standardtopologymodelercreator.java

马尔科夫模型的c语言实现

	/* inside loop */
	modelmaker.setTransition("l_u", "l_bott_u");
	modelmaker.setTransition("l_u", "ohelixi1");
	modelmaker.setTransition("l_u", "l_d");
	modelmaker.setTransition("l_u", "r1");
	modelmaker.setTransition("l_u", "hu1");
	modelmaker.setTransition("l_u", "hd1");
	modelmaker.setTransition("l_u", "e");
	modelmaker.initializeTransitionProbabilities("l_u");

	modelmaker.setTransition("l_bott_u", "l_bott_d");
	modelmaker.setTransition("l_bott_u", "l_d");
	modelmaker.setTransition("l_bott_u", "l11u");
	modelmaker.setTransition("l_bott_u", "l21u");
	modelmaker.setTransition("l_bott_u", "l31u");
	modelmaker.setTransition("l_bott_u", "l41u");
	modelmaker.setTransition("l_bott_u", "l51u");
	modelmaker.setTransition("l_bott_u", "r1");
	modelmaker.setTransition("l_bott_u", "hu1");
	modelmaker.setTransition("l_bott_u", "hd1");
	modelmaker.setTransition("l_bott_u", "e");
	modelmaker.initializeTransitionProbabilities("l_bott_u");

	modelmaker.setTransition("l11u", "l_top_u");
	modelmaker.setTransition("l11u", "l11d");
	modelmaker.setTransition("l11u", "l_bott_d");
	modelmaker.setTransition("l11u", "r1");
	modelmaker.setTransition("l11u", "hu1");
	modelmaker.setTransition("l11u", "hd1");
	modelmaker.setTransition("l11u", "e");
	modelmaker.initializeTransitionProbabilities("l11u");

	modelmaker.setTransition("l21u", "l22u");
	modelmaker.setTransition("l21u", "e");
	modelmaker.initializeTransitionProbabilities("l21u");

	modelmaker.setTransition("l22u", "l_top_u");
	modelmaker.setTransition("l22u", "e");
	modelmaker.initializeTransitionProbabilities("l22u");

	modelmaker.setTransition("l31u", "l32u");
	modelmaker.setTransition("l31u", "e");
	modelmaker.initializeTransitionProbabilities("l31u");

	modelmaker.setTransition("l32u", "l33u");
	modelmaker.setTransition("l32u", "e");
	modelmaker.initializeTransitionProbabilities("l32u");

	modelmaker.setTransition("l33u", "l_top_u");
	modelmaker.setTransition("l33u", "e");
	modelmaker.initializeTransitionProbabilities("l33u");
	
	modelmaker.setTransition("l41u", "l42u");
	modelmaker.setTransition("l41u", "e");
	modelmaker.initializeTransitionProbabilities("l41u");

	modelmaker.setTransition("l42u", "l43u");
	modelmaker.setTransition("l42u", "e");
	modelmaker.initializeTransitionProbabilities("l42u");

	modelmaker.setTransition("l43u", "l44u");
	modelmaker.setTransition("l43u", "e");
	modelmaker.initializeTransitionProbabilities("l43u");

	modelmaker.setTransition("l44u", "l_top_u");
	modelmaker.setTransition("l44u", "e");
	modelmaker.initializeTransitionProbabilities("l44u");

	modelmaker.setTransition("l51u", "l52u");
	modelmaker.setTransition("l51u", "e");
	modelmaker.initializeTransitionProbabilities("l51u");

	modelmaker.setTransition("l52u", "l53u");
	modelmaker.setTransition("l52u", "e");
	modelmaker.initializeTransitionProbabilities("l52u");

	modelmaker.setTransition("l53u", "l54u");
	modelmaker.setTransition("l53u", "e");
	modelmaker.initializeTransitionProbabilities("l53u");

	modelmaker.setTransition("l54u", "l55u");
	modelmaker.setTransition("l54u", "e");
	modelmaker.initializeTransitionProbabilities("l54u");

	modelmaker.setTransition("l55u", "l_top_u");
	modelmaker.setTransition("l55u", "e");
	modelmaker.initializeTransitionProbabilities("l55u");

	modelmaker.setTransition("l_top_u", "g");
	modelmaker.setTransition("l_top_u", "l_top_d");
	modelmaker.setTransition("l_top_u", "l11d");
	modelmaker.setTransition("l_top_u", "e");
	modelmaker.initializeTransitionProbabilities("l_top_u");

	modelmaker.setTransition("g", "l_top_d");
	modelmaker.setTransition("g", "hu1");
	modelmaker.setTransition("g", "hd1");
	modelmaker.setTransition("g", "e");
	Module m1 = modelmaker.getModule("g");
	LinkedList l = m1.getVertices();
	Vertex v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), ((double)(lengthI - 1))/(double)(lengthI));
	modelmaker.initializeTransitionProbabilities("g");
	

	modelmaker.setTransition("l_top_d", "l11d");
	modelmaker.setTransition("l_top_d", "l21d");
	modelmaker.setTransition("l_top_d", "l31d");
	modelmaker.setTransition("l_top_d", "l41d");
	modelmaker.setTransition("l_top_d", "l51d");
	modelmaker.setTransition("l_top_d", "e");
	modelmaker.initializeTransitionProbabilities("l_top_d");

	modelmaker.setTransition("l11d", "l_bott_d");
	modelmaker.setTransition("l11d", "e");
	modelmaker.initializeTransitionProbabilities("l11d");

	modelmaker.setTransition("l21d", "l22u");
	modelmaker.setTransition("l21d", "e");
	modelmaker.initializeTransitionProbabilities("l21d");

	modelmaker.setTransition("l22d", "l_bott_d");
	modelmaker.setTransition("l22d", "e");
	modelmaker.initializeTransitionProbabilities("l22d");

	modelmaker.setTransition("l31d", "l32d");
	modelmaker.setTransition("l31d", "e");
	modelmaker.initializeTransitionProbabilities("l31d");

	modelmaker.setTransition("l32d", "l33d");
	modelmaker.setTransition("l32d", "e");
	modelmaker.initializeTransitionProbabilities("l32d");

	modelmaker.setTransition("l33d", "l_bott_d");
	modelmaker.setTransition("l33d", "e");
	modelmaker.initializeTransitionProbabilities("l33d");
	
	modelmaker.setTransition("l41d", "l42d");
	modelmaker.setTransition("l41d", "e");
	modelmaker.initializeTransitionProbabilities("l41d");

	modelmaker.setTransition("l42d", "l43d");
	modelmaker.setTransition("l42d", "e");
	modelmaker.initializeTransitionProbabilities("l42d");

	modelmaker.setTransition("l43d", "l44d");
	modelmaker.setTransition("l43d", "e");
	modelmaker.initializeTransitionProbabilities("l43d");

	modelmaker.setTransition("l44d", "l_bott_d");
	modelmaker.setTransition("l44d", "e");
	modelmaker.initializeTransitionProbabilities("l44d");

	modelmaker.setTransition("l51d", "l52d");
	modelmaker.setTransition("l51d", "e");
	modelmaker.initializeTransitionProbabilities("l51d");

	modelmaker.setTransition("l52d", "l53d");
	modelmaker.setTransition("l52d", "e");
	modelmaker.initializeTransitionProbabilities("l52d");

	modelmaker.setTransition("l53d", "l54d");
	modelmaker.setTransition("l53d", "e");
	modelmaker.initializeTransitionProbabilities("l53d");

	modelmaker.setTransition("l54d", "l55d");
	modelmaker.setTransition("l54d", "e");
	modelmaker.initializeTransitionProbabilities("l54d");

	modelmaker.setTransition("l55d", "l_bott_d");
	modelmaker.setTransition("l55d", "e");
	modelmaker.initializeTransitionProbabilities("l55d");

	modelmaker.setTransition("l_bott_d", "l_d");
	modelmaker.setTransition("l_bott_d", "l_u");
	modelmaker.setTransition("l_bott_d", "e");
	modelmaker.initializeTransitionProbabilities("l_bott_d");

	modelmaker.setTransition("l_d", "c");
	modelmaker.setTransition("l_d", "ohelixi1");
	modelmaker.setTransition("l_d", "e");
	modelmaker.initializeTransitionProbabilities("l_d");

	modelmaker.setTransition("c", "c_loop");
	modelmaker.setTransition("c", "l_u");
	modelmaker.setTransition("c", "e");
	modelmaker.initializeTransitionProbabilities("c");

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

	
	/* inside reentrant */
	modelmaker.setTransition("r1", "r2");
	modelmaker.setTransition("r1", "e");
	modelmaker.initializeTransitionProbabilities("r1");

	modelmaker.setTransition("r2", "r3");
	modelmaker.setTransition("r2", "e");
	modelmaker.initializeTransitionProbabilities("r2");

	modelmaker.setTransition("r3", "r4");
	modelmaker.setTransition("r3", "e");
	modelmaker.initializeTransitionProbabilities("r3");

	modelmaker.setTransition("r4", "r5");
	modelmaker.setTransition("r4", "r11");
	modelmaker.setTransition("r4", "e");
	modelmaker.initializeTransitionProbabilities("r4");
	
	modelmaker.setTransition("r5", "r6");
	modelmaker.setTransition("r5", "r10");
	modelmaker.setTransition("r5", "r11");
	modelmaker.setTransition("r5", "e");
	modelmaker.initializeTransitionProbabilities("r5");

	modelmaker.setTransition("r6", "r7");
	modelmaker.setTransition("r6", "r9");
	modelmaker.setTransition("r6", "r10");
	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");