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revision 1.7, Wed Dec 16 01:45:19 2009 UTC revision 1.8, Mon Feb 1 20:14:28 2010 UTC
# Line 145  Line 145 
145      my ($self,$model) = @_;      my ($self,$model) = @_;
146    
147      #First getting the compound table which has a list of all compounds in the database as well as alot of compound information      #First getting the compound table which has a list of all compounds in the database as well as alot of compound information
148      my $CompoundTable = $model->GetDBTable("COMPOUNDS");      my $CompoundTable = $model->database()->GetDBTable("COMPOUNDS");
149    
150      #Adding the universal AliasType that will always exist      #Adding the universal AliasType that will always exist
151      $self->PutE(AliasType => "NAME", source => "NONE");      $self->PutE(AliasType => "NAME", source => "NONE");
# Line 230  Line 230 
230  sub LoadReactions {  sub LoadReactions {
231      my ($self,$model) = @_;      my ($self,$model) = @_;
232      #First getting the reaction table which has a list of all reactions in the database as well as alot of reaction information      #First getting the reaction table which has a list of all reactions in the database as well as alot of reaction information
233      my $ReactionTable = $model->GetDBTable("REACTIONS");      my $ReactionTable = $model->database()->GetDBTable("REACTIONS");
234    
235      #Cycling through the compound list and adding each individual compound entity      #Cycling through the compound list and adding each individual compound entity
236      my $Count = 0;      my $Count = 0;
# Line 337  Line 337 
337  sub LoadRoleSets {  sub LoadRoleSets {
338      my ($self,$model) = @_;      my ($self,$model) = @_;
339      my $sapling =$self->db();      my $sapling =$self->db();
340      my $RoleMappings = $model->GetDBTable("CURATED ROLE MAPPINGS");      my $RoleMappings = $model->database()->GetDBTable("CURATED ROLE MAPPINGS");
341      my $NewSet;      my $NewSet;
342      my $SetHash;      my $SetHash;
343      my $LastComplex = -1;      my $LastComplex = -1;
# Line 405  Line 405 
405      my $sapling = $self->db();      my $sapling = $self->db();
406      ## TRS: Get hash of valid genome IDs.      ## TRS: Get hash of valid genome IDs.
407      my $genomeHash = $sapling->GenomeHash();      my $genomeHash = $sapling->GenomeHash();
408      my $ModelList = $model->GetDBTable("MODEL LIST");      my $ModelList = $model->database()->GetDBTable("MODEL LIST");
409      my $ModelStats = $model->GetDBTable("MODEL STATS");      my $ModelStats = $model->database()->GetDBTable("MODEL STATS");
410      for (my $i=0; $i < $ModelStats->size(); $i++) {      for (my $i=0; $i < $ModelStats->size(); $i++) {
411          my $Row = $ModelStats->get_row($i);          my $Row = $ModelStats->get_row($i);
412          if (defined($Row) && defined($Row->{"Model ID"}->[0])) {          if (defined($Row) && defined($Row->{"Model ID"}->[0])) {
# Line 499  Line 499 
499                  #If the model is not obsolete, we add the relationships between model and reaction and featureset                  #If the model is not obsolete, we add the relationships between model and reaction and featureset
500                  if ($LoadingArray[25] == 0) {                  if ($LoadingArray[25] == 0) {
501                      #Loading the model from file                      #Loading the model from file
502                      my $ModelTable = $model->GetDBModel($LoadingArray[0]);                      my $ModelTable = $model->database()->GetDBModel($LoadingArray[0]);
503                      if (! defined $ModelTable) {                      if (! defined $ModelTable) {
504                          $self->Add(missingModelTable => 1);                          $self->Add(missingModelTable => 1);
505                      } else {                      } else {

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