Re: [Biojava-l] Reading Fasta file problem (new to biojava)

[Chris Cole]

On 16/12/09 11:22, Richard Holland wrote:
BufferedReader br = new BufferedReader(new FileReader(args[0]));
Namespace ns = RichObjectFactory.getDefaultNamespace();
RichSequenceIterator iterator = RichSequence.IOTools.readFastaProtein(br,ns);

Thanks, Richard. However, now I get an error:
"BioException cannot be resolved to a type"

Below is the code for the method. What am I missing?

public void read(String filename) {
   try {
      System.out.println("Reading file: " + filename);
      BufferedReader br = new BufferedReader(new FileReader(filename));
                        
      Namespace ns = RichObjectFactory.getDefaultNamespace();
      RichSequenceIterator iter = 
RichSequence.IOTools.readFastaProtein(br,ns);
   }
   catch (FileNotFoundException ex) {
      //can't find file specified by args[0]
      ex.printStackTrace();
   } catch (BioException ex) {
      //error parsing requested format
      ex.printStackTrace();
   }
}
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