+ * @author $author$
+ * @version $Revision$
+ */
+public class JPredFile
+ extends AlignFile
+{
+ Vector ids;
+ Vector conf;
+ Hashtable Scores; // Hash of names and score vectors
+ Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
+ private int QuerySeqPosition;
+
+ /**
+ * Creates a new JPredFile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public JPredFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param QuerySeqPosition DOCUMENT ME!
+ */
+ public void setQuerySeqPosition(int QuerySeqPosition)
+ {
+ this.QuerySeqPosition = QuerySeqPosition;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getQuerySeqPosition()
+ {
+ return QuerySeqPosition;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getScores()
+ {
+ return Scores;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getSymscores()
+ {
+ return Symscores;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initData()
+ {
+ super.initData();
+ Scores = new Hashtable();
+ ids = null;
+ conf = null;
+ }
+
+ /**
+ * parse a JPred concise file into a sequence-alignment like object.
+ */
+ public void parse()
+ throws IOException
+ {
+ // JBPNote log.System.out.println("all read in ");
+ String line;
+ QuerySeqPosition = -1;
+ noSeqs = 0;
+
+ Vector seq_entries = new Vector();
+ Vector ids = new Vector();
+ Hashtable Symscores = new Hashtable();
+
+ while ( (line = nextLine()) != null)
+ {
+ // Concise format allows no comments or non comma-formatted data
+ StringTokenizer str = new StringTokenizer(line, ":");
+ String id = "";
+
+ if (!str.hasMoreTokens())
+ {
+ continue;
+ }
+
+ id = str.nextToken();
+
+ String seqsym = str.nextToken();
+ StringTokenizer symbols = new StringTokenizer(seqsym, ",");
+
+ // decide if we have more than just alphanumeric symbols
+ int numSymbols = symbols.countTokens();
+
+ if (numSymbols == 0)
+ {
+ continue;
+ }
+
+ if (seqsym.length() != (2 * numSymbols))
+ {
+ // Set of scalars for some property
+ if (Scores.containsKey(id))
+ {
+ int i = 1;
+
+ while (Scores.containsKey(id + "_" + i))
+ {
+ i++;
+ }
+
+ id = id + "_" + i;
+ }
+
+ Vector scores = new Vector();
+
+ // Typecheck from first entry
+ int i = 0;
+ String ascore = "dead";
+
+ try
+ {
+ // store elements as floats...
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+
+ Float score = new Float(ascore);
+ scores.addElement( (Object) score);
+ }
+
+ Scores.put(id, scores);
+ }
+ catch (Exception e)
+ {
+ // or just keep them as strings
+ i = scores.size();
+
+ for (int j = 0; j < i; j++)
+ {
+ scores.setElementAt(
+ (Object) ( (Float) scores.elementAt(j)).toString(), j);
+ }
+
+ scores.addElement( (Object) ascore);
+
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+ scores.addElement( (Object) ascore);
+ }
+
+ Scores.put(id, scores);
+ }
+ }
+ else if (id.equals("jnetconf"))
+ {
+ // log.debug System.out.println("here");
+ id = "Prediction Confidence";
+ this.conf = new Vector(numSymbols);
+
+ for (int i = 0; i < numSymbols; i++)
+ {
+ conf.setElementAt(symbols.nextToken(), i);
+ }
+ }
+ else
+ {
+ // Sequence or a prediction string (rendered as sequence)
+ StringBuffer newseq = new StringBuffer();
+
+ for (int i = 0; i < numSymbols; i++)
+ {
+ newseq.append(symbols.nextToken());
+ }
+
+ if (id.indexOf(";") > -1)
+ {
+ seq_entries.addElement(newseq);
+
+ int i = 1;
+ String name = id.substring(id.indexOf(";") + 1);
+
+ while (ids.lastIndexOf(name) > -1)
+ {
+ name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
+ }
+
+ if (QuerySeqPosition==-1)
+ QuerySeqPosition = ids.size();
+ ids.addElement(name);
+ noSeqs++;
+ }
+ else
+ {
+ if (id.equals("JNETPRED"))
+ {
+ id = "Predicted Secondary Structure";
+ }
+
+ seq_entries.addElement(newseq.toString());
+ ids.addElement(id);
+ Symscores.put( (Object) id,
+ (Object)new Integer(ids.size() - 1));
+ }
+ }
+ }
+ /* leave it to the parser user to actually check this.
+ if (noSeqs < 1)
+ {
+ throw new IOException(
+ "JpredFile Parser: No sequence in the prediction!");
+ }*/
+
+ maxLength = seq_entries.elementAt(0).toString().length();
+
+ for (int i = 0; i < ids.size(); i++)
+ {
+ // Add all sequence like objects
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
+ seq_entries.elementAt(i).toString(), 1,
+ seq_entries.elementAt(i).toString().length());
+
+ if (maxLength != seq_entries.elementAt(i).toString().length())
+ {
+ throw new IOException("JPredConcise: Entry (" +
+ ids.elementAt(i).toString() +
+ ") has an unexpected number of columns");
+ }
+
+ if ((newSeq.getName().startsWith("QUERY") || newSeq.getName().startsWith("align;"))&&
+ (QuerySeqPosition == -1))
+ {
+ QuerySeqPosition = seqs.size();
+ }
+
+ seqs.addElement(newSeq);
+ }
+ }
+
+ /**
+ * print
+ *
+ * @return String
+ */
+ public String print()
+ {
+ return "Not Supported";
+ }
+
+ /**
+ * 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();
+ }
+ }
+
+ 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;
+ }
+}
+