[Biojava-l] Using SeqIOTools in a JNLP context

[Keith Turner]

Hello-

I am new to the list.  I enjoy working with the Biojava API, but a problem has arisen for me, and I need some help with it.  I am developing an application to be used in the Java Webstart framework, and this brings with it some interesting file permission issues.  Basically, you use the JNLP interface FileOpenService to open a file from within the secure "sandbox" environment, and then you can get an InputStream out of that.

So I want to take this InputStream (which presumably is from a Fasta file), and read a DNA sequence from it.  However, all the methods that worked when I was running my software as a Java application no longer work in the JNLP environment.  In the past, I was doing:
  InputStreamReader fr = new InputStreamReader(in);
  BufferedReader br = new BufferedReader(fr);
  SequenceIterator stream = SeqIOTools.readFastaDNA(br);
  Sequence seq = stream.nextSequence();
But the program freezes on the SeqIOTools.readFastaDNA(br) call.  No exception is thrown back, it just does nothing.  Does anyone have any suggestions as to how I can solve or work around this problem?  Thank you very much

-Keith Turner