How can I create a List of a custom class with two fields and get output?

I need to make list of a gene sequence in Java and the starting positions of the parts that I care. I use a .txt file as input then search "GT" in the sequence. Once I find it, I want to store it in an array with the corresponding index. I couldn't make it happen. Please guide me.

import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.nio.MappedByteBuffer; import java.nio.channels.FileChannel; import java.nio.charset.Charset; import java.util.ArrayList; import java.util.List; import java.util.logging.Level; import java.util.logging.Logger; class Signal{ public String signal; public int pos; public Signal(String s, int p) { s = signal; p = pos; } public static String inputSequence(String filename) throws IOException{ FileInputStream stream = new FileInputStream(new File(filename)); try { FileChannel fc = stream.getChannel(); MappedByteBuffer bb = fc.map(FileChannel.MapMode.READ_ONLY, 0, fc.size()); return Charset.defaultCharset().decode(bb).toString(); } finally{ stream.close(); } } public static void main(String[] args) { String c1 = "GT"; String seq = null; List<Signal> s2 = new ArrayList<Signal>(); String s1; int i; try { seq = inputSequence(path); } catch (IOException ex) { Logger.getLogger(Signal.class.getName()).log(Level.SEVERE, null, ex); } for (i = 0; i < seq.length() - 2; i++ ) { s1 = seq.substring(i,i+2); if (s1.equals(c1)){ Signal ss = new Signal(s1, i); s2.add(ss); } } System.out.print(s2); } }

-------------Problems Reply------------

Your constructor should be as follows:

public Signal(String s, int p) {
signal = s;
pos = p;
}

After that it should work fine.

You can use indexOf in a loop to find all occurrences of "GT". This is shown below:

String c1 = "GT";
String seq = null;
List<Signal> s2 = new ArrayList<Signal>();

try {
seq = inputSequence(path);
} catch (IOException ex) {
Logger.getLogger(Signal.class.getName()).log(Level.SEVERE, null, ex);
}

int index = seq.indexOf(c1, 0);
do{
if(index != -1){
Signal ss = new Signal(c1, index);
s2.add(ss);
System.out.println(index);
}
index = seq.indexOf(c1, index+2);
}while(index != -1);

System.out.println(s2);

To print out the signals list you need to override toString in your Signal class:

@Override
public String toString(){
return "(" + signal + "," + pos + ")";
}

Category:java Views:0 Time:2011-02-23

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