shadowmsatmhmmcreator.java

马尔科夫模型的c语言实现

	res = modelmaker.createModule("out23_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out24", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out24_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out25", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out25_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out26", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out26_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out27", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out27_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out28", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out28_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out29", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out29_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglobShort", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglobShort_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");

	res = modelmaker.createModule("ohelixi1", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi1_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi2", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi2_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi3", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi3_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi4", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi4_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi5", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi5_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi6", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi6_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi7", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixi7_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");



	//res = modelmaker.createModule("ohelix", HMM.FORWARD_STD, HMM.EVEN, 2, 22, "M");
	res = modelmaker.createModule("ohelix1", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix1_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix2", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix2_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix3", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix3_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix4", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix4_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix5", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix5_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix6", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix6_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix7", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix7_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix8", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix8_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix9", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix9_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix10", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix10_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix11", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix11_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix12", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix12_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix13", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix13_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix14", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix14_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix15", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix15_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix16", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix16_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix17", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix17_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix18", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix18_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix19", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix19_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix20", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix20_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix21", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix21_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix22", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelix22_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");


	res = modelmaker.createModule("ohelixo2", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo2_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo3", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo3_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo4", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo4_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo5", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo5_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo6", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo6_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo7", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ohelixo7_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	
	res = modelmaker.createModule("ihelixi2", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi2_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi3", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi3_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi4", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi4_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi5", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi5_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi6", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi6_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi7", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixi7_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");

	//res = modelmaker.createModule("ihelix", HMM.FORWARD_STD, HMM.EVEN, 2, 22, "M");
	res = modelmaker.createModule("ihelix1", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix1_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix2", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix2_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix3", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix3_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix4", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix4_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix5", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix5_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix6", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix6_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix7", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix7_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix8", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix8_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix9", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix9_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix10", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix10_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix11", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix11_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix12", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix12_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix13", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix13_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix14", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix14_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix15", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix15_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix16", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix16_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix17", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix17_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix18", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix18_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix19", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix19_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix20", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix20_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix21", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix21_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix22", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelix22_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");



	res = modelmaker.createModule("ihelixo1", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo1_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo2", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo2_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo3", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo3_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo4", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo4_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo5", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo5_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo6", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo6_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo7", HMM.SINGLENODE, HMM.EVEN, 1, "M");
	res = modelmaker.createModule("ihelixo7_s", HMM.SINGLELOOP, HMM.EVEN, 1, "M");

	res = modelmaker.createModule("e", HMM.ENDNODE, HMM.ZERO, 1, "0");

	
	
	modelmaker.setTransition("s", "in10");
	modelmaker.setTransition("s", "in10_s");
	modelmaker.setTransition("s", "out10");
	modelmaker.setTransition("s", "out10_s");
	modelmaker.setTransition("s", "outglob10");
	modelmaker.setTransition("s", "outglob10_s");
	modelmaker.initializeTransitionProbabilities("s");
	
	double distribSum = 0.0;
	for(int i = 1; i <= 20; i++) {
	    distribSum += Math.pow(i, (f_i/2 - 1)) * Math.exp((0-i)/q_i);
	}
	double tot = 1.0;

	modelmaker.setTransition("in10", "in11");
	modelmaker.setTransition("in10", "in29");
	modelmaker.setTransition("in10", "ohelixi1");
	modelmaker.setTransition("in10", "in10_s");
	modelmaker.setTransition("in10", "e");
	//tot = setChiSquareDistrib("in10", 1, 2, f_i, q_i, distribSum, tot);
	modelmaker.initializeTransitionProbabilities("in10");

	modelmaker.setTransition("in10_s", "in11");
	modelmaker.setTransition("in10_s", "in29");
	modelmaker.setTransition("in10_s", "ohelixi1");
	modelmaker.setTransition("in10_s", "e");
	Module m1 = modelmaker.getModule("in10_s");
	LinkedList l = m1.getVertices();
	Vertex v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), gapLenProb);
	modelmaker.initializeTransitionProbabilities("in10_s");


	modelmaker.setTransition("in11", "in12");
	modelmaker.setTransition("in11", "in28");
	modelmaker.setTransition("in11", "in29");
	modelmaker.setTransition("in11", "in11_s");
	modelmaker.setTransition("in11", "e");
	//tot = setChiSquareDistrib("in11", 3, 4, f_i, q_i, distribSum, tot);
	modelmaker.initializeTransitionProbabilities("in11");

	modelmaker.setTransition("in11_s", "in12");
	modelmaker.setTransition("in11_s", "in28");
	modelmaker.setTransition("in11_s", "in29");
	modelmaker.setTransition("in11_s", "e");
	m1 = modelmaker.getModule("in11_s");
	l = m1.getVertices();
	v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), gapLenProb);
	modelmaker.initializeTransitionProbabilities("in11_s");


	modelmaker.setTransition("in12", "in13");
	modelmaker.setTransition("in12", "in27");
	modelmaker.setTransition("in12", "in28");
	modelmaker.setTransition("in12", "in12_s");
	modelmaker.setTransition("in12", "e");
	//tot = setChiSquareDistrib("in12", 5, 6, f_i, q_i, distribSum, tot);
	modelmaker.initializeTransitionProbabilities("in12");

	modelmaker.setTransition("in12_s", "in13");
	modelmaker.setTransition("in12_s", "in27");
	modelmaker.setTransition("in12_s", "in28");
	modelmaker.setTransition("in12_s", "e");
	m1 = modelmaker.getModule("in12_s");
	l = m1.getVertices();
	v = ((Vertex)l.get(0));
	v.setTransitionProbability(v.getNumber(), gapLenProb);
	modelmaker.initializeTransitionProbabilities("in12_s");


	modelmaker.setTransition("in13", "in14");
	modelmaker.setTransition("in13", "in26");
	modelmaker.setTransition("in13", "in27");
	modelmaker.setTransition("in13", "in13_s");
	modelmaker.setTransition("in13", "e");
	v.setTransitionProbability(v.getNumber(), gapLenProb);
	//tot = setChiSquareDistrib("in13", 7, 8, f_i, q_i, distribSum, tot);
	modelmaker.initializeTransitionProbabilities("in13");

	modelmaker.setTransition("in13_s", "in14");
	modelmaker.setTransition("in13_s", "in26");
	modelmaker.setTransition("in13_s", "in27");
	modelmaker.setTransition("in13_s", "e");
	m1 = modelmaker.getModule("in13_s");