shadowmsatmhmmcreator.java

马尔科夫模型的c语言实现

import java.io.*;
import java.util.*;

class ShadowMsaTMHMMCreator
{
    

    BufferedReader reader;
    ModelMaker modelmaker;
    String hmmrow;
    

    /* first input parameter is a file with description of init values etc
     * second input parameter is a name of outputdir */
    public ShadowMsaTMHMMCreator(String hmmfile, String outdir)
    {
	try {
	    BufferedReader br = new BufferedReader(new FileReader(hmmfile));
	    hmmrow = br.readLine();
	    StringTokenizer st = new StringTokenizer(hmmrow, "\t ");
	    if(st.countTokens() < 1) {
		printerr("Could not create hmm");
		System.exit(0);
	    }
	    modelmaker = new ModelMaker();
	    
	    /* read name */
	    String hmmName = st.nextToken();
	    
	    /* read priorfiles */
	    LinkedList priorfiles = new LinkedList();
	    LinkedList priorScalers = new LinkedList();
	    for(int i = 0; i < 7; i++) {
		hmmrow = br.readLine();
		st = new StringTokenizer(hmmrow, " \t");
		st.nextToken();
		priorfiles.add(st.nextToken());
		priorScalers.add(st.nextToken());
	    }

	    /* read init distributions */
	    double[][] emissionProbs = new double[8][22];
	    for(int i = 0; i < 8; i++) {
		hmmrow = br.readLine();
		st = new StringTokenizer(hmmrow, "\t ");
		if(st.countTokens() != 23) {
		    printerr("Could not create hmm");
		    System.exit(0);
		}
		st.nextToken();
		for(int j = 0; j < 22; j++) {
		    emissionProbs[i][j] = Double.parseDouble(st.nextToken());
		}
	    }

	    /* read expected looplengths */
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    int lengthOL = Integer.parseInt(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    int lengthOS = Integer.parseInt(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    int lengthI = Integer.parseInt(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    double Po = Double.parseDouble(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    int f_i = Integer.parseInt(st.nextToken());
	    int q_i = Integer.parseInt(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    int f_o = Integer.parseInt(st.nextToken());
	    int q_o = Integer.parseInt(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    double gapOpenerProb = Double.parseDouble(st.nextToken());
	    hmmrow = br.readLine();
	    st = new StringTokenizer(hmmrow, " \t");
	    st.nextToken();
	    double gapLenProb = Double.parseDouble(st.nextToken());
	    
	    createHMM(hmmName, priorfiles, priorScalers, emissionProbs, lengthOL, lengthOS, lengthI, Po, f_i, q_i, f_o, q_o, gapOpenerProb, gapLenProb);
	    saveHMM(outdir);
	}
	catch(IOException e) {
	    printerr("Could not read from hmmfile");
	    System.exit(0);
	}
    }


    /****************input/output handling**********************************/
    private void println(String s)
    {
	System.out.println(s);
    }

    private void newln(){
	System.out.println("");
    }
    private void printerr(String s)
    {
	System.out.println("Error: " + s);
    }
    private void print(String s)
    {
	System.out.print(s);
	System.out.flush();
    }

    private String readln()
    {
	try {
	String s = reader.readLine();
	if(s == "" || s == null) {
	    return null;
	}
	s = s.trim();
	return s;
	}
	catch(IOException e) {
	    P.INTERNAL_ERROR("DataReader.readLine: IOException");
	    return null;
	}
    }
    
    
    /*******************************HMM methods****************************/
    private void createHMM(String name, LinkedList priorfiles, LinkedList priorScalers, double[][] emissionProbs,
			   int lengthOL, int lengthOS, int lengthI, double Po, int f_i, int q_i, int f_o, int q_o, double gapOpenerProb, double gapLenProb)
    {
	modelmaker.createHMM(name);
	modelmaker.setAlphabet(HMM.AMINO_DOUBLE_GAP);
	int res = modelmaker.createModule("s", HMM.STARTNODE, HMM.ZERO, 1, "0");

	res = modelmaker.createModule("in10", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in10_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in11", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in11_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in12", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in12_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in13", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in13_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in14", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in14_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in15", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in15_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in16", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in16_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in17", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in17_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in18", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in18_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in19", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in19_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in20", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in20_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in21", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in21_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in22", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in22_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in23", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in23_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in24", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in24_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in25", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in25_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in26", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in26_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in27", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in27_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in28", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in28_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in29", HMM.SINGLENODE, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("in29_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("inglob1", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	res = modelmaker.createModule("inglob1_s", HMM.SINGLELOOP, HMM.EVEN, 1, "i");
	
	res = modelmaker.createModule("outglob10", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob10_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob11", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob11_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob12", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob12_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob13", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob13_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob14", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob14_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob15", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob15_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob16", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob16_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob17", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob17_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob18", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob18_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob19", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob19_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob20", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob20_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob21", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob21_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob22", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob22_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob23", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob23_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob24", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob24_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob25", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob25_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob26", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob26_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob27", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob27_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob28", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob28_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob29", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglob29_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglobLong", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("outglobLong_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");

	res = modelmaker.createModule("out10", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out10_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out11", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out11_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out12", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out12_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out13", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out13_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out14", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out14_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out15", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out15_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out16", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out16_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out17", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out17_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out18", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out18_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out19", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out19_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out20", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out20_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out21", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out21_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out22", HMM.SINGLENODE, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out22_s", HMM.SINGLELOOP, HMM.EVEN, 1, "o");
	res = modelmaker.createModule("out23", HMM.SINGLENODE, HMM.EVEN, 1, "o");