 it in as a parameter so that we don't end up creating multiple copies of a potentially  
 expensive data structure.  
   
4114  =item options  =item options
4115    
4116  Reference to a hash of command-line options.  Reference to a hash of command-line options.
# Line 4105  Line 4126 
4126    
4127  sub Loader {  sub Loader {
4128      # Get the parameters.      # Get the parameters.
4129      my ($self, $groupName, $source, $options) = @_;      my ($self, $groupName, $options) = @_;
4130      # Compute the loader name.      # Compute the loader name.
4131      my $loaderClass = "${groupName}SproutLoader";      my $loaderClass = "${groupName}SproutLoader";
4132      # Pull in its definition.      # Pull in its definition.
4133      require "$loaderClass.pm";      require "$loaderClass.pm";
4134      # Create an object for it.      # Create an object for it.
4135      my $retVal = eval("$loaderClass->new(\$self, \$source, \$options)");      my $retVal = eval("$loaderClass->new(\$self, \$options)");
4136      # Insure it worked.      # Insure it worked.
4137      Confess("Could not create $loaderClass object: $@") if $@;      Confess("Could not create $loaderClass object: $@") if $@;
4138      # Return it to the caller.      # Return it to the caller.
4139      return $retVal;      return $retVal;
4140  }  }
4141    
4142    
4143  =head3 LoadGroupList  =head3 LoadGroupList
4144    
4145      my @groups = $erdb->LoadGroupList();      my @groups = $erdb->LoadGroupList();
# Line 4130  Line 4152 
4152    
4153  sub LoadGroupList {  sub LoadGroupList {
4154      # Return the list.      # Return the list.
4155      return qw(Genome Subsystem Annotation Property Source Reaction Synonym Drug Feature);      return qw(Genome Subsystem Annotation Property Source Reaction Synonym Feature Drug);
4156  }  }
4157    
4158  =head3 LoadDirectory  =head3 LoadDirectory
# Line 4168  Line 4190 
4190          # We don't have one pre-built, so we build and save it now.          # We don't have one pre-built, so we build and save it now.
4191          $retVal = BioWords->new(exceptions => "$FIG_Config::sproutData/Exceptions.txt",          $retVal = BioWords->new(exceptions => "$FIG_Config::sproutData/Exceptions.txt",
4192                                   stops => "$FIG_Config::sproutData/StopWords.txt",                                   stops => "$FIG_Config::sproutData/StopWords.txt",
4193                                   cache => 1);                                   cache => 0);
4194          $self->{stemmer} = $retVal;          $self->{stemmer} = $retVal;
4195      }      }
4196      # Return the result.      # Return the result.
# Line 4261  Line 4283 
4283      # Get the parameters.      # Get the parameters.
4284      my ($self, $fid) = @_;      my ($self, $fid) = @_;
4285      # Insure we have a genome hash.      # Insure we have a genome hash.
4286      if (! defined $self->{genomeHash}) {      my $genomes = $self->_GenomeHash();
         my %genomeHash = map { $_ => 1 } $self->GetFlat(['Genome'], "", [], 'Genome(id)');  
         $self->{genomeHash} = \%genomeHash;  
     }  
4287      # Get the feature's genome ID.      # Get the feature's genome ID.
4288      my ($genomeID) = FIGRules::ParseFeatureID($fid);      my ($genomeID) = FIGRules::ParseFeatureID($fid);
4289      # Return an indicator of whether or not the genome ID is in the hash.      # Return an indicator of whether or not the genome ID is in the hash.
# Line 4341  Line 4360 
4360      return $retVal;      return $retVal;
4361  }  }
4362    
4363    =head3 _GenomeHash
4364    
4365        my $gHash = $sprout->_GenomeHash();
4366    
4367    Return a hash mapping all NMPDR genome IDs to [[ERDBObjectPm]] genome objects.
4368    
4369    =cut
4370    
4371    sub _GenomeHash {
4372        # Get the parameters.
4373        my ($self) = @_;
4374        # Do we already have a filled hash?
4375        if (! $self->{genomeHashFilled}) {
4376            # No, create it.
4377            my %gHash = map { $_->PrimaryValue('id') => $_ } $self->GetList("Genome", "", []);
4378            $self->{genomeHash} = \%gHash;
4379            # Denote we have it.
4380            $self->{genomeHashFilled} = 1;
4381        }
4382        # Return the hash.
4383        return $self->{genomeHash};
4384    }
4385    
4386    =head3 _GenomeData
4387    
4388        my $genomeData = $sprout->_GenomeData($genomeID);
4389    
4390    Return an [[ERDBObjectPm]] object for the specified genome, or an undefined
4391    value if the genome does not exist.
4392    
4393    =over 4
4394    
4395    =item genomeID
4396    
4397    ID of the desired genome.
4398    
4399    =item RETURN
4400    
4401    Returns either an [[ERDBObjectPm]] containing the genome, or an undefined value.
4402    If the genome exists, it will have been read into the genome cache.
4403    
4404    =back
4405    
4406    =cut
4407    
4408    sub _GenomeData {
4409        # Get the parameters.
4410        my ($self, $genomeID) = @_;
4411        # Are we in the genome hash?
4412        if (! exists $self->{genomeHash}->{$genomeID} && ! $self->{genomeHashFilled}) {
4413            # The genome isn't in the hash, and the hash is not complete, so we try to
4414            # read it.
4415            $self->{genomeHash}->{$genomeID} = $self->GetEntity(Genome => $genomeID);
4416        }
4417        # Return the result.
4418        return $self->{genomeHash}->{$genomeID};
4419    }
4420    
4421    =head3 _CacheGenome
4422    
4423        $sprout->_CacheGenome($genomeID, $genomeData);
4424    
4425    Store the specified genome object in the genome cache if it is already there.
4426    
4427    =over 4
4428    
4429    =item genomeID
4430    
4431    ID of the genome to store in the cache.
4432    
4433    =item genomeData
4434    
4435    An [[ERDBObjectPm]] containing at least the data for the specified genome.
4436    Note that the Genome may not be the primary object in it, so a fully-qualified
4437    field name has to be used to retrieve data from it.
4438    
4439    =back
4440    
4441    =cut
4442    
4443    sub _CacheGenome {
4444        # Get the parameters.
4445        my ($self, $genomeID, $genomeData) = @_;
4446        # Only proceed if we don't already have the genome.
4447        if (! exists $self->{genomeHash}->{$genomeID}) {
4448            $self->{genomeHash}->{$genomeID} = $genomeData;
4449        }
4450    }
4451    
4452  1;  1;

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