/*******************************************************************************  authors      : Peter Pipenbacher  filename     : ghmm++/examples/dna.cpp  created      : DATE: 2002-03-14  $Id: dna.cpp,v 1.2 2003/02/28 15:09:37 wasinee Exp $  Copyright (C) 1998-2001, ZAIK/ZPR, Universit鋞 zu K鰈n    This program is free software; you can redistribute it and/or modify  it under the terms of the GNU General Public License as published by  the Free Software Foundation; either version 2 of the License, or  (at your option) any later version.    This program is distributed in the hope that it will be useful,  but WITHOUT ANY WARRANTY; without even the implied warranty of  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the  GNU General Public License for more details.    You should have received a copy of the GNU General Public License  along with this program; if not, write to the Free Software  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  *******************************************************************************/#include "ghmm++/GHMM.h"#ifdef HAVE_NAMESPACESusing namespace std;#endifint dna_test() {  GHMM_Alphabet alphabet;  alphabet.addSymbol("A");  alphabet.addSymbol("C");  alphabet.addSymbol("T");  alphabet.addSymbol("G");  alphabet.addSymbol("-");  GHMM_DiscreteModel model(&alphabet);  model.addState("StartRegion");  model.addState("EndRegion");  model.getState("StartRegion")->setInitialProbability(0.6);  model.getState("StartRegion")->setOutputProbability("A",0.2);  model.getState("StartRegion")->setOutputProbability("C",0.2);  model.getState("StartRegion")->setOutputProbability("T",0.2);  model.getState("StartRegion")->setOutputProbability("G",0.2);  model.getState("StartRegion")->setOutputProbability("-",0.2);  model.getState("EndRegion")->setInitialProbability(0.4);  model.getState("EndRegion")->setOutputProbability("A",0.0);  model.getState("EndRegion")->setOutputProbability("C",0.5);  model.getState("EndRegion")->setOutputProbability("T",0.0);  model.getState("EndRegion")->setOutputProbability("G",0.5);    model.setTransition("EndRegion","EndRegion",0.9);  model.setTransition("EndRegion","StartRegion",0.1);  model.setTransition("StartRegion","EndRegion",0.1);  model.setTransition("StartRegion","StartRegion",0.9);  if (model.check() != 0)    return 1;  GHMM_Sequences seq(&alphabet);  seq.add("AAACGCGCGCGCGCG");  seq.add("CGCTTGGCGCGCGCGCG");  seq.add("TAGCA-CGCGCGCGCG");  seq.add("-CC-AGCGCGCGCGCG");  seq.add("--CTGATTCGCGCGCGCG");  seq.add("C-G-GGCGCGCGCGCG");  seq.add("A--CGCGCGCGCGCG");  seq.add("------CGCGCGCGCG");  seq.add("CGATAACTTGCGCGCGCG");  seq.add("CGGG--TCGCGCGCGCG");  model.reestimate_baum_welch(&seq);  model.A_print(stdout,""," ","\n");   model.B_print(stdout,""," ","\n");   GHMM_Document doc;  doc.open("dna.xml","w");  doc.writeElement(&model);  doc.writeEndl();  doc.writeEndl();  doc.writeElement(&seq);  doc.writeEndl();  doc.close();  doc.open("dna.xml","r");  doc.readDocument();  doc.close();  GHMM_DiscreteModel* new_model = doc.getDiscreteModel();  GHMM_Sequences* new_seq = doc.getSequences();  doc.open("dna2.xml","w");  doc.writeElement(new_model);  doc.writeEndl();  doc.writeEndl();  doc.writeElement(new_seq);  doc.writeEndl();  doc.close();    cout << "Wrote to dna2.xml" << endl;  delete new_model;  delete new_seq;  //SAFE_DELETE(new_model);  //SAFE_DELETE(new_seq);  return 0;}int main() {  /* Important! initialise rng  */  GHMM_Toolkit::gsl_rng_init();  int result = dna_test();#ifdef WIN32  printf("\nPress ENTER\n");  fgetc(stdin);#endif  return result;}