Odd behaviour appending to System.out PrintStream

Question

I've run into some unexpected behaviour with the System.out PrintStream object. When I append characters to it I'm expecting the characters to be displayed on screen much like I'd expect the characters to be written to a file using a FileOutputStream. What seems to happen is that the characters are written to the PrintStream but the process continues on and on adding some unseen character (newline?). The following code generates the behaviour I"m talking about. The main method is a bit contrived but does the job. You'll likely have to increase your heap size to run this (-Xmx512m worked for me):
{code}
package output.stream.problem;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.io.StringReader;
import java.util.HashMap;
import java.util.Random;
* A class used to introduce transition/transversion errors into DNA sequences. Error types are introduced
* with equal probability and are mutually exclusive.
* @author twb
public class GenomicDNAMutator {
     private HashMap<Integer,Character> mutations=new HashMap<Integer,Character>();
     private Reader sequenceSource;
     private Random rand=new Random();
     private double errorRate=-1;
     public GenomicDNAMutator(String fileName, double errorProbability) {
          try {
               sequenceSource=new FileReader(fileName);
               errorRate=errorProbability;
          } catch (FileNotFoundException fnfe) {
               System.err.println("Could not open file "+fileName);
               fnfe.printStackTrace();
     public GenomicDNAMutator(File file, double errorProbability) {
          try {
               sequenceSource=new FileReader(file);
               errorRate=errorProbability;
          } catch (FileNotFoundException fnfe) {
               System.err.println("Could not open file "+file);
               fnfe.printStackTrace();
     public GenomicDNAMutator(Reader is, double errorProbability) {
          sequenceSource=is;
          errorRate=errorProbability;
     public void process() {
          this.process(System.out);
     public void process(OutputStream os) {
          BufferedWriter bw=new BufferedWriter(new OutputStreamWriter(os));
          BufferedReader br=new BufferedReader(this.sequenceSource);
          char nucleotide;
          char[] a=new char[]{'T','C','G'};
          char[] t=new char[]{'A','C','G'};
          char[] c=new char[]{'A','T','G'};
          char[] g=new char[]{'A','T','C'};
          char[][] errorMatrix=new char[][]{a,t,c,g};
          int matrixIndex=-1;
          try {
               int count=0;
               int i=0;
               while((i=br.read())!=-1) {
                    nucleotide=(char)i;
                    count++;
                    double d=rand.nextDouble();
                    if(d<=this.errorRate) {
                         switch(nucleotide) {
                         case 'A':
                              matrixIndex=0;
                              break;
                         case 'T':
                              matrixIndex=1;
                              break;
                         case 'C':
                              matrixIndex=2;
                              break;
                         case 'G':
                              matrixIndex=3;
                              break;
                         int pos=rand.nextInt(3);
                         this.mutations.put(count,nucleotide);
                         nucleotide=errorMatrix[matrixIndex][pos];
                    bw.append(nucleotide);
               bw.flush();
               bw.close();
          } catch (IOException ioe) {
               System.err.println("Could not read the input source");
     public Reader getIn() {
          return sequenceSource;
     public void setSequenceSource(Reader in) {
          this.sequenceSource = in;
     public static void main(String[] args) throws Exception {
          StringBuilder sb=new StringBuilder();
          for(int i=0;i<30000000;i++) {
               sb.append('A');
          System.out.println("Mock sequence built");
          GenomicDNAMutator gdm=new GenomicDNAMutator(new StringReader(sb.toString()),1d/100d);
          * Run the program using one of the process statements
          gdm.process(new FileOutputStream(new File("c:/text.txt")));
//This one uses the System.out PrintStream object
//          gdm.process();
          System.out.println("done");
{code}
I see this behaviour with java 1.6.0_10-beta and java 1.5.0_11
Thanks for any insight you can give to this.
- Travis

Answer 1

twb wrote:
I've run into some unexpected behaviour with the System.out PrintStream object. When I append characters to it I'm expecting the characters to be displayed on screen much like I'd expect the characters to be written to a file using a FileOutputStream. What seems to happen is that the characters are written to the PrintStream but the process continues on and on adding some unseen character (newline?). The following code generates the behaviour I"m talking about. The main method is a bit contrived but does the job. You'll likely have to increase your heap size to run this (-Xmx512m worked for me):Yes, this is the case. If you look at the javadoc for PrintStream it talks about the "auto-flush on newline" feature. what is your question?