[Bio] / FigKernelPackages / MergeTransactions.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/MergeTransactions.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.1, Thu Sep 1 09:35:43 2005 UTC revision 1.3, Thu Dec 6 13:59:34 2007 UTC
# Line 1  Line 1 
1  #!/usr/bin/perl -w  #!/usr/bin/perl -w
2    #
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    #
18    
19    
20  package MergeTransactions;  package MergeTransactions;
21    
# Line 76  Line 93 
93    
94  =head3 new  =head3 new
95    
96  C<< my $xprc = MergeTransactions->new(\%options, $command, $directory, $idFile); >>      my $xprc = MergeTransactions->new(\%options, $command, $directory, $idFile);
97    
98  Construct a new MergeTransactions object.  Construct a new MergeTransactions object.
99    
# Line 112  Line 129 
129    
130  =head3 Setup  =head3 Setup
131    
132  C<< $xprc->Setup(); >>      $xprc->Setup();
133    
134  Set up to apply the transactions. This includes reading the ID file.  Set up to apply the transactions. This includes reading the ID file.
135    
# Line 128  Line 145 
145    
146  =head3 SetupGenome  =head3 SetupGenome
147    
148  C<< $xprc->SetupGenome(); >>      $xprc->SetupGenome();
149    
150  Set up for processing this genome. This involves opening the output file  Set up for processing this genome. This involves opening the output file
151  for the transaction trace. The transaction trace essentially contains the  for the transaction trace. The transaction trace essentially contains the
# Line 145  Line 162 
162    
163  =head3 TeardownGenome  =head3 TeardownGenome
164    
165  C<< $xprc->TeardownGenome(); >>      $xprc->TeardownGenome();
166    
167  Clean up after processing this genome. This involves closing the transaction  Clean up after processing this genome. This involves closing the transaction
168  trace file and optionally committing any updates.  trace file and optionally committing any updates.
# Line 161  Line 178 
178    
179  =head3 Add  =head3 Add
180    
181  C<< $xprc->Add($newID, $locations, $translation); >>      $xprc->Add($newID, $locations, $translation);
182    
183  Add a new feature to the data store.  Add a new feature to the data store.
184    
# Line 195  Line 212 
212    
213  =head3 Change  =head3 Change
214    
215  C<< $xprc->Change($fid, $newID, $locations, $aliases, $translation); >>      $xprc->Change($fid, $newID, $locations, $aliases, $translation);
216    
217  Replace a feature to the data store. The feature will be marked for deletion and  Replace a feature to the data store. The feature will be marked for deletion and
218  a new feature will be put in its place.  a new feature will be put in its place.
# Line 242  Line 259 
259    
260  =head3 Delete  =head3 Delete
261    
262  C<< $xprc->Delete($fid); >>      $xprc->Delete($fid);
263    
264  Delete a feature from the data store. The feature will be marked as deleted,  Delete a feature from the data store. The feature will be marked as deleted,
265  which will remove it from consideration by most FIG methods. A garbage  which will remove it from consideration by most FIG methods. A garbage

Legend:
Removed from v.1.1  
changed lines
  Added in v.1.3

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3