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revision 1.12, Mon Jan 24 03:52:18 2011 UTC revision 1.21, Mon Nov 28 19:38:35 2011 UTC
# Line 16  Line 16 
16  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
17  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
18  #  #
19  use FIGMODEL;  #use FIGMODEL;
20    
21  package ModelSaplingLoader;  package ModelSaplingLoader;
22      use strict;      use strict;
23      use Tracer;      use Tracer;
24      use ERDB;      use ERDB;
     use HTTP::Date;  
25      use base 'BaseSaplingLoader';      use base 'BaseSaplingLoader';
26    
27  =head1 Sapling ModelLoader Load Group Class  =head1 Sapling Model Load Group Class
28    
29  =head2 Introduction  =head2 Introduction
30    
31  The ModelLoader Load Group includes all of the major mdl tables.  The Model Load Group includes a small set of tables that describe reactions and compounds
32    and how they relate to the models in the main model database.
33    
34  =head3 new  =head3 new
35    
36      my $sl = ModelLoaderSaplingLoader->new($erdb, $options, @tables);      my $sl = ModelSaplingLoader->new($erdb, $options);
37    
38  Construct a new ModelLoaderSaplingLoader object.  Construct a new ModelSaplingLoader object.
39    
40  =over 4  =over 4
41    
# Line 47  Line 47 
47    
48  Reference to a hash of command-line options.  Reference to a hash of command-line options.
49    
 =item tables  
   
 List of tables in this load group.  
   
50  =back  =back
51    
52  =cut  =cut
# Line 59  Line 55 
55      # Get the parameters.      # Get the parameters.
56      my ($class, $erdb, $options) = @_;      my ($class, $erdb, $options) = @_;
57      # Create the table list.      # Create the table list.
58      my @tables = sort qw(StructuralCue IsFoundIn Compound HasAliasOf AliasType      my @tables = qw(Compound Reaction EcNumber Model Media IsTriggeredBy
59                           HasReactionAliasOf Reaction Involves IsTriggeredBy                      IsCategorizedInto IsConsistentWith IsModeledBy Involves
60                           RoleSet IsCombinationOf IsCategorizedInto EcNumber                      IsRequiredBy Complex ComplexName IsSetOf IsExemplarOf);
                          IsConsistentWith IsStimulatedBy  FeatureSet IsSetOf  
                          IsRequiredBy Model IsModeledBy ModelUser); # Encompasses);  
61      # Create the BaseSaplingLoader object.      # Create the BaseSaplingLoader object.
62      my $retVal = BaseSaplingLoader::new($class, $erdb, $options, @tables);      my $retVal = BaseSaplingLoader::new($class, $erdb, $options, @tables);
63        # Create the reaction tracking hash.
64        $retVal->{reactions} = {};
65      # Return it.      # Return it.
66      return $retVal;      return $retVal;
67  }  }
# Line 76  Line 72 
72    
73      $sl->Generate();      $sl->Generate();
74    
75  Generate the data for the mdl files.  Generate the data for the model files.
76    
77  =cut  =cut
78    
# Line 85  Line 81 
81      my ($self) = @_;      my ($self) = @_;
82      # Get the database object.      # Get the database object.
83      my $erdb = $self->db();      my $erdb = $self->db();
     # Get the source object.  
     my $fig = $self->source();  
84      # Is this the global section?      # Is this the global section?
     my $model = new FIGMODEL;  
85      if ($self->global()) {      if ($self->global()) {
86          #Loading the compound entities and relationships          # Load the tables from the model dump files.
87          $self->LoadCompounds($model);          $self->LoadModelFiles();
         #Loading the reaction, and EC number entities and relationships  
         $self->LoadReactions($model);  
88      } else {      } else {
89          # Get the section ID.          # Get the section ID.
90          my $genomeID = $self->section();          my $genomeID = $self->section();
# Line 101  Line 92 
92      }      }
93  }  }
94    
95  sub LoadCompounds {  =head3 LoadModelFiles
     my ($self,$model) = @_;  
96    
97      #First getting the compound table which has a list of all compounds in the database as well as alot of compound information      $sl->LoadModelFiles();
     my $CompoundTable = $model->database()->GetDBTable("COMPOUNDS");  
98    
99      #Adding the universal AliasType that will always exist  Load the data from the six model dump files.
     $self->PutE(AliasType => "NAME", source => "NONE");  
     $self->PutE(AliasType => "SEARCHNAME", source => "NONE");  
     $self->PutE(AliasType => "KEGG", source => "http://www.kegg.com/");  
     $self->PutE(AliasType => "ARGONNE", source => "OBSOLETE IDs");  
100    
101      #Cycling through the compound list and adding each individual compound entity  =cut
     for (my $i=0; $i < $CompoundTable->size(); $i++) {  
         my $Row = $CompoundTable->get_row($i);  
         if (defined($Row) && defined($Row->{"DATABASE"}->[0]) && $Row->{"DATABASE"}->[0] =~ m/cpd\d\d\d\d\d/) {  
             my $Object = FIGMODELObject->load($model->{"compound directory"}->[0].$Row->{"DATABASE"}->[0],"\t");  
             my @LoadingArray = ($Row->{"DATABASE"}->[0],$Row->{"DATABASE"}->[0],0,"",0,"",0,10000000,10000000,"");  
             $self->Track(compoundRow => $LoadingArray[0], 1000);  
             if (defined($Row->{"NAME"}->[0])) {  
                 $LoadingArray[1] = $Row->{"NAME"}->[0];  
             }  
             if (defined($Object->{"MASS"}->[0])) {  
                 $LoadingArray[2] = $Object->{"MASS"}->[0];  
             }  
             if (defined($Object->{"FORMULA"}->[0])) {  
                 $LoadingArray[3] = $Object->{"FORMULA"}->[0];  
             }  
             if (defined($Object->{"CHARGE"}->[0])) {  
                 $LoadingArray[4] = $Object->{"CHARGE"}->[0];  
             }  
             if (defined($Object->{"CHARGE"}->[0]) && defined($Object->{"FORMULA"}->[0])) {  
                 $LoadingArray[5] = FIGMODEL::ConvertToNeutralFormula($Object->{"FORMULA"}->[0],$Object->{"CHARGE"}->[0]);  
             }  
             if (-e $model->{"Argonne molfile directory"}->[0].$Row->{"DATABASE"}->[0].".mol" || -e $model->{"Argonne molfile directory"}->[0]."pH7/".$Row->{"DATABASE"}->[0].".mol") {  
                 $LoadingArray[6] = 1;  
             }  
             if (defined($Object->{"DELTAG"}->[0])) {  
                 $LoadingArray[7] = $Object->{"DELTAG"}->[0];  
             }  
             if (defined($Object->{"DELTAGERR"}->[0])) {  
                 $LoadingArray[8] = $Object->{"DELTAGERR"}->[0];  
             }  
             if (defined($Row->{"STRINGCODE"}->[0])) {  
                 $LoadingArray[9] = $Row->{"STRINGCODE"}->[0];  
             }  
             $self->PutE(Compound => $LoadingArray[0], label => $LoadingArray[1], mass => $LoadingArray[2], chargedFormula => $LoadingArray[3], charge => $LoadingArray[4],neutralFormula => $LoadingArray[5], hasMolfile => $LoadingArray[6], deltaG => $LoadingArray[7], deltaGerr => $LoadingArray[8], stringcode => $LoadingArray[9]);  
             #Adding the relationship between compound and structural cue  
             if (defined($Object->{"STRUCTURAL_CUES"})) {  
                 foreach my $Cue (@{$Object->{"STRUCTURAL_CUES"}}) {  
                     my @TempArray = split(/:/,$Cue);  
                     if (@TempArray == 2) {  
                         $self->PutR(IsFoundIn => $TempArray[0],$LoadingArray[0],count => $TempArray[1]);  
                     }  
                 }  
             }  
             #Adding the relationship between compound and alias type  
             if (defined($Object->{"NAME"})) {  
                 foreach my $Name (@{$Object->{"NAME"}}) {  
                     $self->PutR(HasAliasOf => $LoadingArray[0],"NAME",alias => $Name);  
                     my @SearchNames = FIGMODEL::ConvertToSearchNames($Name);  
                     foreach my $SearchName (@SearchNames) {  
                         $self->PutR(HasAliasOf => $LoadingArray[0],"SEARCHNAME",alias => $SearchName);  
                     }  
                 }  
             }  
             if (defined($Object->{"DBLINKS"})) {  
                 foreach my $Link (@{$Object->{"DBLINKS"}}) {  
                     my @TempArray = split(/:/,$Link);  
                     if (@TempArray >= 2) {  
                         if ($TempArray[0] ne "KEGG" && $TempArray[0] ne "ARGONNE") {  
                             $self->PutE(AliasType => $TempArray[0], source => "PUBLISHED MODEL");  
                         }  
                         if ($TempArray[0] eq "ARGONNE") {  
                             splice(@TempArray,1,1);  
                         }  
                         for (my $j=1; $j < @TempArray; $j++) {  
                             $self->PutR(HasAliasOf => $LoadingArray[0],$TempArray[0],alias => $TempArray[$j]);  
                         }  
                     }  
                 }  
             }  
         }  
     }  
 }  
102    
103  sub LoadReactions {  # hash of ubiquitous compounds.
104      my ($self,$model) = @_;  use constant UBIQUITOUS => {
105      #First getting the reaction table which has a list of all reactions in the database as well as alot of reaction information      cpd00001 => 'OH-',
106      my $ReactionTable = $model->database()->GetDBTable("REACTIONS");      cpd00002 => 'ATP',
107        cpd00003 => 'Nicotinamideadeninedinucleotide',
108        cpd00004 => 'Nicotinamideadeninedinucleotide-reduced',
109        cpd00005 => 'Nicotinamideadeninedinucleotidephosphate-reduced',
110        cpd00006 => 'Nicotinamideadeninedinucleotidephosphate',
111        cpd00007 => 'Oxygen',
112        cpd00008 => 'ADP',
113        cpd00009 => 'Orthophosphoric acid',
114        cpd00010 => 'CoenzymeA',
115        cpd00011 => 'Carbon dioxide',
116        cpd00012 => 'PPi',
117        cpd00018 => 'AMP',
118        cpd00020 => 'Pyruvic Acid',
119        cpd00022 => 'Acetyl-CoA',
120        cpd00025 => 'Hydrogen peroxide',
121        cpd00067 => 'H+',
122        cpd00971 => 'Sodium',
123        cpd15352 => '2-Demethylmenaquinone',
124        cpd15353 => '2-Demethylmenaquinol',
125        cpd15499 => 'Menaquinol',
126        cpd15500 => 'Menaquinone',
127        cpd15560 => 'Ubiquinone-8',
128        cpd15561 => 'Ubiquinol-8',
129    };
130    
131      #Cycling through the compound list and adding each individual compound entity  sub LoadModelFiles {
132      my $Count = 0;      # Get the parameters.
133      for (my $i=0; $i < $ReactionTable->size(); $i++) {      my ($self) = @_;
134          my $Row = $ReactionTable->get_row($i);      # Get the sapling database.
135          if (defined($Row) && defined($Row->{"DATABASE"}->[0]) && $Row->{"DATABASE"}->[0] =~ m/rxn\d\d\d\d\d/) {      my $erdb = $self->db();
136              my $Object = FIGMODELObject->load($model->{"reaction directory"}->[0].$Row->{"DATABASE"}->[0],"\t");      # Get the model dump file directory.
137              my @LoadingArray = ($Row->{"DATABASE"}->[0],"","","","","",10000000,10000000,10000000,"R");      my $dir = $erdb->LoadDirectory() . "/models";
138              $self->Track(reactionRow => $LoadingArray[0], 1000);      # First we read the compounds.
139              if (defined($Object->{"DEFINITION"}->[0])) {      my $ih = $self->CheckFile("$dir/CompoundName.txt", qw(CompoundID Name));
140                  $LoadingArray[1] = $Object->{"DEFINITION"}->[0];      while (! eof $ih) {
141              }          # Get the next compound.
142              if (defined($Object->{"EQUATION"}->[0])) {          my ($id, $label) = $self->ReadLine($ih);
143                  my ($Direction,$Equation,$ReverseEquation,$FullEquation,$EquationCompartment,$Error) = $model->ConvertEquationToCode($Object->{"EQUATION"}->[0],{"Test" => "Test"});          # Create a compound record for it.
144                  $LoadingArray[2] = $Equation;          $self->PutE(Compound => $id, label => $label, ubiquitous => (UBIQUITOUS->{$id} ? 1 : 0));
145              }      }
146              if (defined($Object->{"OPERATOR"}->[0])) {      # Next, the compound-reactions relationship. We create the reactions here, too.
147                  $LoadingArray[3] = $Object->{"OPERATOR"}->[0];      $ih = $self->CheckFile("$dir/CompoundReaction.txt", qw(CompoundID ReactionID
148              }                             Stoichiometry Cofactor));
149              if (defined($Object->{"PATHWAY"}->[0])) {      while (! eof $ih) {
150                  $LoadingArray[4] = join(";",@{$Object->{"PATHWAY"}});          # Get the next link.
151              }          my ($compound, $reaction, $stoich, $cofactor) = $self->ReadLine($ih);
152              if (defined($Row->{"KEGG MAPS"}->[0])) {          # Insure the reaction exists.
153                  $LoadingArray[5] = join(";",@{$Row->{"KEGG MAPS"}});          $self->CreateReaction($reaction);
154              }          # Check for product or substrate.
155              if (defined($Object->{"DELTAG"}->[0])) {          my $product;
156                  $LoadingArray[6] = $Object->{"DELTAG"}->[0];          if ($stoich < 0) {
157              }              $product = 0;
158              if (defined($Object->{"MMDELTAG"}->[0])) {              $stoich = -$stoich;
                 $LoadingArray[7] = $Object->{"MMDELTAG"}->[0];  
             }  
             if (defined($Object->{"DELTAGERR"}->[0])) {  
                 $LoadingArray[8] = $Object->{"DELTAGERR"}->[0];  
             }  
             if (defined($Object->{"THERMODYNAMIC REVERSIBILITY"}->[0])) {  
                 my $code = $Object->{"THERMODYNAMIC REVERSIBILITY"}->[0];  
                 if ($code eq '<=>') {  
                     $LoadingArray[9] = "R";  
                 } elsif ($code eq '<=') {  
                     $LoadingArray[9] = "B";  
                 } elsif ($code eq '=>') {  
                     $LoadingArray[9] = "F";  
                 }  
             }  
             $self->PutE(Reaction => $LoadingArray[0], definition => $LoadingArray[1], code => $LoadingArray[2], operator => $LoadingArray[3], pathway => $LoadingArray[4],keggMap => $LoadingArray[5], deltaG => $LoadingArray[6], MMdeltaG => $LoadingArray[7], deltaGerr => $LoadingArray[8], predictedReversibility => $LoadingArray[9]);  
             #Adding relationship between compounds and reactions  
             my ($Reactants,$Products) = $model->GetReactionSubstrateData($LoadingArray[0]);  
             if (! defined $Reactants) {  
                 $self->Add(missingReactants => 1);  
             } else {  
                 for (my $j=0; $j < @{$Reactants}; $j++) {  
                     $self->PutR(Involves => $LoadingArray[0],$Reactants->[$j]->{"DATABASE"}->[0],product => 0,stoichiometry => $Reactants->[$j]->{"COEFFICIENT"}->[0],main => 1,compartment => $Reactants->[$j]->{"COMPARTMENT"}->[0],discriminator => $Count);  
                     #TODO:Properly identify main reactants in reactions  
                     $Count++;  
                 }  
             }  
             if (! defined $Products) {  
                 $self->Add(missingProducts => 1);  
159              } else {              } else {
160                  for (my $j=0; $j < @{$Products}; $j++) {              $product = 1;
                     $self->PutR(Involves => $LoadingArray[0],$Products->[$j]->{"DATABASE"}->[0],product => 1,stoichiometry => $Products->[$j]->{"COEFFICIENT"}->[0],main => 1,compartment => $Products->[$j]->{"COMPARTMENT"}->[0],discriminator => $Count);  
                     #TODO:Properly identify main reactants in reactions  
                     $Count++;  
                 }  
161              }              }
162              #Adding relationship between EC number and reactions          # Connect the reaction to the compound.
163              if (defined($Object->{"ENZYME"})) {          $self->PutR(Involves => $reaction, $compound, product => $product,
164                  foreach my $Enzyme (@{$Object->{"ENZYME"}}) {                      stoichiometry => $stoich, cofactor => $cofactor);
165                     if ($Enzyme =~ /,/) {      }
166                      #TODO:Invalid enzyme      # Before we go on, we need to get a map of the modelSEED role IDs to
167        # the SEED role IDs. This is found in the Role.txt file, along with the
168        # exemplar data.
169        my %roleHash;
170        $ih = $self->CheckFile("$dir/Role.txt", qw(RoleID Name ExemplarID));
171        while (! eof $ih) {
172            # Get the next role's record.
173            my ($roleID, $role, $exemplarList) = $self->ReadLine($ih);
174            # Map the role ID to the role name (which is the SEED's ID).
175            $roleHash{$roleID} = $role;
176            # If there is are exemplars, store them.
177            if ($exemplarList && $exemplarList ne 'NONE') {
178                for my $exemplar (split /\s*,\s*/, $exemplarList) {
179                    $self->PutR(IsExemplarOf => $exemplar, $role);
180                }
181            }
182        }
183        # The next step is to create the complexes. We load into memory a
184        # hash mapping the complexes to their reactions. This is later
185        # used to insure we have reaction-to-role coverage.
186        my %cpxHash;
187        $ih = $self->CheckFile("$dir/ReactionComplex.txt", qw(ReactionID ComplexID));
188        while (! eof $ih) {
189            # Get the next reaction/complex pair.
190            my ($rxn, $cpx) = $self->ReadLine($ih);
191            # Is this a new complex?
192            if (! exists $cpxHash{$cpx}) {
193                # Yes. Create a record for it.
194                $self->PutE(Complex => $cpx);
195                $cpxHash{$cpx} = [];
196            }
197            # Insure the reaction exists.
198            $self->CreateReaction($rxn);
199            # Connect the complex to the reaction.
200            $self->PutR(IsSetOf => $cpx, $rxn);
201            push @{$cpxHash{$cpx}}, $rxn;
202        }
203        # Here we connect the complexes to the roles. Along the way, we
204        # create a hash listing of all of a reaction's roles. That hash
205        # will be used to check for missing reaction/role links later on.
206        my %rxnHash;
207        $ih = $self->CheckFile("$dir/ComplexRole.txt", qw(RoleID ComplexID));
208        while (! eof $ih) {
209            # Get the next role/complex pair.
210            my ($roleID, $cpx) = $self->ReadLine($ih);
211            # Connect the role to the complex.
212            $self->PutR(IsTriggeredBy => $cpx, $roleHash{$roleID}, optional => 0);
213            # Denote that this role is connected to the complex's reactions.
214            for my $rxn (@{$cpxHash{$cpx}}) {
215                push @{$rxnHash{$rxn}}, $roleID;
216            }
217        }
218        # We don't need the complex hash any more. Instead, we're going to
219        # use it to track single-reaction complexes we create.
220        %cpxHash = ();
221        # Now we fill in the missing reaction-to-role connections.
222        $ih = $self->CheckFile("$dir/ReactionRole.txt", qw(ReactionID Role));
223        while (! eof $ih) {
224            # Get the next reaction/role pair.
225            my ($reaction, $role) = $self->ReadLine($ih);
226            # Insure the reaction exists.
227            $self->CreateReaction($reaction);
228            # Is this reaction already connected to this role?
229            my $roleList = $rxnHash{$reaction};
230            if (! $roleList || ! (grep { $roleHash{$_} eq $role } @{$rxnHash{$reaction}})) {
231                # No, so we have to do it the hard way.
232                if (! exists $cpxHash{$reaction}) {
233                    # Here the reaction has not had a complex created, so we
234                    # must create one.
235                    $self->Add(pseudoComplex => 1);
236                    $self->PutE(Complex => $reaction);
237                    $self->PutR(IsSetOf => $reaction, $reaction);
238                }
239                # Connect the reaction's complex to this role.
240                $self->PutR(IsTriggeredBy => $reaction, $role);
241                $self->Add(missingTrigger => 1);
242            }
243        }
244        # Now we create the models.
245        $ih = $self->CheckFile("$dir/ModelGenome.txt", qw(ModelID Name GenomeID));
246        while (! eof $ih) {
247            # Get the next model.
248            my ($model, $name, $genome) = $self->ReadLine($ih);
249            # Create the model.
250            $self->PutE(Model => $model);
251            # Connect it to the genome. Again, the genomes are created elsewhere.
252            $self->PutR(IsModeledBy => $genome, $model);
253        }
254        # Next we connect the reactions to models.
255        $ih = $self->CheckFile("$dir/ModelReaction.txt", qw(ModelID ReactionID));
256        while (! eof $ih) {
257            # Get the next line.
258            my ($model, $reaction) = $self->ReadLine($ih);
259            # Only proceed if a reaction is present.
260            if ($reaction) {
261                # Insure the reaction exists.
262                $self->CreateReaction($reaction);
263                # Connect the reaction to the model.
264                $self->PutR(IsRequiredBy => $reaction, $model);
265            }
266        }
267    }
268    
269    =head3 CheckFile
270    
271        my $ih = $sl->CheckFile($fileName, @fieldNames);
272    
273    Read the header record of the specified file and verify that the field names match
274    the names in the input list. If they do not, an error will be thrown; if they do, an
275    open file handle will be returned, positioned on the first data record.
276    
277    =over 4
278    
279    =item fileName
280    
281    Name for the input file. The file is in standard tab-delimited format. The first record
282    contains the field names and the remaining records contain the data.
283    
284    =item fieldNames
285    
286    List of the field names expected, in order.
287    
288    =item RETURN
289    
290    Returns the open file handle if successful. If there is a mismatch, throws an error.
291    
292    =back
293    
294    =cut
295    
296    sub CheckFile {
297        # Get the parameters.
298        my ($self, $fileName, @fieldNames) = @_;
299        # Open the file.
300        my $retVal = Open(undef, "<$fileName");
301        $self->Add(files => 1);
302        # Read in the file header.
303        my @actualFields = Tracer::GetLine($retVal);
304        # This will be set to TRUE if there's a mismatch.
305        my $error = 0;
306        for (my $i = 0; $i <= $#fieldNames; $i++) {
307            if ($fieldNames[$i] ne $actualFields[$i]) {
308                Trace("Field match error: expected $fieldNames[$i], found $actualFields[$i].") if T(0);
309                $error = 1;
310            }
311        }
312        # Was there an error?
313        if ($error) {
314            # Yes, so abort.
315            Confess("Invalid field name header in $fileName.");
316                     } else {                     } else {
317                      $Enzyme =~ s/\s//g;          # No, so trace the open.
318                      $self->PutE(EcNumber => $Enzyme, obsolete => 0, replacedby => "NONE");          Trace("Processing $fileName.") if T(ERDBLoadGroup => 2);
                     $self->PutR(IsCategorizedInto => $LoadingArray[0],$Enzyme,source => "KEGG");  
                    }  
                 }  
             }  
             #Adding the relationship between reaction and alias type  
             if (defined($Object->{"NAME"})) {  
                 foreach my $Name (@{$Object->{"NAME"}}) {  
                     $self->PutR(HasReactionAliasOf => $LoadingArray[0],"NAME",alias => $Name);  
                 }  
             }  
             if (defined($Object->{"DBLINKS"})) {  
                 foreach my $Link (@{$Object->{"DBLINKS"}}) {  
                     my @TempArray = split(/:/,$Link);  
                     if (@TempArray >= 2) {  
                         if ($TempArray[0] ne "KEGG" && $TempArray[0] ne "ARGONNE") {  
                             $self->PutE(AliasType => $TempArray[0], source => "PUBLISHED MODEL");  
                         }  
                         if ($TempArray[0] eq "ARGONNE") {  
                             splice(@TempArray,1,1);  
                         }  
                         for (my $j=1; $j < @TempArray; $j++) {  
                             $self->PutR(HasReactionAliasOf => $LoadingArray[0],$TempArray[0],alias => $TempArray[$j]);  
                         }  
                     }  
                 }  
             }  
319          }          }
320        # Return the file handle.
321        return $retVal;
322      }      }
323    
324    =head3 ReadLine
325    
326        my @fields = $sl->ReadLine($ih);
327    
328    Read a line of data from an input file.
329    
330    =over 4
331    
332    =item ih
333    
334    Open file handle for the input file.
335    
336    =item RETURN
337    
338    Returns a list of the field values for the next record in the file.
339    
340    =back
341    
342    =cut
343    
344    sub ReadLine {
345        # Get the parameters.
346        my ($self, $ih) = @_;
347        # Read the line.
348        my @retVal = Tracer::GetLine($ih);
349        # Count this record.
350        $self->Track(records => $retVal[0], 1000);
351        # Return the data.
352        return @retVal;
353  }  }
354    
355    
356  sub FixDate {  =head3 CheckReaction
357      my ($date) = @_;  
358      my $retVal = ($date eq 'NA' ? 0 : $date);      $sl->CheckReaction($reaction);
359      return $retVal;  
360    Insure we have created a rectord for the specified reaction.
361    
362    =over 4
363    
364    =item reaction
365    
366    ID of the reaction in question.
367    
368    =back
369    
370    =cut
371    
372    sub CreateReaction {
373        # Get the parameters.
374        my ($self, $reaction) = @_;
375        # Get the reaction hash.
376        my $reactionH = $self->{reactions};
377        # See if this reaction is new.
378        if (! $reactionH->{$reaction}) {
379            # It is, so create it.
380            $self->PutE(Reaction => $reaction);
381            # Insure we don't create it again.
382            $reactionH->{$reaction} = 1;
383        }
384  }  }
385    
386  1;  1;

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