12 static OptionS OptS;  variable
53   return (&OptS);  in decodeCML()
81   fprintf(stderr, "\nUsage: %s [OPTIONS] < SeqFile  > Outfile\n", OptS.ExeName);  in usage()
90 	  OptS.ExeName);  in usage()
97 	  OptS.barrier_heuristic,OptS.dangle, OptS.grouping, OptS.lookahead);  in usage()
104 …        OptS.maxkeep,OptS.noLonelyPairs,OptS.transcribed, OptS.transcription_rate,OptS.windowsize);  in usage()
130   strcpy(OptS.ExeName, name);  in initializeOptions()
132   OptS.init_structure=0;  in initializeOptions()
133   OptS.interrupt_trajectory=0;  in initializeOptions()
134   OptS.printfront=0;  in initializeOptions()
135   OptS.testseq      = 0;  in initializeOptions()
136   OptS.verbose      = 0;  in initializeOptions()
139   OptS.barrier_heuristic= 'M';  in initializeOptions()
140   OptS.dangle=0;  in initializeOptions()
141   strcpy(OptS.grouping,"standard");  in initializeOptions()
142   OptS.lookahead=1;  in initializeOptions()
144   OptS.maxkeep = 1;  in initializeOptions()
145   OptS.noLonelyPairs=2;  in initializeOptions()
146   OptS.transcribed=1;  in initializeOptions()
147   OptS.transcription_rate=200.0;  in initializeOptions()
148   OptS.windowsize=0;  in initializeOptions()
163          OptS.init_structure = 1;   in processOptions()
166          OptS.interrupt_trajectory = 1;   in processOptions()
169 	OptS.printfront = 1;  in processOptions()
172 	OptS.testseq = 1;  in processOptions()
175 	OptS.verbose = 1;  in processOptions()
186 	else { OptS.barrier_heuristic = tmp; }  in processOptions()
194 	else { OptS.dangle = tmp; }  in processOptions()
202 	else { strcpy(OptS.grouping,tmp); }  in processOptions()
210 	else { OptS.lookahead = tmp; }  in processOptions()
219 	else { OptS.maxkeep = tmp; }  in processOptions()
227 	else { OptS.noLonelyPairs = tmp; }  in processOptions()
235 	else { OptS.transcribed = tmp; }  in processOptions()
243 	else { OptS.transcription_rate = tmp; }  in processOptions()
251 	else { OptS.windowsize = tmp;}  in processOptions()
258       OptS.verbose++;  in processOptions()
261       OptS.testseq = 1;  in processOptions()
271     strcpy(OptS.PhylipFile,  argv[optind++]);  in processOptions()
272     strcpy(OptS.DumpFile,    argv[optind++]);  in processOptions()