vertex.java

马尔科夫模型的c语言实现

		emissions[i] = initDistrib[i];
	    }
	    break;
	case 2:
	    for(int i = 0; i < emissions_2.length;i++) {
		emissions_2[i] = initDistrib[i];
	    }
	    break;
	case 3:
	    for(int i = 0; i < emissions_3.length;i++) {
		emissions_3[i] = initDistrib[i];
	    }
	    break;
	case 4:
	    for(int i = 0; i < emissions_4.length;i++) {
		emissions_4[i] = initDistrib[i];
	    }
	    break;
	}
    }
    
    public void lock()
    {
	if(vertexType == HMM.STANDARD) {
	    vertexType = HMM.LOCKED;
	}
    }

    public void normalizeEmissProbs(int alphabet)
    {
	double[] emiss = null;
	
	switch(alphabet) {
	case 1:
	    emiss = emissions;
	    break;
	case 2:
	    emiss = emissions_2;
	    break;
	case 3:
	    emiss = emissions_3;
	    break;
	case 4:
	    emiss = emissions_4;
	    break;  
	}
	double sum = 0.0;
	for(int i = 0; i < emiss.length; i++) {
	    sum += emiss[i];
	}
	if(sum != 0.0) {
	    for(int i = 0; i < emiss.length; i++) {
		emiss[i] = emiss[i] / sum;
	    }
	}
    }

    public void normalizeTransProbs()
    {
	double sum = 0.0;
	for(int i = 0; i < transitionList.size(); i++) {
	    sum += ((Transition)transitionList.get(i)).probability;
	}
	if(sum != 0.0) {
	    for(int i = 0; i < transitionList.size(); i++) {
		((Transition)transitionList.get(i)).probability =  ((Transition)transitionList.get(i)).probability / sum;
	    }
	}
    }
    
    public void setInitialEmissionProbs(int distribType)
    {
	/* Initialize emission probabilities to zero for all possible emissions */
	if(distribType == HMM.ZERO) {
	    if(vertexType != HMM.START && vertexType != HMM.END) {
		vertexType = HMM.SILENT;
	    }
	    for(int i = 0; i < emissions.length; i++) {
		emissions[i] = 0.0;
	    }
	}
	/* Initialize emission probabilities evenly for all possible emissions */
	else if (distribType == HMM.EVEN) {
	    vertexType = HMM.STANDARD;
	    int nrEmissions = emissions.length;
	    double initProb = (double)1/nrEmissions;
	    for(int i = 0; i < emissions.length; i++) {
		emissions[i] = initProb;
	    }
	}

	/* Initialize emission probabilities randomly */
	else if (distribType == HMM.RANDOM) {
	    vertexType = HMM.STANDARD;
	    int nrEmissions = emissions.length;
	    double sum = 0;
	    for(int i = 0; i < emissions.length; i++) {
		double initProb = Math.random();
		emissions[i] = initProb;
		sum = sum + initProb;
	    }
	    for(int i = 0; i < emissions.length; i++) {
		emissions[i] = emissions[i] / sum;
	    }
	    
	}
    }

    public void setInitialEmissionProbs(int nr, int distribType)
    {
	switch(nr) {
	case 1:
	    /* Initialize emission probabilities to zero for all possible emissions */
	    if(distribType == HMM.ZERO) {
		if(vertexType != HMM.START && vertexType != HMM.END) {
		    vertexType = HMM.SILENT;
		}
		for(int i = 0; i < emissions.length; i++) {
		    emissions[i] = 0.0;
		}
	    }
	    /* Initialize emission probabilities evenly for all possible emissions */
	    else if (distribType == HMM.EVEN) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions.length;
		double initProb = (double)1/nrEmissions;
		for(int i = 0; i < emissions.length; i++) {
		    emissions[i] = initProb;
		}
	    }
	    
	    /* Initialize emission probabilities randomly */
	    else if (distribType == HMM.RANDOM) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions.length;
		double sum = 0;
		for(int i = 0; i < emissions.length; i++) {
		    double initProb = Math.random();
		    emissions[i] = initProb;
		    sum = sum + initProb;
		}
		for(int i = 0; i < emissions.length; i++) {
		    emissions[i] = emissions[i] / sum;
		}
		
	    }
	    break;
	case 2:
	    /* Initialize emission probabilities to zero for all possible emissions */
	    if(distribType == HMM.ZERO) {
		if(vertexType != HMM.START && vertexType != HMM.END) {
		    vertexType = HMM.SILENT;
		}
		for(int i = 0; i < emissions_2.length; i++) {
		    emissions_2[i] = 0.0;
		}
	    }
	    /* Initialize emission probabilities evenly for all possible emissions */
	    else if (distribType == HMM.EVEN) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions_2.length;
		double initProb = (double)1/nrEmissions;
		for(int i = 0; i < emissions_2.length; i++) {
		    emissions_2[i] = initProb;
		}
	    }
	    
	    /* Initialize emission probabilities randomly */
	    else if (distribType == HMM.RANDOM) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions_2.length;
		double sum = 0;
		for(int i = 0; i < emissions_2.length; i++) {
		    double initProb = Math.random();
		    emissions_2[i] = initProb;
		    sum = sum + initProb;
		}
		for(int i = 0; i < emissions_2.length; i++) {
		    emissions_2[i] = emissions_2[i] / sum;
		}
		
	    }
	    break;
	case 3:
	    /* Initialize emission probabilities to zero for all possible emissions */
	    if(distribType == HMM.ZERO) {
		if(vertexType != HMM.START && vertexType != HMM.END) {
		    vertexType = HMM.SILENT;
		}
		for(int i = 0; i < emissions_3.length; i++) {
		    emissions_3[i] = 0.0;
		}
	    }
	    /* Initialize emission probabilities evenly for all possible emissions */
	    else if (distribType == HMM.EVEN) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions_3.length;
		double initProb = (double)1/nrEmissions;
		for(int i = 0; i < emissions_3.length; i++) {
		    emissions_3[i] = initProb;
		}
	    }
	    
	    /* Initialize emission probabilities randomly */
	    else if (distribType == HMM.RANDOM) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions_3.length;
		double sum = 0;
		for(int i = 0; i < emissions_3.length; i++) {
		    double initProb = Math.random();
		    emissions_3[i] = initProb;
		    sum = sum + initProb;
		}
		for(int i = 0; i < emissions_3.length; i++) {
		    emissions_3[i] = emissions_3[i] / sum;
		}
		
	    }
	    break;
	case 4:
	    /* Initialize emission probabilities to zero for all possible emissions */
	    if(distribType == HMM.ZERO) {
		if(vertexType != HMM.START && vertexType != HMM.END) {
		    vertexType = HMM.SILENT;
		}
		for(int i = 0; i < emissions_4.length; i++) {
		    emissions_4[i] = 0.0;
		}
	    }
	    /* Initialize emission probabilities evenly for all possible emissions */
	    else if (distribType == HMM.EVEN) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions_4.length;
		double initProb = (double)1/nrEmissions;
		for(int i = 0; i < emissions_4.length; i++) {
		    emissions_4[i] = initProb;
		}
	    }
	    
	    /* Initialize emission probabilities randomly */
	    else if (distribType == HMM.RANDOM) {
		vertexType = HMM.STANDARD;
		int nrEmissions = emissions_4.length;
		double sum = 0;
		for(int i = 0; i < emissions_4.length; i++) {
		    double initProb = Math.random();
		    emissions_4[i] = initProb;
		    sum = sum + initProb;
		}
		for(int i = 0; i < emissions_4.length; i++) {
		    emissions_4[i] = emissions_4[i] / sum;
		}
		
	    }
	    break;
	}
    }

    public void setPreliminaryInitialEmissionProbs(int distribType)
    {
	/* Initialize emission probabilities to zero for all possible emissions */
	if(distribType == HMM.ZERO) {
	    if(vertexType != HMM.START && vertexType != HMM.END) {
		vertexType = HMM.SILENT;
	    }
	    for(int i = 0; i < emissions.length; i++) {
		emissions[i] = 0.0;
	    }
	    for(int i = 0; i < emissions_2.length; i++) {
		emissions_2[i] = 0.0;
	    }
	    for(int i = 0; i < emissions_3.length; i++) {
		emissions_3[i] = 0.0;
	    }
	    for(int i = 0; i < emissions_4.length; i++) {
		emissions_4[i] = 0.0;
	    }
	}
	/* Initialize emission probabilities evenly for all possible emissions */
	else if (distribType == HMM.EVEN) {
	    vertexType = HMM.STANDARD;
	    int nrEmissions = emissions.length;
	    double initProb = (double)1/nrEmissions;
	    for(int i = 0; i < emissions.length; i++) {
		emissions[i] = initProb;
	    }
	    nrEmissions = emissions_2.length;
	    if(nrEmissions != 0) {
		initProb = (double)1/nrEmissions;
	    }
	    else {
		initProb = 0.0;
	    }
	    for(int i = 0; i < emissions_2.length; i++) {
		emissions_2[i] = initProb;
	    }
	    nrEmissions = emissions_3.length;
	    if(nrEmissions != 0) {
		initProb = (double)1/nrEmissions;
	    }
	    else {
		initProb = 0.0;
	    }
	    for(int i = 0; i < emissions_3.length; i++) {
		emissions_3[i] = initProb;
	    }
	    nrEmissions = emissions_4.length;
	    if(nrEmissions != 0) {
		initProb = (double)1/nrEmissions;
	    }
	    else {
		initProb = 0.0;
	    }
	    for(int i = 0; i < emissions_4.length; i++) {
		emissions_4[i] = initProb;
	    }
	    
	}

	/* Initialize emission probabilities randomly */
	else if (distribType == HMM.RANDOM) {
	    vertexType = HMM.STANDARD;
	    int nrEmissions = emissions.length;
	    double sum = 0;
	    for(int i = 0; i < emissions.length; i++) {
		double initProb = Math.random();
		emissions[i] = initProb;
		sum = sum + initProb;
	    }
	    for(int i = 0; i < emissions.length; i++) {
		emissions[i] = emissions[i] / sum;
	    }
	    nrEmissions = emissions_2.length;
	    sum = 0;
	    for(int i = 0; i < emissions_2.length; i++) {
		double initProb = Math.random();
		emissions_2[i] = initProb;
		sum = sum + initProb;
	    }
	    for(int i = 0; i < emissions_2.length; i++) {
		emissions_2[i] = emissions_2[i] / sum;
	    }
	    nrEmissions = emissions_3.length;
	    sum = 0;
	    for(int i = 0; i < emissions_3.length; i++) {
		double initProb = Math.random();
		emissions_3[i] = initProb;
		sum = sum + initProb;
	    }
	    for(int i = 0; i < emissions_3.length; i++) {
		emissions_3[i] = emissions_3[i] / sum;
	    }
	    nrEmissions = emissions_4.length;
	    sum = 0;
	    for(int i = 0; i < emissions_4.length; i++) {
		double initProb = Math.random();
		emissions_4[i] = initProb;
		sum = sum + initProb;
	    }
	    for(int i = 0; i < emissions_4.length; i++) {
		emissions_4[i] = emissions_4[i] / sum;
	    }
	    
	}
    }
}