import org.biojava.bio.BioException; import org.biojavax.bio.seq.RichSequence; import org.biojavax.bio.seq.RichSequenceIterator; import org.biojavax.bio.seq.RichSequence.IOTools; import java.io.*; import javax.swing.JFileChooser; public class FastaReader { public static BufferedReader openFile() { JFileChooser chooser = new JFileChooser("."); int retval = chooser.showOpenDialog(null); BufferedReader br = null; if (retval == JFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); try { br = new BufferedReader(new FileReader(file)); } catch (FileNotFoundException e) { System.out.println("Trouble reading " + file.getName()); e.printStackTrace(); } } return br; } public static RichSequenceIterator readFastaDNA(BufferedReader br) throws BioException { return IOTools.readFastaDNA(br, null); } }