standardtmhmmcreator.java

马尔科夫模型的c语言实现

	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", "outglob10");
	modelmaker.setTransition("ohelixo7", "out10");
	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", "in10");
	modelmaker.initializeTransitionProbabilities("ihelixi7");

	modelmaker.setTransition("ohelix", "ohelixo2");
	Forward_std f1 = ((Forward_std)modelmaker.getModule("ohelix"));
	f1.setPoisson(Po, -1);
	modelmaker.initializeTransitionProbabilities("ohelix");
	
	modelmaker.setTransition("ihelix", "ihelixi2");
	f1 = ((Forward_std)modelmaker.getModule("ihelix"));
	f1.setPoisson(Po, -1);
	modelmaker.initializeTransitionProbabilities("ihelix");	

	

	
	LinkedList distribGroup = new LinkedList();
	distribGroup.add("in10");
	distribGroup.add("in11");
	distribGroup.add("in12");
	distribGroup.add("in13");
	distribGroup.add("in14");
	distribGroup.add("in15");
	distribGroup.add("in16");
	distribGroup.add("in17");
	distribGroup.add("in18");
	distribGroup.add("in19");
	distribGroup.add("in20");
	distribGroup.add("in21");
	distribGroup.add("in22");
	distribGroup.add("in23");
	distribGroup.add("in24");
	distribGroup.add("in25");
	distribGroup.add("in26");
	distribGroup.add("in27");
	distribGroup.add("in28");
	distribGroup.add("in29");
	modelmaker.addDistributionGroup(distribGroup);
	
	distribGroup = new LinkedList();
	distribGroup.add("out10");
	distribGroup.add("out11");
	distribGroup.add("out12");
	distribGroup.add("out13");
	distribGroup.add("out14");
	distribGroup.add("out15");
	distribGroup.add("out16");
	distribGroup.add("out17");
	distribGroup.add("out18");
	distribGroup.add("out19");
	distribGroup.add("out20");
	distribGroup.add("out21");
	distribGroup.add("out22");
	distribGroup.add("out23");
	distribGroup.add("out24");
	distribGroup.add("out25");
	distribGroup.add("out26");
	distribGroup.add("out27");
	distribGroup.add("out28");
	distribGroup.add("out29");
	modelmaker.addDistributionGroup(distribGroup);
	
	distribGroup = new LinkedList();
	distribGroup.add("outglob10");
	distribGroup.add("outglob11");
	distribGroup.add("outglob12");
	distribGroup.add("outglob13");
	distribGroup.add("outglob14");
	distribGroup.add("outglob15");
	distribGroup.add("outglob16");
	distribGroup.add("outglob17");
	distribGroup.add("outglob18");
	distribGroup.add("outglob19");
	distribGroup.add("outglob20");
	distribGroup.add("outglob21");
	distribGroup.add("outglob22");
	distribGroup.add("outglob23");
	distribGroup.add("outglob24");
	distribGroup.add("outglob25");
	distribGroup.add("outglob26");
	distribGroup.add("outglob27");
	distribGroup.add("outglob28");
	distribGroup.add("outglob29");
	modelmaker.addDistributionGroup(distribGroup);

	distribGroup = new LinkedList();
	distribGroup.add("ohelixo2");
	distribGroup.add("ohelixo3");
	distribGroup.add("ohelixo4");
	distribGroup.add("ohelixo5");
	distribGroup.add("ohelixo6");
	distribGroup.add("ohelixo7");
	distribGroup.add("ihelixo1");
	distribGroup.add("ihelixo2");
	distribGroup.add("ihelixo3");
	distribGroup.add("ihelixo4");
	distribGroup.add("ihelixo5");
	distribGroup.add("ihelixo6");
	distribGroup.add("ihelixo7");
	modelmaker.addDistributionGroup(distribGroup);	
	
	distribGroup = new LinkedList();
	distribGroup.add("ihelixi2");
	distribGroup.add("ihelixi3");
	distribGroup.add("ihelixi4");
	distribGroup.add("ihelixi5");
	distribGroup.add("ihelixi6");
	distribGroup.add("ihelixi7");
	distribGroup.add("ohelixi1");
	distribGroup.add("ohelixi2");
	distribGroup.add("ohelixi3");
	distribGroup.add("ohelixi4");
	distribGroup.add("ohelixi5");
	distribGroup.add("ohelixi6");
	distribGroup.add("ohelixi7");
	modelmaker.addDistributionGroup(distribGroup);
	
	distribGroup = new LinkedList();
	distribGroup.add("ihelix");
	distribGroup.add("ohelix");
	modelmaker.addDistributionGroup(distribGroup);

	distribGroup = new LinkedList();
	distribGroup.add("inglob1");
	distribGroup.add("outglobLong");
	distribGroup.add("outglobShort");	
	modelmaker.addDistributionGroup(distribGroup);
	

	LinkedList transTieGroup = new LinkedList();
	transTieGroup.add("ihelix");
	transTieGroup.add("ohelix");
	modelmaker.addTransTieGroup(transTieGroup);

	if(priorfiles.size() >= 1 && !((String)priorfiles.get(0)).equals("null")) {
	    String prifile = ((String)priorfiles.get(0));
	    double priScaler = Double.parseDouble(((String)priorScalers.get(0)));
	    modelmaker.addPriorfile(prifile); 
	    Module m = modelmaker.getModule("in10");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in11");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in12");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in13");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in14");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in15");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in16");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in17");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in18");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in19");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in20");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in21");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in22");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in23");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in24");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in25");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in26");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in27");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in28");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	    m = modelmaker.getModule("in29");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[3]);
	}

	if(priorfiles.size() >= 2 && !((String)priorfiles.get(1)).equals("null")) {
	    String prifile = ((String)priorfiles.get(1));
	    double priScaler = Double.parseDouble(((String)priorScalers.get(1)));
	    modelmaker.addPriorfile(prifile); 
	    Module m = modelmaker.getModule("outglob10");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob11");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob12");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob13");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob14");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob15");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob16");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob17");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob18");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob19");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob20");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob21");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob22");
	    m.setPriorfile(prifile);
	    m.setEmissPriorScaler(priScaler);
	    m.setDistribType(HMM.MANUAL, emissionProbs[4]);
	    m = modelmaker.getModule("outglob23");