read files

[amoon]

hello every bady
I have a big problems please help me
I have a file like this:
> YAL005C YAR002W
> YAL005C YPL240C
> YLR335W YAL005C
> YLR335W YGL097W
> YLR335W YMR047C
> YNL064C YAL005C
> YLR335W YAR002W
> YGL097W YAR002W
> YMR047C YAR002W
which is names for protins
and I want to read this file to get matrix as output
for every protins and it is intaractions protins
for example; protein YAL005C interacts
> with YAR002W, YPL240C, YLR335W and YNL064C and doesn't interact
> with the other 2.
> * The output will be 7X7 matrix
>
> 1 1 1 1 0 0 1
> 1 1 0 1 1 1 0
> 1 0 1 0 0 0 0
> 1 1 0 1 1 1 0
> 0 1 0 1 1 0 0
> 0 1 0 1 0 1 0
> 1 0 0 0 0 0 1
how can i writ the cod
I wait ASAP

[JosAH]

Consider a TreeMap<String, Set<String>>; the keys are the protein codes,
the values are Sets of proteins that 'interact' with the key proteins.

Adding a new protein pair can be done as follows:

[code=java]
public void add(Map<String> map, Set<String>>, String protein, String otherProtein) {

Set<String others;
if ((others= map.get(protein )) == null)
map.put(protein , others= new HashSet<String> ());
others.put(othe rProtein);
}
[/code]

Producing a matrix given that map is easy.

kind regards,

Jos

[amoon]

Dear Jos

I don't want to add protins I want to get the interaction protins in a matrix
package tASk1;
import java.util.*;
import java.io.*;
import java.util.Scann er;


public class read {
public static void main(String args[]){
try{
FileInputStream fstream = new FileInputStream ("interactions. txt");
DataInputStream in = new DataInputStream (fstream);
BufferedReader br = new BufferedReader( new InputStreamRead er(in));
String strLine;
Protein p=new Protein();
while ((strLine=br.re adLine())!=null ){
if(p.getPNameIn Col1().contentE quals("YAL005C" )&&(p.getPNameI nCol2().content Equals("YAR002W ")));
System.out.prin tln(strLine);
}
in.close();
}catch (Exception e){
System.err.prin tln("Error: "+e.getMessage( ));
}}






}


I do this code put my problems in the if statment
help me

[r035198x]

Dear Jos

I don't want to add protins I want to get the interaction protins in a matrix
package tASk1;
import java.util.*;
import java.io.*;
import java.util.Scann er;


public class read {
public static void main(String args[]){
try{
FileInputStream fstream = new FileInputStream ("interactions. txt");
DataInputStream in = new DataInputStream (fstream);
BufferedReader br = new BufferedReader( new InputStreamRead er(in));
String strLine;
Protein p=new Protein();
while ((strLine=br.re adLine())!=null ){
if(p.getPNameIn Col1().contentE quals("YAL005C" )&&(p.getPNameI nCol2().content Equals("YAR002W ")));
System.out.prin tln(strLine);
}
in.close();
}catch (Exception e){
System.err.prin tln("Error: "+e.getMessage( ));
}}






}


I do this code put my problems in the if statment
help me

Please use code tags for posting code.
The correct methods of reading a text file are described here.

[JosAH]

Dear Jos

I don't want to add protins I want to get the interaction protins in a matrix

Maybe you don't realize it yet but you do want to add those proteins to that map.
Given that map you can generate the matrix without even thinking.

I think you just have problems with reading a text file.

kind regards,

Jos

[amoon]

maybe I always get error in the if statmen whcih is under while loop
can u help me in that

[JosAH]

maybe I always get error in the if statmen whcih is under while loop
can u help me in that

I really can't say in advance; what's the exact error message? Mondays are my
non-psychic days ... ;-)

kind regards,

Jos

[r035198x]

maybe I always get error in the if statmen whcih is under while loop
can u help me in that

It would help if you were reading the responses being given to you.