Applet: StackOverflowError when calling readObject()

[verteidi]

Hello everyone,
I have been searching this forum for a solution to my problem, but unfortunately couldn't find anything so far. It would be very kind if you could take a look at this.
I am trying to read an object, that I have saved before in a file called "eco.net", in an applet with the readObject() method:

import java.applet.*;
import java.io.*;
 
public class TestApplet extends Applet
{
     public void init()
     {
         try{
            FileInputStream fis = new FileInputStream("eco.net");
            ObjectInputStream ois = new ObjectInputStream(fis);
 
            BioNet bioNet = (BioNet) ois.readObject();
            ois.close();
        } catch (IOException e) {
            e.printStackTrace();
        } catch (ClassNotFoundException e) {
            e.printStackTrace();
        }
     }
}
 

The command-line output of this is:

java.lang.StackOverflowError
        at java.io.ObjectInputStream$BlockDataInputStream.readByte(ObjectInputStream.java:2718)
        at java.io.ObjectInputStream.readHandle(ObjectInputStream.java:1428)
        at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1490)
        at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1732)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)
        at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1667)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1323)
        at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1945)
        at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1869)
        at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1753)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)
        at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1945)
...
 

These kind of errors continue for more than 1000 lines.
If I try to read the same object in a normal application, this works flawlessly:

import java.io.*;
 
public class Test
{
     public static void main(String[] args)
     {
         try{
            FileInputStream fis = new FileInputStream("eco.net");
            ObjectInputStream ois = new ObjectInputStream(fis);
 
            BioNet bioNet = (BioNet) ois.readObject();
            ois.close();
        } catch (IOException e) {
            e.printStackTrace();
        } catch (ClassNotFoundException e) {
            e.printStackTrace();
        }
     }
} 
 

I made sure that the classes I am creating the object "eco.net" from implement the Serializable interface, as I read that this is likely to cause problems.
A bit more information about the object that I am trying to read:
I am trying to create a Java-representation of a biochemical network "BioNet". This uses the classes "Compound" and "Reaction", which are themselves interlinked. Please tell me if it would help you to see the whole code (it is quite a lot, that's why I didn't post it already). The actual writing of the object in a file is done with this code:

import java.io.*;
 
public class BuildBioNet {
 
    public static void main(String[] args) {
        try {
 
            FileOutputStream fos = new FileOutputStream("eco.net");
            ObjectOutputStream oos = new ObjectOutputStream(fos);
 
            BioNet eco = new BioNet();
            eco.buildFromFile("ecoInfo.ref","ecoBioNet.txt");
 
            oos.writeObject(eco);
 
            // Flush and close the ObjectOutputStream.
            oos.flush();
            oos.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}
 

The file size of "eco.net" is 325kB, if this is of any importance. I am using Java version 1.5.0.
Thank you very very much,any help is appreciated - this problem is driving me mad for days already.
Regards,
Kai

[BigDaddyLH]

I would dump the applet and try to get this working in a standalone application -- it will be easier to debug. Try using a smaller file. Also try raising your max memory: see options -XMs and -XMx: http://java.sun.com/javase/6/docs/te...dows/java.html

[verteidi]

Thank you for your quick answer. I tried raising the maximum memory to 120Mb without effect, I still get the same error message for the applet. My goal is to create a web-tool for external users that work with the biochemical network (a graph creation and manipulation tool), so I would like to keep the applet. It is already working as a standalone application. I have been working with objects of similar size already and it worked without problems, I just can't figure out, why it is not working with this one. Thank you again!

[JosAH]

Thank you for your quick answer. I tried raising the maximum memory to 120Mb without effect, I still get the same error message for the applet. My goal is to create a web-tool for external users that work with the biochemical network (a graph creation and manipulation tool), so I would like to keep the applet. It is already working as a standalone application. I have been working with objects of similar size already and it worked without problems, I just can't figure out, why it is not working with this one. Thank you again!

Did you also try to increase the stack size? (use the -XMs option). Graphs
are read recursively, i.e. when a node is connected to another node (through an
edge) the ObjectInputStream calls itself recursively to read that other node.

kind regards,

Jos

[verteidi]

Thank you! I already suspected it to be a recursion problem, but couldn't connect it with my network. I will try to change its structure again, so perhaps I can avoid deep recursion. It became a lot clearer to me now.
By the way, changing the stack size was without effect, as well.
Have a nice day still and thank you again!

[verteidi]

It worked! I separated the processes 'creating and reading the BioNet' and 'connecting the nodes'. Only after retrieving the "eco.net" object I am establishing the final structure. No StackOverflowError any more.
Thank you all for the final clue and all the help, now I can finally sleep without nightmares of Stacks falling on my head again.