standardtopologymodelercreator.java

马尔科夫模型的c语言实现

	modelmaker.setTransition("R6", "e");
	modelmaker.initializeTransitionProbabilities("R6");

	modelmaker.setTransition("R7", "R_loop");
	modelmaker.setTransition("R7", "R8");
	modelmaker.setTransition("R7", "R9");
	modelmaker.setTransition("R7", "e");
	modelmaker.initializeTransitionProbabilities("R7");

	modelmaker.setTransition("R_loop", "R8");
	modelmaker.setTransition("R_loop", "e");
	m1 = modelmaker.getModule("R_loop");
	l = m1.getVertices();
	v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), ((double)(R_LOOP - 1))/(double)(R_LOOP));
	modelmaker.initializeTransitionProbabilities("R_loop");

	modelmaker.setTransition("R8", "R9");
	modelmaker.setTransition("R8", "e");
	modelmaker.initializeTransitionProbabilities("R8");

	modelmaker.setTransition("R9", "R10");
	modelmaker.setTransition("R9", "e");
	modelmaker.initializeTransitionProbabilities("R9");

	modelmaker.setTransition("R10", "R11");
	modelmaker.setTransition("R10", "e");
	modelmaker.initializeTransitionProbabilities("R10");

	modelmaker.setTransition("R11", "R12");
	modelmaker.setTransition("R11", "e");
	modelmaker.initializeTransitionProbabilities("R11");

	modelmaker.setTransition("R12", "R13");
	modelmaker.setTransition("R12", "e");
	modelmaker.initializeTransitionProbabilities("R12");

	modelmaker.setTransition("R13", "R14");
	modelmaker.setTransition("R13", "e");
	modelmaker.initializeTransitionProbabilities("R13");

	modelmaker.setTransition("R14", "L_u");
	modelmaker.setTransition("R14", "e");
	modelmaker.initializeTransitionProbabilities("R14");


	/* inside interface helix */
	modelmaker.setTransition("Hu1", "Hu2");
	modelmaker.setTransition("Hu1", "Hd2");
	modelmaker.setTransition("Hu1", "e");
	modelmaker.initializeTransitionProbabilities("Hu1");

	modelmaker.setTransition("Hu2", "Hu3");
	modelmaker.setTransition("Hu2", "Hd3");
	modelmaker.setTransition("Hu2", "e");
	modelmaker.initializeTransitionProbabilities("Hu2");

	modelmaker.setTransition("Hu3", "Hu4");
	modelmaker.setTransition("Hu3", "Hd4");
	modelmaker.setTransition("Hu3", "e");
	modelmaker.initializeTransitionProbabilities("Hu3");

	modelmaker.setTransition("Hu4", "Hu5");
	modelmaker.setTransition("Hu4", "Hd5");
	modelmaker.setTransition("Hu4", "L_u");
	modelmaker.setTransition("Hu4", "G");
	modelmaker.setTransition("Hu4", "e");
	modelmaker.initializeTransitionProbabilities("Hu4");
	
	modelmaker.setTransition("Hu5", "Hu6");
	modelmaker.setTransition("Hu5", "Hd6");
	modelmaker.setTransition("Hu5", "L_u");
	modelmaker.setTransition("Hu5", "G");
	modelmaker.setTransition("Hu5", "e");
	modelmaker.initializeTransitionProbabilities("Hu5");

	modelmaker.setTransition("Hu6", "Hu7");
	modelmaker.setTransition("Hu6", "Hd7");
	modelmaker.setTransition("Hu6", "L_u");
	modelmaker.setTransition("Hu6", "G");
	modelmaker.setTransition("Hu6", "e");
	modelmaker.initializeTransitionProbabilities("Hu6");
	
	modelmaker.setTransition("Hu7", "Hu8");
	modelmaker.setTransition("Hu7", "Hd8");
	modelmaker.setTransition("Hu7", "L_u");
	modelmaker.setTransition("Hu7", "G");
	modelmaker.setTransition("Hu7", "e");
	modelmaker.initializeTransitionProbabilities("Hu7");

	modelmaker.setTransition("Hu8", "Hu9");
	modelmaker.setTransition("Hu8", "Hd9");
	modelmaker.setTransition("Hu8", "L_u");
	modelmaker.setTransition("Hu8", "G");
	modelmaker.setTransition("Hu8", "e");
	modelmaker.initializeTransitionProbabilities("Hu8");

	modelmaker.setTransition("Hu9", "Hu10");
	modelmaker.setTransition("Hu9", "Hd10");
	modelmaker.setTransition("Hu9", "L_u");
	modelmaker.setTransition("Hu9", "G");
	modelmaker.setTransition("Hu9", "e");
	modelmaker.initializeTransitionProbabilities("Hu9");

	modelmaker.setTransition("Hu10", "Hu11");
	modelmaker.setTransition("Hu10", "Hd11");
	modelmaker.setTransition("Hu10", "L_u");
	modelmaker.setTransition("Hu10", "G");
	modelmaker.setTransition("Hu10", "e");
	modelmaker.initializeTransitionProbabilities("Hu10");

	modelmaker.setTransition("Hu11", "Hu12");
	modelmaker.setTransition("Hu11", "Hd12");
	modelmaker.setTransition("Hu11", "L_u");
	modelmaker.setTransition("Hu11", "G");
	modelmaker.setTransition("Hu11", "e");
	modelmaker.initializeTransitionProbabilities("Hu11");

	modelmaker.setTransition("Hu12", "Hu_loop");
	modelmaker.setTransition("Hu12", "Hd_loop");
	modelmaker.setTransition("Hu12", "L_u");
	modelmaker.setTransition("Hu12", "G");
	modelmaker.setTransition("Hu12", "e");
	modelmaker.initializeTransitionProbabilities("Hu12");
	
	modelmaker.setTransition("Hu_loop", "Hd_loop");
	modelmaker.setTransition("Hu_loop", "L_u");
	modelmaker.setTransition("Hu_loop", "G");
	modelmaker.setTransition("Hu_loop", "e");
	m1 = modelmaker.getModule("Hu_loop");
	l = m1.getVertices();
	v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), ((double)(HU_LOOP - 1))/(double)(HU_LOOP));
	modelmaker.initializeTransitionProbabilities("Hu_loop");

	modelmaker.setTransition("Hd1", "Hd2");
	modelmaker.setTransition("Hd1", "Hu2");
	modelmaker.setTransition("Hd1", "e");
	modelmaker.initializeTransitionProbabilities("Hd1");

	modelmaker.setTransition("Hd2", "Hd3");
	modelmaker.setTransition("Hd2", "Hu3");
	modelmaker.setTransition("Hd2", "e");
	modelmaker.initializeTransitionProbabilities("Hd2");

	modelmaker.setTransition("Hd3", "Hd4");
	modelmaker.setTransition("Hd3", "Hu4");
	modelmaker.setTransition("Hd3", "e");
	modelmaker.initializeTransitionProbabilities("Hd3");

	modelmaker.setTransition("Hd4", "Hd5");
	modelmaker.setTransition("Hd4", "Hu5");
	modelmaker.setTransition("Hd4", "L_u");
	modelmaker.setTransition("Hd4", "G");
	modelmaker.setTransition("Hd4", "e");
	modelmaker.initializeTransitionProbabilities("Hd4");
	
	modelmaker.setTransition("Hd5", "Hd6");
	modelmaker.setTransition("Hd5", "Hu6");
	modelmaker.setTransition("Hd5", "L_u");
	modelmaker.setTransition("Hd5", "G");
	modelmaker.setTransition("Hd5", "e");
	modelmaker.initializeTransitionProbabilities("Hd5");

	modelmaker.setTransition("Hd6", "Hd7");
	modelmaker.setTransition("Hd6", "Hu7");
	modelmaker.setTransition("Hd6", "L_u");
	modelmaker.setTransition("Hd6", "G");
	modelmaker.setTransition("Hd6", "e");
	modelmaker.initializeTransitionProbabilities("Hd6");
	
	modelmaker.setTransition("Hd7", "Hd8");
	modelmaker.setTransition("Hd7", "Hu8");
	modelmaker.setTransition("Hd7", "L_u");
	modelmaker.setTransition("Hd7", "G");
	modelmaker.setTransition("Hd7", "e");
	modelmaker.initializeTransitionProbabilities("Hd7");

	modelmaker.setTransition("Hd8", "Hd9");
	modelmaker.setTransition("Hd8", "Hu9");
	modelmaker.setTransition("Hd8", "L_u");
	modelmaker.setTransition("Hd8", "G");
	modelmaker.setTransition("Hd8", "e");
	modelmaker.initializeTransitionProbabilities("Hd8");

	modelmaker.setTransition("Hd9", "Hd10");
	modelmaker.setTransition("Hd9", "Hu10");
	modelmaker.setTransition("Hd9", "L_u");
	modelmaker.setTransition("Hd9", "G");
	modelmaker.setTransition("Hd9", "e");
	modelmaker.initializeTransitionProbabilities("Hd9");

	modelmaker.setTransition("Hd10", "Hd11");
	modelmaker.setTransition("Hd10", "Hu11");
	modelmaker.setTransition("Hd10", "L_u");
	modelmaker.setTransition("Hd10", "G");
	modelmaker.setTransition("Hd10", "e");
	modelmaker.initializeTransitionProbabilities("Hd10");

	modelmaker.setTransition("Hd11", "Hd12");
	modelmaker.setTransition("Hd11", "Hu12");
	modelmaker.setTransition("Hd11", "L_u");
	modelmaker.setTransition("Hd11", "G");
	modelmaker.setTransition("Hd11", "e");
	modelmaker.initializeTransitionProbabilities("Hd11");

	modelmaker.setTransition("Hd12", "Hd_loop");
	modelmaker.setTransition("Hd12", "Hu_loop");
	modelmaker.setTransition("Hd12", "L_u");
	modelmaker.setTransition("Hd12", "G");
	modelmaker.setTransition("Hd12", "e");
	modelmaker.initializeTransitionProbabilities("Hd12");
	
	modelmaker.setTransition("Hd_loop", "Hu_loop");
	modelmaker.setTransition("Hd_loop", "L_u");
	modelmaker.setTransition("Hd_loop", "G");
	modelmaker.setTransition("Hd_loop", "e");
	m1 = modelmaker.getModule("Hd_loop");
	l = m1.getVertices();
	v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), ((double)(HD_LOOP - 1))/(double)(HD_LOOP));
	modelmaker.initializeTransitionProbabilities("Hd_loop");


	modelmaker.setTransition("ohelixi1", "ohelixi2");
	modelmaker.initializeTransitionProbabilities("ohelixi1");
	modelmaker.setTransition("ohelixi2", "ohelixi3");
	modelmaker.initializeTransitionProbabilities("ohelixi2");
	modelmaker.setTransition("ohelixi3", "ohelixi4");
	modelmaker.initializeTransitionProbabilities("ohelixi3");
	modelmaker.setTransition("ohelixi4", "ohelixi5");
	modelmaker.initializeTransitionProbabilities("ohelixi4");
	modelmaker.setTransition("ohelixi5", "ohelixi6");
	modelmaker.initializeTransitionProbabilities("ohelixi5");	
	modelmaker.setTransition("ohelixi6", "ohelixi7");
	modelmaker.initializeTransitionProbabilities("ohelixi6");
	modelmaker.setTransition("ohelixi7", "ohelix");
	modelmaker.initializeTransitionProbabilities("ohelixi7");	

	modelmaker.setTransition("ihelixo1", "ihelixo2");
	modelmaker.initializeTransitionProbabilities("ihelixo1");
	modelmaker.setTransition("ihelixo2", "ihelixo3");
	modelmaker.initializeTransitionProbabilities("ihelixo2");
	modelmaker.setTransition("ihelixo3", "ihelixo4");
	modelmaker.initializeTransitionProbabilities("ihelixo3");
	modelmaker.setTransition("ihelixo4", "ihelixo5");
	modelmaker.initializeTransitionProbabilities("ihelixo4");
	modelmaker.setTransition("ihelixo5", "ihelixo6");
	modelmaker.initializeTransitionProbabilities("ihelixo5");
	modelmaker.setTransition("ihelixo6", "ihelixo7");
	modelmaker.initializeTransitionProbabilities("ihelixo6");
	modelmaker.setTransition("ihelixo7", "ihelix");
	modelmaker.initializeTransitionProbabilities("ihelixo7");

	modelmaker.setTransition("ohelixo2", "ohelixo3");
	modelmaker.initializeTransitionProbabilities("ohelixo2");
	modelmaker.setTransition("ohelixo3", "ohelixo4");
	modelmaker.initializeTransitionProbabilities("ohelixo3");
	modelmaker.setTransition("ohelixo4", "ohelixo5");
	modelmaker.initializeTransitionProbabilities("ohelixo4");
	modelmaker.setTransition("ohelixo5", "ohelixo6");
	modelmaker.initializeTransitionProbabilities("ohelixo5");	
	modelmaker.setTransition("ohelixo6", "ohelixo7");
	modelmaker.initializeTransitionProbabilities("ohelixo6");
	modelmaker.setTransition("ohelixo7", "L_u");
	modelmaker.initializeTransitionProbabilities("ohelixo7");	
	
	modelmaker.setTransition("ihelixi2", "ihelixi3");
	modelmaker.initializeTransitionProbabilities("ihelixi2");
	modelmaker.setTransition("ihelixi3", "ihelixi4");
	modelmaker.initializeTransitionProbabilities("ihelixi3");
	modelmaker.setTransition("ihelixi4", "ihelixi5");
	modelmaker.initializeTransitionProbabilities("ihelixi4");
	modelmaker.setTransition("ihelixi5", "ihelixi6");
	modelmaker.initializeTransitionProbabilities("ihelixi5");
	modelmaker.setTransition("ihelixi6", "ihelixi7");
	modelmaker.initializeTransitionProbabilities("ihelixi6");
	modelmaker.setTransition("ihelixi7", "l_u");
	modelmaker.initializeTransitionProbabilities("ihelixi7");

	modelmaker.setTransition("ohelix", "ohelixo2");
	Forward_std f1 = ((Forward_std)modelmaker.getModule("ohelix"));
	modelmaker.initializeTransitionProbabilities("ohelix");
	
	modelmaker.setTransition("ihelix", "ihelixi2");
	f1 = ((Forward_std)modelmaker.getModule("ihelix"));
	modelmaker.initializeTransitionProbabilities("ihelix");	

	

	LinkedList distribGroup = new LinkedList();
	distribGroup.add("G");
	distribGroup.add("g");
	modelmaker.addDistributionGroup(distribGroup);
	
	distribGroup = new LinkedList();
	distribGroup.add("c");
	distribGroup.add("c_loop");
	modelmaker.addDistributionGroup(distribGroup);

	distribGroup = new LinkedList();
	distribGroup.add("C");
	distribGroup.add("C_loop");
	modelmaker.addDistributionGroup(distribGroup);

	distribGroup = new LinkedList();
	distribGroup.add("hd1");
	distribGroup.add("hd2");
	distribGroup.add("hd3");
	distribGroup.add("hd4");
	distribGroup.add("hd5");
	distribGroup.add("hd6");
	distribGroup.add("hd7");
	distribGroup.add("hd8");
	distribGroup.add("hd9");
	distribGroup.add("hd10");
	distribGroup.add("hd11");
	distribGroup.add("hd12");
	distribGroup.add("hd_loop");
	modelmaker.addDistributionGroup(distribGroup);
	
	distribGroup = new LinkedList();
	distribGroup.add("hu1");
	distribGroup.add("hu2");
	distribGroup.add("hu3");
	distribGroup.add("hu4");
	distribGroup.add("hu5");
	distribGroup.add("hu6");
	distribGroup.add("hu7");
	distribGroup.add("hu8");
	distribGroup.add("hu9");
	distribGroup.add("hu10");
	distribGroup.add("hu11");
	distribGroup.add("hu12");
	distribGroup.add("hu_loop");
	modelmaker.addDistributionGroup(distribGroup);