+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args)
+ {
+ try
+ {
+ JPredFile blc = new JPredFile(args[0], "File");
+
+ for (int i = 0; i < blc.seqs.size(); i++)
+ {
+ System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName() +
+ "\n" +
+ ( (Sequence) blc.seqs.elementAt(i)).getSequenceAsString() +
+ "\n");
+ }
+ }
+ catch (java.io.IOException e)
+ {
+ System.err.println("Exception " + e);
+ // e.printStackTrace(); not java 1.1 compatible!
+ }
+ }
+
+ Vector annotSeqs = null;
+ /**
+ * removeNonSequences
+ */
+ public void removeNonSequences()
+ {
+ if (annotSeqs != null)
+ {
+ return;
+ }
+ annotSeqs = new Vector();
+ Vector newseqs = new Vector();
+ int i = 0;
+ int j = seqs.size();
+ for (; i < QuerySeqPosition; i++)
+ {
+ annotSeqs.addElement(seqs.elementAt(i));
+ }
+ // check that no stray annotations have been added at the end.
+ {
+ SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
+ if (sq.getName().toUpperCase().startsWith("JPRED"))
+ {
+ annotSeqs.addElement(sq);
+ seqs.removeElementAt(--j);
+ }
+ }
+ for (; i < j; i++)
+ {
+ newseqs.addElement(seqs.elementAt(i));
+ }
+
+ seqs.removeAllElements();
+ seqs = newseqs;
+ }