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revision 1.5, Mon Dec 5 19:06:30 2005 UTC revision 1.6, Thu Dec 6 13:59:34 2007 UTC
# Line 78  Line 78 
78    
79  =head3 new  =head3 new
80    
81  C<< my $xprc = TransactionProcessor->new(\%options, $command, $idFile); >>      my $xprc = TransactionProcessor->new(\%options, $command, $idFile);
82    
83  Construct a new Transaction Processor object.  Construct a new Transaction Processor object.
84    
# Line 131  Line 131 
131    
132  =head3 FIG  =head3 FIG
133    
134  C<< my $fig = $xprc->FIG; >>      my $fig = $xprc->FIG;
135    
136  Return the FIG object used to access and manipulate the data store.  Return the FIG object used to access and manipulate the data store.
137    
# Line 146  Line 146 
146    
147  =head3 GenomeID  =head3 GenomeID
148    
149  C<< my $genomeID = $xprc->GenomeID; >>      my $genomeID = $xprc->GenomeID;
150    
151  Return the ID of the current genome. The current genome is specified by the  Return the ID of the current genome. The current genome is specified by the
152  L</StartGenome> method.  L</StartGenome> method.
# Line 162  Line 162 
162    
163  =head3 CurrentFileName  =head3 CurrentFileName
164    
165  C<< my $name = $xprc->CurrentFileName; >>      my $name = $xprc->CurrentFileName;
166    
167  Return the name of the transaction file currently being read. There is a  Return the name of the transaction file currently being read. There is a
168  difference file for each genome being processed.  difference file for each genome being processed.
# Line 178  Line 178 
178    
179  =head3 IncrementStat  =head3 IncrementStat
180    
181  C<< $xprc->IncrementStat($name); >>      $xprc->IncrementStat($name);
182    
183  Increment the named statistics in the organism statistics object.  Increment the named statistics in the organism statistics object.
184    
# Line 201  Line 201 
201    
202  =head3 AddStats  =head3 AddStats
203    
204  C<< $xprc->AddStats($name1, $name2, ... $nameN); >>      $xprc->AddStats($name1, $name2, ... $nameN);
205    
206  Insure statistics with the specified names exist in the organism statistics  Insure statistics with the specified names exist in the organism statistics
207  object.  object.
# Line 225  Line 225 
225    
226  =head3 AddMessage  =head3 AddMessage
227    
228  C<< $xprc->AddMessage($message); >>      $xprc->AddMessage($message);
229    
230  Add the specified message to the organism statistics object.  Add the specified message to the organism statistics object.
231    
# Line 248  Line 248 
248    
249  =head3 StartGenome  =head3 StartGenome
250    
251  C<< my  = $xprc->StartGenome($genomeID, $orgFileName); >>      my  = $xprc->StartGenome($genomeID, $orgFileName);
252    
253  Start processing a particular genome.  Start processing a particular genome.
254    
# Line 281  Line 281 
281    
282  =head3 EndGenome  =head3 EndGenome
283    
284  C<< my $orgStats = $xprc->EndGenome(); >>      my $orgStats = $xprc->EndGenome();
285    
286  Terminate processing for the current genome and return its statistics object.  Terminate processing for the current genome and return its statistics object.
287    
# Line 304  Line 304 
304    
305  =head3 Option  =head3 Option
306    
307  C<< my $value = $xprc->Option($optionName); >>      my $value = $xprc->Option($optionName);
308    
309  Return the value of the specified command-line option.  Return the value of the specified command-line option.
310    
# Line 332  Line 332 
332    
333  =head3 GetRealID  =head3 GetRealID
334    
335  C<< my $realID = $xprc->GetRealID($ftype, $ordinal, $key); >>      my $realID = $xprc->GetRealID($ftype, $ordinal, $key);
336    
337  Compute the real ID of a new feature. This involves interrogating the ID hash and  Compute the real ID of a new feature. This involves interrogating the ID hash and
338  formatting a full-blown ID out of little bits of information.  formatting a full-blown ID out of little bits of information.
# Line 382  Line 382 
382    
383  =head3 ParseNewID  =head3 ParseNewID
384    
385  C<< my ($ftype, $ordinal, $key) = $xprc->ParseNewID($newID); >>      my ($ftype, $ordinal, $key) = $xprc->ParseNewID($newID);
386    
387  Extract the feature type and ordinal number from an incoming new ID.  Extract the feature type and ordinal number from an incoming new ID.
388    
# Line 428  Line 428 
428    
429  =head3 CheckTranslation  =head3 CheckTranslation
430    
431  C<< my $actualTranslation = $xprc->CheckTranslation($ftype, $locations, $translation); >>      my $actualTranslation = $xprc->CheckTranslation($ftype, $locations, $translation);
432    
433  If we are processing a PEG, insure we have a translation for the peg's locations.  If we are processing a PEG, insure we have a translation for the peg's locations.
434    
# Line 484  Line 484 
484    
485  =head3 ReadIDHash  =head3 ReadIDHash
486    
487  C<< $xprc->ReadIDHash(); >>      $xprc->ReadIDHash();
488    
489  Read the ID hash data from the ID file.  Read the ID hash data from the ID file.
490    
# Line 513  Line 513 
513    
514  =head3 Directory  =head3 Directory
515    
516  C<< my $dirName = $xprc->Directory; >>      my $dirName = $xprc->Directory;
517    
518  Name of the directory containing the transaction files.  Name of the directory containing the transaction files.
519    
# Line 528  Line 528 
528    
529  =head3 IDHash  =head3 IDHash
530    
531  C<< my $idHash = $xprc->IDHash; >>      my $idHash = $xprc->IDHash;
532    
533  Return a reference to the ID hash. The ID hash is used to extract the base  Return a reference to the ID hash. The ID hash is used to extract the base
534  value for new IDs when processing and to count the IDs needed when counting.  value for new IDs when processing and to count the IDs needed when counting.
# Line 544  Line 544 
544    
545  =head3 IncrementID  =head3 IncrementID
546    
547  C<< $xprc->IncrementID($ftype); >>      $xprc->IncrementID($ftype);
548    
549  Increment the ID hash counter for the specified feature type and the current genome.  Increment the ID hash counter for the specified feature type and the current genome.
550    
# Line 573  Line 573 
573    
574  =head3 IDFileName  =head3 IDFileName
575    
576  C<< my $idFileName = $xprc->IDFileName; >>      my $idFileName = $xprc->IDFileName;
577    
578  Return the name of the ID file.  Return the name of the ID file.
579    
# Line 588  Line 588 
588    
589  =head3 Show  =head3 Show
590    
591  C<< my $printout = $xprc->Show(); >>      my $printout = $xprc->Show();
592    
593  Return a display of the global statistics object. The display will be in printable  Return a display of the global statistics object. The display will be in printable
594  form with embedded new-lines.  form with embedded new-lines.

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