Printing DNA data

[hcadet]

Hello everyone I am taking a class in Java and I have to print DNA and underneath it I need to print a (*) where I find a match. Here is the output to be more clear.

>gi|116268103|ref|NP_001070736.1| zinc finger FYVE domain-containing protein 19 [Homo sapiens]
contains the zinc finger site: CSGCLSFSAAVPRTGNTQQKVCKQC
at locations:
103 128

MNYDSQQPPLPPLPYAGCRRASGFPALGRGGTVPVGVWGGAGQGREGRSW
                                                  
GEGPRGPGLGRRDLSSADPAVLGATMESRCYGCAVKFTLFKKEYGCKNCG
                                                  
RAFCSGCLSFSAAVPRTGNTQQKVCKQCHEVLTRGSSANASKWSPPQNYK
   *************************                      
KRVAALEAKQKPSTSQSQGLTRQDQMIAERLARLRQENKPKLVPSQAEIE
                                                  
ARLAALKDERQGSIPSTQEMEARLAALQGRVLPSQTPQPAHHTPDTRTQA
                                                  
QQTQDLLTQLAAEVAIDESWKGGGPAASLQNDLNQGGPGSTNSKRQANWS
                                                  
LEEEKSRLLAEAALELREENTRQERILALAKRLAMLRGQDPERVTLQDYR
                                                  
LPDSDDDEDEETAIQRVLQQLTEEASLDEASGFNIPAEQASRPWTQPRGA
                                                  
EPEAQDVDPRPEAEEEELPWCCICNEDATLRCAGCDGDLFCARCFREGHD
                                                  
AFELKEHQTSAYSPPRAGQEH

if you see where the stars are that's what I need to accomplish, I can print the data but how do I go about printing things underneath a string. Here is the code that would generate the data.

/*
3)Modification the print out of the sequence to include a label 
underneath the zinc finger consensus sequence. 
*/

import java.util.*;
import java.io.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class hwk4_3 {


	public static void main(String[] args) 
	{

	
		try{	
				ArrayList<String> a = new ArrayList<String>();	
								
				// Open the file that is the first 
				// command line parameter
				FileInputStream fstream = new FileInputStream("zinkFinger.txt");
				// Get the object of DataInputStream
				DataInputStream in = new DataInputStream(fstream);
				BufferedReader br = new BufferedReader(new InputStreamReader(in));
    			
				String seqLine;	
				  
					//Read File Line By Line
					while ((seqLine = br.readLine()) != null) 
					{  
						//adds the lines of the file to this array
						//System.out.println("\n " + seqLine );
						a.add(seqLine);
					}in.close();
						
				String listString = "";

					for (String s : a)
					{
						listString += s +"\n\n";
					}
					
					//Sets the first header to be printed out.
					int fd = listString.indexOf(">");
					int endheader = listString.indexOf("]");
					endheader++;
					
					//sets the first sequence to be printed and parsed
					int endheader2 = listString.indexOf("]");
					endheader2++;
					int sd = listString.indexOf(">", endheader2 );
					
					do
					{
					
						//Separates all headers from the sequence for print.
						String header = listString.substring(fd, endheader);
						fd = listString.indexOf(">", endheader);
						endheader = listString.indexOf("]", fd);
						endheader++;	
						///////////////////////////////////////////////////
						
						//separates all the sequences from the headers for print.
						String subseq = listString.substring( endheader2, sd );
						endheader2 = listString.indexOf("]", endheader2);
						sd = listString.indexOf(">", endheader2++);
						
						
						//Pattern match of the sequences
						Pattern p = Pattern.compile ("C[A-Z]{2}C[A-Z]{17}C[A-Z]{2}C");
						Matcher m = p.matcher("");
						m.reset( subseq ); //reset the input
			
							if ( m.find() )
							{
								//Header print of the match.
								System.out.print("\n " + header);
								for (int i = 0; i<=10
								//The pattern and the location print of the match.
								System.out.print("\n Contains the zinc finger site:" + m.group());
								System.out.print("\n At locations:\n " + m.start() + " " + m.end() +"\n");
								
								System.out.print(" " + m.group().replaceAll("************************"));
								//The actual sequence print of the match.
								//System.out.print(" " + subseq);
							
								
							}
					
					}while( sd != -1 );				
			}catch (Exception e){//Catch exception if any
			    	System.err.println("Error: " + e.getMessage());
		    }
     }
}

*
I am using replaceAll() but that is not the solution. Can someone please help?


Thank you so much,

Hernando Cadet

Moderator Edit: Code tags added

[Eranga]

Can you please elaborate more your matching criteria. I'm not clear with that. What asterisk you want to find?

[hcadet]

okay so the matching criteria is a zing finger or a regular expression.

Pattern p = Pattern.compile ("C[A-Z]{2}C[A-Z]{17}C[A-Z]{2}C");
Matcher m = p.matcher("");

Above is the regular expression. Once I find a match on the sequence, I need to show the match by printing asterisks underneath the match.

I am thinking two dimensional array but I am not sure.

Thanks;

[Fubarable]

Or a StringBuilder object could work -- or even a simple second String, either one. You'd add a " " if no match, and add "*" if in the region of the match.

[Eranga]

Looking at OPs requirement temporary string variable could be enough.

[hcadet]

"StringBuilder object could work" -- or even a simple second String, either one. You'd add a " " if no match, and add "*" if in the region of the match.

Looking at OPs requirement temporary string variable could be enough.

All suggestions seem to make sense but looking at the code above can you please give me an example of how I would be using what you just suggested?



Thank you so much;
:cool:

[Eranga]

Initialize a string variable. In each line of your original string, validate your pattern. Do necessary changes on it if any. Then concatenate with the temporary string.

[hcadet]

okay so I will be using the Array still, right? Let me try it with the array.

[hcadet]

Hello guys I must say I am new to java and is kind of hard to understand the concepts for me.

[Eranga]

Hello guys I must say I am new to java and is kind of hard to understand the concepts for me.

That's why we helped you here. But you must put some effort first of all. If you comes with any error let us know. What you've done so far?