[Cdk-devel] [ cdk-Bugs-895973 ] java.lang.OutOfMemoryError with IteratingMDLReader

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Bugs item #895973, was opened at 2004-02-12 20:06
Message generated for change (Comment added) made by egonw
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Category: cdk-io module
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
>Assigned to: Egon Willighagen (egonw)
Summary: java.lang.OutOfMemoryError with IteratingMDLReader

Initial Comment:
Hello,

I get an java.lang.OutOfMemoryError if I access the
IteratingMDLReader.next() function. Example program:

FileReader fileReader = new FileReader( args[1] );
IteratingMDLReader reader = new IteratingMDLReader(
fileReader );
while( reader.hasNext() )
  reader.next();

The first call of reader.next() leads to the
OutOfMemoryError.

I really appreaciate any help.

Uli

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>Comment By: Egon Willighagen (egonw)
Date: 2004-02-13 13:34

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I've applied to suggested fixes (Thanx Sulev!). About the 
throws Exception. It's specified by the Iterator 
interface, and indeed should have been implemented as 
such. 

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Comment By: Sulev Sild (sulev)
Date: 2004-02-13 13:21

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One more thing. According to the Iterator interface
specification, this method should throw
NoSuchElementException if there is no next element. With the
current implementation an empty molecule is returned which
is against the spec.


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Comment By: Sulev Sild (sulev)
Date: 2004-02-13 13:18

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The next() method has problem that no next line is read in
the while cycle. Thus the first line is appended to the
buffer over and over, eventually overflowing. Add
"currentLine = input.readLine();" after
"buffer.append(currentLine);".

There is another problem in this method as well.
"input.readLine();" will strip  newline and parsing of the
molecule will fail. Therefore "buffer.append(currentLine);"
should be replaced with "buffer.append(currentLine + "\n");"

After these changes, it should work OK.

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Comment By: Christoph Steinbeck (steinbeck)
Date: 2004-02-12 21:57

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It would be great to learn something about the boundary
conditions of the occurence of this bug. How many where
present in the file? Can we get a copy of this file?

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You can respond by visiting: 
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