matchcolumnidentifyer.java

来自「马尔科夫模型的c语言实现」· Java 代码 · 共 92 行

class MatchColumnIdentifyer
{
    
    MSA msa;


    public MatchColumnIdentifyer(MSA msa)
    {
	this.msa = msa;
    }



    public boolean[] getMatchColumns(String constructionMethod)
    {
	if(constructionMethod.startsWith("F")) {
	    return getMatchColumnsFast();
	}
	else if(constructionMethod.startsWith("H")) {
	    return getMatchColumnsHand();
	}
	else if(constructionMethod.startsWith("M")) {
	    return getMatchColumnsMAP();
	}
	else if(constructionMethod.startsWith("Q")) {
	    return getMatchColumnsQuery();
	}
	else {
	    P.MESSAGE("No such match column identifyer exists");
	    System.exit(0);
	}




	return null;
    }




    private boolean[] getMatchColumnsFast()
    {
	return null;
    }

    private boolean[] getMatchColumnsHand()
    {
	return null;
    }

    private boolean[] getMatchColumnsMAP()
    {
	return null;
    }

    private boolean[] getMatchColumnsQuery()
    {
	/* return the columns for which the query sequence has non gap residues
	 * the query seq is always taken to be the first seq in the alignment */
	boolean[] matchColumns = new boolean[msa.nrColumns];

	for(int i = 0; i < msa.nrColumns; i++) {
	    if(!(msa.theMsa[0][i].letter_1.equals("-")) && !(msa.theMsa[0][i].letter_1.equals(" ")) &&
	       !(msa.theMsa[0][i].letter_1.equals(".")) && !(msa.theMsa[0][i].letter_1.equals("_"))) {
		matchColumns[i] = true;
	    }
	    else {
		matchColumns[i] = false;
	    }
	}


	return matchColumns;
    }
    
    public int getNrOfMatchColumns(boolean[] mc)
    {
	int nr = 0;

	for(int i = 0; i < mc.length; i++) {
	    if(mc[i]) {
		nr++;
	    }
	}

	return nr;
    }


}