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 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
