/sPlot/src/Splot.java

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import java.beans.PropertyChangeSupport;

import java.io.BufferedReader;

import java.io.BufferedWriter;

import java.io.File;

import java.io.FileReader;

import java.io.FileWriter;

import java.io.IOException;

import java.io.PrintWriter;

import java.text.DateFormat;

import java.text.SimpleDateFormat;

import java.util.Calendar;



import javax.swing.JOptionPane;



public class Splot {

//Input

	private int w_size;				//window size

	private int nmer_size;

	private boolean use_complementary;

//Parameters 

	private int num_possible_nmers;

	private float min_percent_nt_in_w = (float)0.1;

	private int min_num_nmers_in_w=50;

	

//Output

	private int len_X;

	private int len_Y;

	

	private char[][] seq_inX_w;		//Holds all X window sequences [# of windows][sequence for each window]

	private int w_num_X;				//Number of windows for X sequence

	

	private char[][] seq_inY_w;		//Holds all Y window sequences [# of windows][sequence for each window]

	private int w_num_Y;				//Number of windows for Y sequence 

	

	private static String[] X_geneSynonyms;

	private static String[] Y_geneSynonyms;

	

	private float[][] score;

	private int[] hisPlot;

	private float[] avgCorrX;

	private float[] avgCorrY;

	private float[] stdev_pearCorrX;

	private float[] stdev_pearCorrY;

	

	private boolean[] valid_X;

	private boolean[] valid_Y;

	

	private float[][] nmer_counts_X;

	private float[][] nmer_counts_Y;

	

	private float[] w_meanVals_X;

	private float[] w_meanVals_Y;

	

	private float[] X_square;

	private float[] Y_square;

	private static String X_header;

	private static String Y_header;

	

//FileWriters 

	private PrintWriter writeGC;



//Sean's stuff

	private String args[];

	public final PropertyChangeSupport pcs = new PropertyChangeSupport( this );

	private boolean process = false;

	

	// Some OO changes

	public Splot(String[] args_i){

		/* 

		 * String[] args

	     * 0 - Sequence X

	     * 1 - Sequence Y

	     * 2 - nmer_size

	     * 3 - w_size	//VALUE=-1 IF USING GENE

	     * 4 - use_complementary

	     * 5 - gene file X 

	     * 6 - gene file Y 

	     * 7 - Dir for scoreMatrix file  

	     * 8 - Dir for avg+stdev file  

	     * 9 - Dir for window_GC_content file

	     * 10 - Dir for maxCorr_w_pairs file 

	     * 11 - Dir for geneScoreMatrix file

	     * 12 - Dir for geneAvgStdev file

	     * 13 - Dir for gene_GC_content file

	     * 14 - Dir for maxCorr_gene_pairs file

		 * 

		 */

		

		this.args = args_i;

	}

	

	public void init(){

		System.err.println("heLL!");

		int one=1;	 

        nmer_size = Integer.parseInt(args[2]);

        w_size = Integer.parseInt(args[3]);

        if(w_size!=-1)

        {

                    parse_X(args[0]);

                    if(process) return;

                    parse_Y(args[1]);

                    if(process) return;

                    

                    use_complementary = Boolean.valueOf(args[4]);

                    score = new float[w_num_X][w_num_Y];

                    valid_X = new boolean[w_num_X];

                    valid_Y = new boolean[w_num_Y];



                    num_possible_nmers = one<<(nmer_size*2);

                    nmer_counts_X = new float[w_num_X][num_possible_nmers];

                    nmer_counts_Y = new float[w_num_Y][num_possible_nmers];



                    w_meanVals_X = new float[w_num_X];

                    w_meanVals_Y = new float[w_num_Y];

                    X_square = new float[w_num_X];

                    Y_square = new float[w_num_Y];	

                    

                    compute();

                    

                    //writeScoreMatrix(args[7]);

                    //write_Avg_Stdev(args[8]);

                    //write_GC_w_content(args[9]);

                    //write_max_w_Corr(args[10]);

        }

        else

        {

        			Prepare_Sequences_var_window_X(args[0], args[5]);

        			if(process) return;

        			Prepare_Sequences_var_window_Y(args[1], args[6]);

        			if(process) return;

        			use_complementary = Boolean.valueOf(args[4]);

                    

                    score = new float[w_num_X][w_num_Y]; //508952576 33030144

                    valid_X = new boolean[w_num_X]; //C:\\DOCUME~1\\ADMINI~1\\LOCALS~1\\Temp\\NC_009925.fna

                    valid_Y = new boolean[w_num_Y];

                    

                    // TEST WITH N-MER SIZE 3

                    num_possible_nmers = one<<(nmer_size*2);

                    nmer_counts_X = new float[w_num_X][num_possible_nmers];

                    nmer_counts_Y = new float[w_num_Y][num_possible_nmers];

                    w_meanVals_X = new float[w_num_X];

                    w_meanVals_Y = new float[w_num_Y];

                    X_square = new float[w_num_X];

                    Y_square = new float[w_num_Y];

                    

                    S_Plot_Correlation_var_windows();

                    //writeGeneMatrix(args[11]);

                    //write_Gene_Avg_Stdev(args[12]);

                    //write_GC_gene_content(args[13]);

                    //write_max_gene_Corr(args[14]);

        }

	}

	

	public void parse_X(String xSquence){

		File f_X = new File(xSquence);

		BufferedReader in = getReader(f_X);

		

		StringBuilder sb = new StringBuilder();

		String line = getLine(in);

		while (line!=null) {

			line = getLine(in);

			if(line!=null){

				len_X += (long)line.length();

				sb.append(line);

			}

		}

		StringBuilder sb2 = sb;

			

			w_num_X=len_X/w_size;

			if(((len_X%w_size)/(float)w_size)>=min_percent_nt_in_w) w_num_X++;

			seq_inX_w = new char[w_num_X][w_size+1];

			

			int k = 0;

			int j = 0;

			for(int i=0; i<w_num_X; i++){

				for(j=0; j<w_size; j++){

					seq_inX_w[i][j] = sb2.charAt(k);

					if(k<(len_X-1)){k++;}

						else{break;}

				}

				seq_inX_w[i][j]='\0';

			}

	}

	public void parse_Y(String ySequence){

		File f_Y = new File(ySequence);

		BufferedReader in = getReader(f_Y);

		

		StringBuilder sb = new StringBuilder();

		String line = getLine(in);

			while (line!=null) {

				line = getLine(in);

				if(line!=null){

					len_Y += (long)line.length();

					sb.append(line);

					}

			}

			StringBuilder sb2 = sb;

			

			w_num_Y=len_Y/w_size;

			if(((len_Y%w_size)/(float)w_size)>=min_percent_nt_in_w) w_num_Y++;

			seq_inY_w = new char[w_num_Y][w_size+1];

			

			int k = 0;

			int j = 0;

			for(int i=0; i<w_num_Y; i++){

				for(j=0; j<w_size; j++){

					seq_inY_w[i][j] = sb2.charAt(k);

					if(k<(len_Y-1)){k++;}

						else{break;}

				}

				seq_inY_w[i][j]='\0';

			}

	}

	public void getTime() {

		Calendar cal = Calendar.getInstance();

	    SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss:SS");

		System.out.println(sdf.format(cal.getTime()));

	}

	public void compute(){

		int i, j;

		int n_x, n_y;

		char c;

		String sNmer = new String();

		boolean okay = true;

		

		/*

			Sean

		*/

		frame.progressBar.setStringPainted(true);

		frame.progressBar.setMinimum(0);

		frame.progressBar.setMaximum(w_num_Y+w_num_X+w_num_X);

		

		///---------------------------X

		

		for(n_x=0;n_x<w_num_X;n_x++){

			i=-1;

			for(;;){

				i++;

				if(seq_inX_w[n_x][i]=='\0') {break;}

				c=seq_inX_w[n_x][i];

				if(c=='a'||c=='A'){sNmer+="00";}

					else if(c=='t'||c=='T'){sNmer+="01";}

					else if(c=='g'||c=='G'){sNmer+="10";}

					else if(c=='c'||c=='C'){sNmer+="11";}

					else continue;



				

				for(j=1;j<nmer_size;j++){

					i++;

					if(seq_inX_w[n_x][i]=='\0'){break;}

					c=seq_inX_w[n_x][i];



					okay=true;

					if(c=='a'||c=='A'){sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer+="11";}

						else okay=false;

					

					if(!okay){j=nmer_size;}

					

				} //first nmer found

				

				if(okay){

				nmer_counts_X[n_x][Integer.parseInt(sNmer,2)]++;

				}

				

				if(use_complementary&&okay){nmer_counts_X[n_x][Integer.parseInt(giveR_ComplementX(n_x,i),2)]++;}

				

				for(;;){

					i++;

					if(seq_inX_w[n_x][i]=='\0') {

						i--;

						break; }

					

					c=seq_inX_w[n_x][i];

					if(c=='a'||c=='A'){sNmer=sNmer.substring(2);sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer=sNmer.substring(2);sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer=sNmer.substring(2);sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer=sNmer.substring(2);sNmer+="11";}

						else break;



					

					nmer_counts_X[n_x][Integer.parseInt(sNmer,2)]++;

					if(use_complementary){nmer_counts_X[n_x][Integer.parseInt(giveR_ComplementX(n_x,i),2)]++;}

					

				}

				

				sNmer = new String();

				

			}

			

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++){

				w_meanVals_X[n_x]+=nmer_counts_X[n_x][nmer_i]; }



			if(w_meanVals_X[n_x]<min_num_nmers_in_w) {valid_X[n_x]=true; continue;}

			if(w_meanVals_X[n_x]/i<min_percent_nt_in_w) {valid_X[n_x]=true; continue;}

			

			w_meanVals_X[n_x] = w_meanVals_X[n_x]/num_possible_nmers; 

			

			pcs.firePropertyChange("progress", null, n_x);	// progressbar stuff

		

		}//end window loop

		

		///---------------------Y

		sNmer = new String();

		

		for(n_y=0;n_y<w_num_Y;n_y++){ 

			i=-1;

			for(;;){

				i++;

				if(seq_inY_w[n_y][i]=='\0'){break;}

				c=seq_inY_w[n_y][i];

				if(c=='a'||c=='A'){sNmer+="00";}

					else if(c=='t'||c=='T'){sNmer+="01";}

					else if(c=='g'||c=='G'){sNmer+="10";}

					else if(c=='c'||c=='C'){sNmer+="11";}

					else continue;



				

				for(j=1;j<nmer_size;j++){

					i++;

					if(seq_inY_w[n_y][i]=='\0')break;

					c=seq_inY_w[n_y][i];



					okay=true;

					if(c=='a'||c=='A'){sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer+="11";}

						else okay=false;

					

					if(!okay){j=nmer_size;}

					

				}//found first nmer

				

				if(okay){

				nmer_counts_Y[n_y][Integer.parseInt(sNmer,2)]++;

				}

				if(use_complementary&&okay){nmer_counts_Y[n_y][Integer.parseInt(giveR_ComplementY(n_y,i),2)]++;}

				

				for(;;){

					i++;

					if(seq_inY_w[n_y][i]=='\0') {

						i--;

						break; }

					

					c=seq_inY_w[n_y][i];

					if(c=='a'||c=='A'){sNmer=sNmer.substring(2);sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer=sNmer.substring(2);sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer=sNmer.substring(2);sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer=sNmer.substring(2);sNmer+="11";}

						else break;

					

					nmer_counts_Y[n_y][Integer.parseInt(sNmer,2)]++;

					if(use_complementary){nmer_counts_Y[n_y][Integer.parseInt(giveR_ComplementY(n_y,i),2)]++;}

					

				}

				

				sNmer = new String();

				

			}

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++){w_meanVals_Y[n_y]+=nmer_counts_Y[n_y][nmer_i];}



			if(w_meanVals_Y[n_y]<min_num_nmers_in_w){valid_Y[n_y]=true; continue;}

			if(w_meanVals_Y[n_y]/i<min_percent_nt_in_w){valid_Y[n_y]=true; continue;}

			

			w_meanVals_Y[n_y] = w_meanVals_Y[n_y]/num_possible_nmers; 

		

			pcs.firePropertyChange("progress", null, (w_num_X + n_y)); // progressbar

			

		}//end of window loop



		///Computations-----------X 

		for(n_x=0;n_x<w_num_X;n_x++)		// for each window on X axis loop

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

			{

				if(valid_X[n_x]) continue;

					nmer_counts_X[n_x][nmer_i]=nmer_counts_X[n_x][nmer_i]-w_meanVals_X[n_x];

					X_square[n_x]+=nmer_counts_X[n_x][nmer_i]*nmer_counts_X[n_x][nmer_i];

			}



		///Computations------------Y

		for(n_y=0;n_y<w_num_Y;n_y++)		// for each window on Y axis loop

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

			{

				if(valid_Y[n_y]) continue;

					nmer_counts_Y[n_y][nmer_i]=nmer_counts_Y[n_y][nmer_i]-w_meanVals_Y[n_y];

					Y_square[n_y]+=nmer_counts_Y[n_y][nmer_i]*nmer_counts_Y[n_y][nmer_i];

			}

	//Computations------------Score

		float minScore=0;

		boolean firstTime=true;

		for(n_x=0;n_x<w_num_X;n_x++){		// for each window on X axis loop

			for(n_y=0;n_y<w_num_Y;n_y++)		// for each window on Y axis loop

			{

				if(valid_X[n_x]){continue;}

				if(valid_Y[n_y]){continue;}



				for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

							score[n_x][n_y]+=nmer_counts_X[n_x][nmer_i]*nmer_counts_Y[n_y][nmer_i];



				score[n_x][n_y]=score[n_x][n_y]/(float)Math.sqrt((X_square[n_x]*Y_square[n_y]));

				

				if(firstTime){minScore=score[n_x][n_y]; firstTime=false;}

				if(score[n_x][n_y]<minScore){minScore=score[n_x][n_y];}



			}

			

			pcs.firePropertyChange("progress", null, (w_num_X + w_num_Y + n_x)); // progressbar

			

		}



		//-----------------------Clear memory 

		valid_X = null;

		valid_Y = null;

		nmer_counts_X = null;

		nmer_counts_Y = null;

		w_meanVals_X = null;

		w_meanVals_Y = null;

		X_square = null;    

		Y_square = null;

		

	}

	

	public void Prepare_Sequences_var_window_X(String xSequence, String xGenes)

	{

		int i,j,k,l,m;

		boolean overOrigin=false;

		

		//genes for sequence x

		File f_g = new File(xGenes);

		BufferedReader in = getReader(f_g);

		

		String line = getLine(in); //gets the first line

		line=getLine(in); //gets the number of genes + word protein

		String [] result = line.split(" ");

		w_num_X=Integer.parseInt(result[0]);

		

		int[][] w_pos=new int [w_num_X][2];

		X_geneSynonyms = new String [w_num_X];

		boolean[] strand=new boolean [w_num_X];

		line=getLine(in);	//gets the column headings

		for(i=0; i<w_num_X; i++)

		{

			line=getLine(in);	//gets a gene

			j=line.indexOf("."); //location of end of start

			k=line.indexOf("\t"); //location of end of end

			l=line.indexOf("\t",k+1); 

			l=line.indexOf("\t",l+1); 

			l=line.indexOf("\t",l+1); 

			l=line.indexOf("\t",l+1); 

			l=line.indexOf("\t",l+1);

			m=line.lastIndexOf("\t",l-1); 

			result[0]=line.substring(0,j);

			w_pos[i][0]=Integer.parseInt(result[0]);

			w_pos[i][0]--;

			result[0]=line.substring(j+2,k);

			w_pos[i][1]=Integer.parseInt(result[0]);

			w_pos[i][1]--;

			result[0]=line.substring(k+1,k+2);

			if(result[0]=="+") strand[i]=true;

			else strand[i]=false;

			X_geneSynonyms[i]=line.substring(m+1,l);

		}

		

		//sequence x

		File f_s = new File(xSequence);

		in = getReader(f_s);

		

		StringBuilder sb = new StringBuilder();

		X_header = getLine(in);

		while(line!=null)

		{

			line=getLine(in);

			if(line!=null)

			{

				len_X += (long)line.length();

				sb.append(line);

			}

		}

		StringBuilder sb2 = sb; 

		

		//set up arrays

		seq_inX_w=new char [w_num_X][];



		for(i=0; i<w_num_X; i++)

		{

			if(w_pos[i][1]>=w_pos[i][0])

			{

				seq_inX_w[i]=new char[(w_pos[i][1]-w_pos[i][0]+2)]; //why add two?

				overOrigin=false;

			}

			else

			{

				seq_inX_w[i]=new char[(len_X-w_pos[i][0])+w_pos[i][1]+2]; //changed from (length-end)+start to (length-start)+end! -vinnie 

				overOrigin=true;

			}

		}

		for(i=0; i<w_num_X; i++)

		{

			if(strand[i]) //original strand

			{

				if(overOrigin==false) 

				{

					for(j=0; j<w_pos[i][1]-w_pos[i][0]+1; j++){

						seq_inX_w[i][j]=sb2.charAt(w_pos[i][0]+j);

					}

					seq_inX_w[i][j]='\0';

				}

				else

				{

					k=0;

					for(j=w_pos[i][0]; j<len_X; j++)

					{

						seq_inX_w[i][k]=sb2.charAt(j);

						k++;

					}

					for(j=0; j<=w_pos[i][1]; j++)

					{

						seq_inX_w[i][k]=sb2.charAt(j);

						k++;

					}

					seq_inX_w[i][k]='\0';

				}

			}

			else //complementary strand

			{

				if(overOrigin==false)

				{

					for(j=0; j<w_pos[i][1]-w_pos[i][0]+1; j++)

					{

						seq_inX_w[i][j]=sb2.charAt(w_pos[i][1]-w_pos[i][0]-j); 

						switch(seq_inX_w[i][j]){

						case 'a': case 'A': seq_inX_w[i][j]='T'; break;

						case 't': case 'T': seq_inX_w[i][j]='A'; break;

						case 'g': case 'G': seq_inX_w[i][j]='C'; break;

						case 'c': case 'C': seq_inX_w[i][j]='G'; break;

						default: seq_inX_w[i][j]='N';

						}

					}

					seq_inX_w[i][j]='\0';

				}

				else 

				{

					k=0;

					j=w_pos[i][1];

					while(j>=0)

					{

						seq_inX_w[i][k]= sb2.charAt(j);

						j--;

						switch(seq_inX_w[i][k]){

						case 'a': case 'A': seq_inX_w[i][k]='T'; break;

						case 't': case 'T': seq_inX_w[i][k]='A'; break;

						case 'g': case 'G': seq_inX_w[i][k]='C'; break;

						case 'c': case 'C': seq_inX_w[i][k]='G'; break;

						default: seq_inX_w[i][k]='N';

						}

						k++;

					}

					for(j=len_X-1; j>=w_pos[i][0]; j--)

					{

						seq_inX_w[i][k]=sb2.charAt(j);

						switch(seq_inX_w[i][k]){

						case 'a': case 'A': seq_inX_w[i][k]='T'; break;

						case 't': case 'T': seq_inX_w[i][k]='A'; break;

						case 'g': case 'G': seq_inX_w[i][k]='C'; break;

						case 'c': case 'C': seq_inX_w[i][k]='G'; break;

						default: seq_inX_w[i][k]='N';

						}

						k++;

					}

					seq_inX_w[i][k]='\0';

				} 

			}

		}

	}

	public void Prepare_Sequences_var_window_Y(String ySequence, String yGenes)

	{

		int i,j,k,l,m;

		boolean overOrigin=false;

		

		//genes for sequence y

		File f_g = new File(yGenes);

		BufferedReader in = getReader(f_g);

		

		String line = getLine(in); //gets the first line

		line=getLine(in); //gets the number of genes + word protein

		String [] result = line.split(" ");

		w_num_Y=Integer.parseInt(result[0]);

		

		int[][] w_pos=new int [w_num_Y][2];

		boolean[] strand=new boolean [w_num_Y];

		Y_geneSynonyms = new String [w_num_Y];

		

		line=getLine(in);	//get the column headings

		for(i=0; i<w_num_Y; i++)

		{

			line=getLine(in);	//gets a gene

			j=line.indexOf("."); //location of end of start

			k=line.indexOf("\t"); //location of end of end

			l=line.indexOf("\t",k+1); 

			l=line.indexOf("\t",l+1); 

			l=line.indexOf("\t",l+1); 

			l=line.indexOf("\t",l+1); 

			l=line.indexOf("\t",l+1);

			m=line.lastIndexOf("\t",l-1);

			result[0]=line.substring(0,j);

			w_pos[i][0]=Integer.parseInt(result[0]);

			w_pos[i][0]--;

			result[0]=line.substring(j+2,k);

			w_pos[i][1]=Integer.parseInt(result[0]);

			w_pos[i][1]--;

			result[0]=line.substring(k+1,k+2);

			if(result[0]=="+") strand[i]=true;

			else strand[i]=false;

			Y_geneSynonyms[i]=line.substring(m+1,l);

		}

		

		//sequence y

		File f_s = new File(ySequence);

		in = getReader(f_s);

		

		StringBuilder sb = new StringBuilder();

		Y_header = getLine(in);

		while(line!=null)

		{

			line=getLine(in);

			if(line!=null)

			{

				len_Y += (long)line.length();

				sb.append(line);

			}

		}

		StringBuilder sb2 = sb; 

		

		//set up the array ready to read in

		seq_inY_w=new char [w_num_Y][];

		for(i=0; i<w_num_Y; i++)

		{

			if(w_pos[i][1]>=w_pos[i][0])

			{

				seq_inY_w[i]=new char[(w_pos[i][1]-w_pos[i][0]+2)];

				overOrigin=false;

			}

			else

			{

				seq_inY_w[i]=new char[(len_Y-w_pos[i][0])+w_pos[i][1]+2];

				overOrigin=true;

			}

		}

		for(i=0; i<w_num_Y; i++)

		{

			if(strand[i]) //original strand

			{

				if(overOrigin==false)

				{

					for(j=0; j<w_pos[i][1]-w_pos[i][0]+1; j++){

					seq_inY_w[i][j]=sb2.charAt(w_pos[i][0]+j);

					}

					seq_inY_w[i][j]='\0';

				}

				else

				{

					k=0;

					for(j=w_pos[i][0]; j<len_Y; j++)

					{

						seq_inY_w[i][k]=sb2.charAt(j);

						k++;

					}

					for(j=0; j<=w_pos[i][1]; j++)

					{

						seq_inY_w[i][k]=sb2.charAt(j);

						k++;

					}

					seq_inY_w[i][k]='\0';

				}

			}

			else //complementary strand

			{

				if(overOrigin==false)

				{

					for(j=0; j<w_pos[i][1]-w_pos[i][0]+1; j++)

					{

						seq_inY_w[i][j]=sb2.charAt(w_pos[i][1]-w_pos[i][0]-j);

						switch(seq_inY_w[i][j]){

						case 'a': case 'A': seq_inY_w[i][j]='T'; break;

						case 't': case 'T': seq_inY_w[i][j]='A'; break;

						case 'g': case 'G': seq_inY_w[i][j]='C'; break;

						case 'c': case 'C': seq_inY_w[i][j]='G'; break;

						default: seq_inY_w[i][j]='N';

						}

					}

					seq_inY_w[i][j]='\0';

				}

				else

				{

					k=0;

					j=w_pos[i][1];

					

					while(j>=0)

					{

						seq_inY_w[i][k]= sb2.charAt(j);

						j--;

						switch(seq_inY_w[i][k]){

						case 'a': case 'A': seq_inY_w[i][k]='T'; break;

						case 't': case 'T': seq_inY_w[i][k]='A'; break;

						case 'g': case 'G': seq_inY_w[i][k]='C'; break;

						case 'c': case 'C': seq_inY_w[i][k]='G'; break;

						default: seq_inY_w[i][k]='N';

						}

						k++;

					}

					for(j=len_Y-1; j>=w_pos[i][0]; j--)

					{

						seq_inY_w[i][k]=sb2.charAt(j);

						switch(seq_inY_w[i][k]){

						case 'a': case 'A': seq_inY_w[i][k]='T'; break;

						case 't': case 'T': seq_inY_w[i][k]='A'; break;

						case 'g': case 'G': seq_inY_w[i][k]='C'; break;

						case 'c': case 'C': seq_inY_w[i][k]='G'; break;

						default: seq_inY_w[i][k]='N';

						}

						k++;

					}

					seq_inY_w[i][k]='\0';

				} 

			}

		}

	}

	public void S_Plot_Correlation_var_windows()

	{

		int i, j;

		int n_x, n_y;

		char c;

		String sNmer = new String();

		boolean okay = true;

		

		frame.progressBar.setStringPainted(true);

		frame.progressBar.setMinimum(0);

		frame.progressBar.setMaximum(w_num_Y+w_num_X+w_num_X);

		

		///---------------------------X

		for(n_x=0;n_x<w_num_X;n_x++){

			i=-1;

			for(;;){

				i++;

				if(seq_inX_w[n_x][i]=='\0') {break;}

				c=seq_inX_w[n_x][i];

				if(c=='a'||c=='A'){sNmer+="00";}

					else if(c=='t'||c=='T'){sNmer+="01";}

					else if(c=='g'||c=='G'){sNmer+="10";}

					else if(c=='c'||c=='C'){sNmer+="11";}

					else continue;



				

				for(j=1;j<nmer_size;j++){

					i++;

					if(seq_inX_w[n_x][i]=='\0'){break;}

					c=seq_inX_w[n_x][i];



					okay=true;

					if(c=='a'||c=='A'){sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer+="11";}

						else okay=false;

					

					if(!okay){j=nmer_size;}

					

				} //first nmer found

				

				if(okay){

				nmer_counts_X[n_x][Integer.parseInt(sNmer,2)]++;

				}

				

				if(use_complementary&&okay){nmer_counts_X[n_x][Integer.parseInt(giveR_ComplementX(n_x,i),2)]++;}

				

				for(;;){

					i++;

					if(seq_inX_w[n_x][i]=='\0') {

						i--;

						break; }

					

					c=seq_inX_w[n_x][i];

					if(c=='a'||c=='A'){sNmer=sNmer.substring(2);sNmer+="00";}

					else if(c=='t'||c=='T'){sNmer=sNmer.substring(2);sNmer+="01";}

					else if(c=='g'||c=='G'){sNmer=sNmer.substring(2);sNmer+="10";}

					else if(c=='c'||c=='C'){sNmer=sNmer.substring(2);sNmer+="11";}

					else break;

					

					nmer_counts_X[n_x][Integer.parseInt(sNmer,2)]++;

					if(use_complementary){nmer_counts_X[n_x][Integer.parseInt(giveR_ComplementX(n_x,i),2)]++;}	

				}

				sNmer = new String();

			}



			//validation checks

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++){w_meanVals_X[n_x]+=nmer_counts_X[n_x][nmer_i];}

			if(w_meanVals_X[n_x]<min_num_nmers_in_w) {valid_X[n_x]=true; continue;}

			if(w_meanVals_X[n_x]/i<min_percent_nt_in_w) {valid_X[n_x]=true; continue;}

			

			//take % because other variable window may be significantly different size

			w_meanVals_X[n_x]=0;

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

			{

				nmer_counts_X[n_x][nmer_i]=(nmer_counts_X[n_x][nmer_i]/(float)i);

				w_meanVals_X[n_x]+=nmer_counts_X[n_x][nmer_i];

			}

			w_meanVals_X[n_x]=w_meanVals_X[n_x]/num_possible_nmers;

		

			pcs.firePropertyChange("progress", null, n_x);	// progressbar stuff

			

		}//end window loop

		

		///---------------------Y

		sNmer = new String();

		for(n_y=0;n_y<w_num_Y;n_y++){ 

			i=-1;

			for(;;){

				i++;

				if(seq_inY_w[n_y][i]=='\0'){break;}

				c=seq_inY_w[n_y][i];

				if(c=='a'||c=='A'){sNmer+="00";}

					else if(c=='t'||c=='T'){sNmer+="01";}

					else if(c=='g'||c=='G'){sNmer+="10";}

					else if(c=='c'||c=='C'){sNmer+="11";}

					else continue;



				

				for(j=1;j<nmer_size;j++){

					i++;

					if(seq_inY_w[n_y][i]=='\0')break;

					c=seq_inY_w[n_y][i];



					okay=true;

					if(c=='a'||c=='A'){sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer+="11";}

						else okay=false;

					

					if(!okay){j=nmer_size;}

					

				}//found first nmer

				

				if(okay){

				nmer_counts_Y[n_y][Integer.parseInt(sNmer,2)]++;

				}

				if(use_complementary&&okay){nmer_counts_Y[n_y][Integer.parseInt(giveR_ComplementY(n_y,i),2)]++;}

				

				for(;;){

					i++;

					if(seq_inY_w[n_y][i]=='\0') {

						i--;

						break; }

					

					c=seq_inY_w[n_y][i];

					if(c=='a'||c=='A'){sNmer=sNmer.substring(2);sNmer+="00";}

						else if(c=='t'||c=='T'){sNmer=sNmer.substring(2);sNmer+="01";}

						else if(c=='g'||c=='G'){sNmer=sNmer.substring(2);sNmer+="10";}

						else if(c=='c'||c=='C'){sNmer=sNmer.substring(2);sNmer+="11";}

						else break;

					

					nmer_counts_Y[n_y][Integer.parseInt(sNmer,2)]++;

					if(use_complementary){nmer_counts_Y[n_y][Integer.parseInt(giveR_ComplementY(n_y,i),2)]++;}

					

				}

				

				sNmer = new String();

				

			}

			//validation

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++){w_meanVals_Y[n_y]+=nmer_counts_Y[n_y][nmer_i];}

			if(w_meanVals_Y[n_y]<min_num_nmers_in_w){valid_Y[n_y]=true; continue;}

			if(w_meanVals_Y[n_y]/i<min_percent_nt_in_w){valid_Y[n_y]=true; continue;}



			//take % because other variable window may be significantly different size

			w_meanVals_Y[n_y]=0;

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

			{

				nmer_counts_Y[n_y][nmer_i]=(nmer_counts_Y[n_y][nmer_i]/(float)i);

				w_meanVals_Y[n_y]+=nmer_counts_Y[n_y][nmer_i];

			}			

			w_meanVals_Y[n_y] = w_meanVals_Y[n_y]/num_possible_nmers;

			

			pcs.firePropertyChange("progress", null, (w_num_X + n_y)); // progressbar

			

		}//end of window loop



	///Computations-----------X 

		for(n_x=0;n_x<w_num_X;n_x++)		// for each window on X axis loop

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

			{

				if(valid_X[n_x]) continue;

					nmer_counts_X[n_x][nmer_i]=nmer_counts_X[n_x][nmer_i]-w_meanVals_X[n_x];

					X_square[n_x]+=nmer_counts_X[n_x][nmer_i]*nmer_counts_X[n_x][nmer_i];

			}

		

	///Computations------------Y

		for(n_y=0;n_y<w_num_Y;n_y++)		// for each window on Y axis loop

			for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

			{

				if(valid_Y[n_y]) continue;

					nmer_counts_Y[n_y][nmer_i]=nmer_counts_Y[n_y][nmer_i]-w_meanVals_Y[n_y];

					Y_square[n_y]+=nmer_counts_Y[n_y][nmer_i]*nmer_counts_Y[n_y][nmer_i];

			}





	//Computations------------Score

		for(n_x=0;n_x<w_num_X;n_x++){		// for each window on X axis loop

			for(n_y=0;n_y<w_num_Y;n_y++)		// for each window on Y axis loop

			{

				if(valid_X[n_x]){continue;}

				if(valid_Y[n_y]){continue;}



				for(int nmer_i=0;nmer_i<num_possible_nmers;nmer_i++)

							score[n_x][n_y]+=nmer_counts_X[n_x][nmer_i]*nmer_counts_Y[n_y][nmer_i];



				score[n_x][n_y]=score[n_x][n_y]/(float)Math.sqrt((X_square[n_x]*Y_square[n_y]));

			}

			

			pcs.firePropertyChange("progress", null, (w_num_X + w_num_Y + n_x)); // progressbar

			

		}

		

	//-----------------------Clear memory 

		valid_X = null;

		valid_Y = null;

		nmer_counts_X = null;

		nmer_counts_Y = null;

		w_meanVals_X = null;

		w_meanVals_Y = null;

		X_square = null;    

		Y_square = null;



	}	



	public void writeScoreMatrix(String writeLocation){

		String f_score = writeLocation;

		File F_score = new File(f_score);

		try{

			if(F_score.createNewFile()){System.out.println("File F_score was created");}

				else{System.out.println("File F_score was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: writeScoreMatrix");}

		

		PrintWriter out = openWriter(F_score);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("Pearson Correlation Values");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Window Size:\t" + w_size);

		out.println("Nmer Size:\t" + nmer_size);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();		

		

		out.print("\t0");

		for(int p=1;p<w_num_Y;p++){out.print("\t"+p);}

		out.println();

		

		for(int k=0; k<w_num_X; k++){

			StringBuilder sb2 = new StringBuilder();

			sb2.append(k);

			for(int l=0;l<w_num_Y;l++){

				String v = "\t" + score[k][l];

				sb2.append(v);

				if(l==(w_num_Y-1)){out.println(sb2);}

				}

			}

		out.close();

	}

	public void writeGeneMatrix(String writeLocation){

		String f_geneMatrix = writeLocation;

		File F_geneMatrix = new File(f_geneMatrix);

		try{

			if(F_geneMatrix.createNewFile()){System.out.println("File F_geneMatrix was created");}

				else{System.out.println("File F_geneMatrix was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: writeGeneMatrix");}

		

		PrintWriter out = openWriter(F_geneMatrix);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("Pearson Correlation Gene Values");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Nmer Size:\t3");

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();		

		

		String syn;

		for(int p=0;p<w_num_Y;p++){

			 syn = Y_geneSynonyms[p];

			 out.print("\t"+syn);

			}

		out.println();

		

		for(int k=0; k<w_num_X; k++){

			StringBuilder sb2 = new StringBuilder();

			syn = X_geneSynonyms[k];

			sb2.append(syn);

			for(int l=0;l<w_num_Y;l++){

				String v = "\t" + score[k][l];

				sb2.append(v);

				if(l==(w_num_Y-1)){out.println(sb2);}

				}

			}

		out.close();

	}	

	public void write_Avg_Stdev(String writeLocation){

		calcAvg_window_Corr();

		stdev_pearCorrX = new float [w_num_X];

		stdev_pearCorrY = new float [w_num_Y];

		

		String f_avg_stdev = writeLocation;

		File F_avg_stdev = new File(f_avg_stdev);

		try{

			if(F_avg_stdev.createNewFile()){System.out.println("File F_avg_stdev was created");}

				else{System.out.println("File F_avg_stdev was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: write_Avg_Stdev");}

		

		PrintWriter out = openWriter(F_avg_stdev);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("Average and Standard Deviations");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Window Size:\t" + w_size);

		out.println("Nmer Size:\t" + nmer_size);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();

		

		out.println("Sequence X:");

		out.println("Window\tAvg\tStdev");

		

		float sum_of_the_difference=0;

		for(int i=0;i<w_num_X;i++){

			for(int j=0;j<w_num_Y;j++){

				sum_of_the_difference+=Math.abs(score[i][j]-avgCorrX[i]);

			}

			stdev_pearCorrX[i]=sum_of_the_difference/(float)w_num_Y;

			sum_of_the_difference=0;

		}

		

		sum_of_the_difference=0;

		for(int i=0;i<w_num_Y;i++){

			for(int j=0;j<w_num_X;j++){

				sum_of_the_difference+=Math.abs(score[j][i]-avgCorrY[i]);

			}

			stdev_pearCorrY[i]=sum_of_the_difference/(float)w_num_X;

			sum_of_the_difference=0;

		}

		

		for(int i=0;i<w_num_X;i++){

			out.println(i+"\t"+avgCorrX[i]+"\t"+stdev_pearCorrX[i]);

		}

		

		out.println();

		out.println();

		out.println("Sequence Y:");

		out.println("Window\tAvg\tStdev");

		for(int i=0;i<w_num_Y;i++){

			out.println(i+"\t"+avgCorrY[i]+"\t"+stdev_pearCorrY[i]);

		}



		avgCorrX = null;

		avgCorrY = null;

		stdev_pearCorrX = null;

		stdev_pearCorrY = null;

		out.close();

	}

	public void write_Gene_Avg_Stdev(String writeLocation){

		calcAvg_window_Corr();

		String f_gene_avg_stdev = writeLocation;

		File F_gene_avg_stdev = new File(f_gene_avg_stdev);

		try{

			if(F_gene_avg_stdev.createNewFile()){System.out.println("File F_gene_avg_stdev was created");}

				else{System.out.println("File F_gene_avg_stdev was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: write_Gene_Avg_Stdev");}

		

		PrintWriter out = openWriter(F_gene_avg_stdev);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("Gene Average and Standard Deviations");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Nmer Size:\t" + 3);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();

		

		out.println("Sequence X:");

		out.println("Gene\tAvg\tStdev");

		

		//finding stdev of each window in Sequence X 

		float sum_of_the_difference=0;

		for(int i=0;i<w_num_X;i++){

			for(int j=0;j<w_num_Y;i++){

				sum_of_the_difference+=Math.abs(score[i][j]-avgCorrX[i]);

			}

			stdev_pearCorrX[i]=sum_of_the_difference/(float)w_num_Y;

			sum_of_the_difference=0;

		}

		

		//finding stdev of each window in Sequence Y

		sum_of_the_difference=0;

		for(int i=0;i<w_num_Y;i++){

			for(int j=0;j<w_num_X;i++){

				sum_of_the_difference+=Math.abs(score[j][i]-avgCorrY[i]);

			}

			stdev_pearCorrY[i]=sum_of_the_difference/(float)w_num_X;

			sum_of_the_difference=0;

		}

		

		//writing out avg and stdev for each window in sequence X

		for(int i=0;i<w_num_X;i++){

			out.println(X_geneSynonyms[i]+"\t"+avgCorrX[i]+"\t"+stdev_pearCorrX[i]);

		}

		

		out.println();

		out.println();

		out.println("Sequence Y:");

		out.println("Gene\tAvg\tStdev");

		

		//writing out avg and stdev for each window in sequence Y

		for(int i=0;i<w_num_Y;i++){

			out.println(Y_geneSynonyms[i]+"\t"+avgCorrY[i]+"\t"+stdev_pearCorrY[i]);

		}

		out.println();

		

		avgCorrX = null;

		avgCorrY = null;

		stdev_pearCorrX = null;

		stdev_pearCorrY = null;

		out.close();

	}

	public void write_GC_w_content(String writeLocation){

		String f_w_GC_content = writeLocation;

		File F_w_GC_content = new File(f_w_GC_content);

		try{

			if(F_w_GC_content.createNewFile()){System.out.println("File F_w_GC_content was created");}

				else{System.out.println("File F_w_GC_content was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: write_GC_w_content");}

		

		PrintWriter out = openWriter(F_w_GC_content);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("G+C window content");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Window size:\t"+w_size);

		out.println("Nmer Size:\t" + nmer_size);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();

		out.println("Sequence X:");

		out.println("Window\tG+C");

		

		//writing out the GC content of each window in sequence X

		for(int i=0;i<w_num_X;i++){

			out.println(i+"\t"+calcGC(i,true));

		}

		

		out.println();

		out.println();

		out.println("Sequence Y:");

		out.println("Window\tG+C");

		

		//writing out the GC content of each window in sequence Y

		for(int i=0;i<w_num_Y;i++){

			out.println(i+"\t"+calcGC(i,false));

		}

		out.println();

		out.close();

	}

	public void write_GC_gene_content(String writeLocation){

		

		String f_gene_GC_content = writeLocation;

		File F_gene_GC_content = new File(f_gene_GC_content);

		

		try{

			if(F_gene_GC_content.createNewFile()){System.out.println("File F_gene_GC_content was created");}

				else{System.out.println("File F_gene_GC_content was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: write_GC_gene_content");}

		

		PrintWriter out = openWriter(F_gene_GC_content);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("G+C gene content");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Nmer Size:\t" + 3);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();

		out.println("Sequence X:");

		out.println("Gene\tG+C");

		

		//writing out the GC content of each gene in sequence X

		for(int i=0;i<w_num_X;i++){

			out.println(X_geneSynonyms[i]+"\t"+calcGC(i,true));

		}

		

		out.println();

		out.println();

		out.println("Sequence Y:");

		out.println("Gene\tG+C");

		

		//writing out the GC content of each gene in sequence Y

		for(int i=0;i<w_num_Y;i++){

			out.println(Y_geneSynonyms[i]+"\t"+calcGC(i,false));

		}

		out.println();

		out.close();

	}

	public void write_max_w_Corr(String writeLocation){

		String f_maxCorrs = writeLocation;

		File F_maxCorrs = new File(f_maxCorrs);

		try{

			if(F_maxCorrs.createNewFile()){System.out.println("File F_maxCorrs was created");}

				else{System.out.println("File F_maxCorrs was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: writeScoreMatrix");}

		

		PrintWriter out = openWriter(F_maxCorrs);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("Highest Correlated Windows");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Window Size:\t" + w_size);

		out.println("Nmer Size:\t" + nmer_size);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();

		

		float maxScore=score[0][0];

		int max_Ypos=0,max_Xpos=0;

		

		//writing out the highest correlated window in Y for every window in X   

		out.println("Sequence X:");

		out.println("window in X\tValue\twindow in Y");

		for(int k=0; k<w_num_X; k++){

			for(int l=0;l<w_num_Y;l++){

				if(score[k][l]>maxScore){

					maxScore=score[k][l];

					max_Ypos=l;

					}

				}

			out.println(k+"\t"+score[k][max_Ypos]+"\t"+max_Ypos);

			if((k+1)!=w_num_X){maxScore=score[k+1][0];}

		}

		maxScore = score[0][0];

		

		out.println();

		out.println();

		

		//writing out the highest correlated window in X for every window in Y

		out.println("Sequence Y:");

		out.println("window in Y\tValue\twindow in X");

		for(int k=0; k<w_num_Y; k++){

			for(int l=0;l<w_num_X;l++){

				if(score[l][k]>maxScore){

					maxScore=score[l][k];

					max_Xpos=l;

					}

				}

			out.println(k+"\t"+score[max_Xpos][k]+"\t"+max_Xpos);

			if((k+1)!=w_num_Y){maxScore=score[0][k+1];}

		}

		out.close();

		

	}

	public void write_max_gene_Corr(String writeLocation){

		String f_maxCorrs = writeLocation;

		File F_maxCorrs = new File(f_maxCorrs);

		try{

			if(F_maxCorrs.createNewFile()){System.out.println("File F_maxCorrs was created");}

				else{System.out.println("File F_maxCorrs was not created");}

		}

		catch(IOException e){System.out.println("I/O Error: writeScoreMatrix");}

		

		PrintWriter out = openWriter(F_maxCorrs);

		

		Calendar cal = Calendar.getInstance();

	    DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

		

		out.print("Highest Correlated Genes");

		out.println("\t\t\t" + df.format(cal.getTime()));

		out.println();

		out.println("Sequence X:\t" + X_header);

		out.println("Sequence Y:\t" + Y_header);

		out.println();

		out.println("Nmer Size:\t" + 3);

		out.println("Compl. considered:\t" + use_complementary);

		out.println();

		out.println();

		out.println();

		

		float maxScore=score[0][0];

		int max_Ypos=0,max_Xpos=0;

		

		//writing out the highest correlated window in Y for every window in X   

		out.println("Sequence X:");

		out.println("window in X\tValue\twindow in Y");

		for(int k=0; k<w_num_X; k++){

			for(int l=0;l<w_num_Y;l++){

				if(score[k][l]>maxScore){

					maxScore=score[k][l];

					max_Ypos=l;

					}

				}

			out.println(X_geneSynonyms[k]+"\t"+score[k][max_Ypos]+"\t"+Y_geneSynonyms[max_Ypos]);

			if((k+1)!=w_num_X){maxScore=score[k+1][0];}

		}

		maxScore = score[0][0];

		

		out.println();

		out.println();

	

		//writing out the highest correlated window in X for every window in Y

		out.println("Sequence Y:");

		out.println("window in Y\tValue\twindow in X");

		for(int k=0; k<w_num_Y; k++){

			for(int l=0;l<w_num_X;l++){

				if(score[l][k]>maxScore){

					maxScore=score[l][k];

					max_Xpos=l;

					}

				}

			out.println(Y_geneSynonyms[k]+"\t"+score[max_Xpos][k]+"\t"+max_Xpos);

			if((k+1)!=w_num_Y){maxScore=score[0][k+1];}

		}

		

		out.close();

		X_geneSynonyms = null;

		Y_geneSynonyms = null;		

	}

	

	

	public void calcAvg_window_Corr(){

		float numerator = 0;

		avgCorrX = new float [w_num_X];

		avgCorrY = new float [w_num_Y];

		

		//Calculating averages for the X sequence

		for(int k=0; k<w_num_X; k++){

			for(int l=0;l<w_num_Y;l++){

				numerator = score[k][l] + numerator;

			}

			avgCorrX[k] = numerator/(float)w_num_Y; 

			numerator = 0;

		}

		

		//Calculating averages for the Y sequence

		for(int k=0; k<w_num_Y; k++){

			for(int l=0;l<w_num_X;l++){

				numerator = score[l][k] + numerator;

			}

			avgCorrY[k] = numerator/(float)w_num_X; 

			numerator = 0;

		}

	}

	public float calcGC(int w_num, boolean XorY)

	{

		int gc=0;

		int i=-1;

		float perGC=0;

		

		if(XorY){	//XorY=true means your looking in the X sequence 

			do{

				i++;

				if((seq_inX_w[w_num][i]=='c')||(seq_inX_w[w_num][i]=='C')||

						(seq_inX_w[w_num][i]=='g')||(seq_inX_w[w_num][i]=='G')) {gc++;}

			

			}while(seq_inX_w[w_num][i]!='\0');

			

			perGC = 100*((float)gc/(float)i);

		}//end if

		

		if(!XorY){	//XorY=false means your looking in the Y sequence 

			do{

				i++;

				if((seq_inY_w[w_num][i]=='c')||(seq_inY_w[w_num][i]=='C')||

						(seq_inY_w[w_num][i]=='g')||(seq_inY_w[w_num][i]=='G')) {gc++;}

			

			}while(seq_inY_w[w_num][i]!='\0');

			

			perGC = 100*((float)gc/(float)i);

		}//end if

		

		return perGC;

	}

	

	

	/*public static void hisPlot(){

		int index;

		float maxScore=score[0][0];

		

		for(int k=0; k<w_num_X; k++){

			for(int l=0;l<w_num_Y;l++){

				if(score[k][l]>maxScore){maxScore=score[k][l];}

				}

			

			index=(int)((10-(maxScore*10))*2);

			hisPlot[index]++;

			//System.out.println((int)((10-(maxScore*10))*2));

			if((k+1)!=w_num_X){maxScore=score[k+1][0];}

		}

		

		System.out.println();

		System.out.println();

		for(int i=0;i<hisPlot.length;i++){

			System.out.println(hisPlot[i]);

		}

	}

	*/

	

	public void alignMax(){

		int max_Ypos=0;

		float Xgc,Ygc;

		float maxScore=score[0][0];

		

		String path4_test_writeOut = "C:\\Documents and Settings\\NTUser\\Desktop\\FileTests\\Maxes&GC.txt";

		File writeOut_X_Y = new File(path4_test_writeOut);

		try{

			if(writeOut_X_Y.createNewFile()){System.out.println("Maxes&GC was created");}

				else{System.out.println("File Maxes&GC was not created");}

		}

		catch(IOException e){System.out.println("I/O Error");}

		

		writeGC = openWriter(writeOut_X_Y);

		writeGC.print("\t\t\t");

		//write accession 

		writeGC.print("\n");

		

		for(int k=0; k<w_num_X; k++){

			for(int l=0;l<w_num_Y;l++){

				if(score[k][l]>maxScore){

					maxScore=score[k][l];

					max_Ypos=l;

					}

				}

			Xgc = calcGC(k,true);

			Ygc = calcGC(max_Ypos,false);

			writeWindowGC_Max(Xgc,Ygc,k,max_Ypos,maxScore);

			if((k+1)!=w_num_X){maxScore=score[k+1][0];}

		}

		

		System.out.println();

		System.out.println();

		for(int i=0;i<hisPlot.length;i++){

			System.out.println(hisPlot[i]);

		}

		writeGC.close();

	}



	

	public void writeWindowGC_Max(float GC_X, float GC_Y, int windowX, int windowY, float max){

		

	    writeGC.print(GC_X+"\t"+windowX+"\t"+max+"\t"+windowY+"\t"+GC_Y+"\t\n");

	}

	

	

	public String giveR_ComplementX(int window, int nt){ 

		

		String reverseCNmer = new String();

		char c;

		int endNmerIndex = nt-nmer_size;

		

		for(int q=nt;q>endNmerIndex;q--){

			c=seq_inX_w[window][q];

			if(c=='a'||c=='A'){reverseCNmer+="01";}

				else if(c=='t'||c=='T'){reverseCNmer+="00";}

				else if(c=='g'||c=='G'){reverseCNmer+="11";}

				else if(c=='c'||c=='C'){reverseCNmer+="10";}

		}

		return reverseCNmer;

	}

	

	public String giveR_ComplementY(int window, int nt){ 

		

		String reverseCNmer = new String();

		char c;

		int endNmerIndex = nt-nmer_size;

		

		for(int q=nt;q>endNmerIndex;q--){

			c=seq_inY_w[window][q];

			if(c=='a'||c=='A'){reverseCNmer+="01";}

				else if(c=='t'||c=='T'){reverseCNmer+="00";}

				else if(c=='g'||c=='G'){reverseCNmer+="11";}

				else if(c=='c'||c=='C'){reverseCNmer+="10";}

		}

		return reverseCNmer;

	}	

	

	public PrintWriter openWriter(File name){ //probably don't need this method

		try{

			PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(name)), true); 

			return out;

		}

		catch(IOException e){

			System.out.println("PrintWriter could not find parsed_f_X");

			System.exit(0);

		}

		return null;

	}	

	public BufferedReader getReader(File file){

		BufferedReader in = null;

		try{

			in = new BufferedReader(new FileReader(file));

		}

		catch(IOException e){

			JOptionPane.showMessageDialog(frame.displayPanel,

					"BufferedReader I/O Error or coundn't find the file.", "Error",

				    JOptionPane.ERROR_MESSAGE);

			process = true;

		}

		return in;

		

	}	

	public String getLine(BufferedReader in){

		String line = null;

		try{line = in.readLine();}

		catch(IOException e){

			JOptionPane.showMessageDialog(frame.displayPanel,

					"bReader couldn't read next line.", "Error",

				    JOptionPane.ERROR_MESSAGE);

			process = true;

		}

		if(line==null){return null;}

			else{return line;}

	}	

	public void writeOutNmerCounts(){

		

		String path4_test_writeOut = "C:\\Documents and Settings\\NTUser\\Desktop\\FileTests\\NmerCounts.txt";

		File writeOutNmerCounts = new File(path4_test_writeOut);

		try{

			if(writeOutNmerCounts.createNewFile()){System.out.println("writeOutNmerCounts was created");}

				else{System.out.println("File writeOut_X_Y was not created");}

		}

		catch(IOException e){System.out.println("I/O Error");}

		

		PrintWriter out = openWriter(writeOutNmerCounts);

		

		for(int k=0; k<w_num_X; k++){

			StringBuilder sb2 = new StringBuilder();

			sb2.append(k);

			for(int l=0;l<num_possible_nmers;l++){

				String v = "\t" + nmer_counts_X[k][l];

				sb2.append(v);

				if(l==(num_possible_nmers-1)){out.println(sb2);}

				}

			}

		out.close();

	}

	

	//This method should be executed only when the entire genome is being looked at. It will make one tab-delimited file containing all the windows of both genomes.

	public void write_windows(String writeLocation){

        String f_wind_contents = writeLocation;

        File F_wind_contents = new File(f_wind_contents);

        try{

            if(F_wind_contents.createNewFile()){System.out.println("File F_wind_contents was created");}

                else{System.out.println("File F_wind_contents was not created");}

        }

        catch(IOException e){System.out.println("I/O Error: write_windows");}

       

        PrintWriter out = openWriter(F_wind_contents);

       

        Calendar cal = Calendar.getInstance();

        DateFormat df = DateFormat.getDateTimeInstance(DateFormat.FULL, DateFormat.MEDIUM);

       

        out.print("Sequence partitions");

        out.println("\t\t\t" + df.format(cal.getTime()));

        out.println();

        out.println("Sequence X:\t" + X_header);

        out.println("Sequence Y:\t" + Y_header);

        out.println();

        out.println("Window size:\t" + w_size);

        out.println("Nmer Size:\t" + nmer_size);

        out.println("Compl. considered:\t" + use_complementary);

        out.println();

        out.println();

        out.println();

       

        out.println("Sequence X window partitions: ");

        int i,j=0;

        for(i=0;i<w_num_X;i++){

            out.println("> " +i);

            for(j=0;j<w_size;j++){

                out.print(seq_inX_w[i][j]);

            }

            out.println();

        }

       

        out.println();

        out.println();

        out.println("Sequence Y window partitions: ");

       

        for(i=0;i<w_num_Y;i++){

            out.println("> " +i);

            for(j=0;j<w_size;j++){

                out.print(seq_inY_w[i][j]);

            }

            out.println();

        }

       

    }



	//This method should only be executed when only the gene are being looked at. It will make one tab-delimited file containing all the gene sequences for both genomes.

    public void write_GeneWindows(String writeLocation){

        String f_gene_contents = writeLocation;

        File F_gene_contents = new File(f_gene_contents);

        try{

            if(F_gene_contents.createNewFile()){System.out.println("File F_gene_contents was created");}

                else{System.out.printl…