/*
* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* JalviewX / Vamsas Project
* JPred.seq.concise reader
*/
-
package jalview.io;
-import jalview.datamodel.*;
-import jalview.util.*;
-
import java.io.*;
import java.util.*;
-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;
- public void setQuerySeqPosition(int QuerySeqPosition)
- {
- this.QuerySeqPosition = QuerySeqPosition;
- }
+import jalview.datamodel.*;
- public int getQuerySeqPosition()
- {
- return QuerySeqPosition;
- }
- public Hashtable getScores() {
- return Scores;
- }
- public Hashtable getSymscores() {
- return Symscores;
- }
- public JPredFile(String inStr)
- {
- super(inStr);
- }
+/**
+ * DOCUMENT ME!
+ *
+ * @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);
+ }
- public void initData()
- {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param QuerySeqPosition DOCUMENT ME!
+ */
+ public void setQuerySeqPosition(int QuerySeqPosition)
+ {
+ this.QuerySeqPosition = QuerySeqPosition;
+ }
- super.initData();
- Scores = new Hashtable();
- ids = null;
- conf = null;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getQuerySeqPosition()
+ {
+ return QuerySeqPosition;
+ }
- public JPredFile(String inFile, String type)
- throws IOException
- {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getScores()
+ {
+ return Scores;
+ }
- super(inFile, type);
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getSymscores()
+ {
+ return Symscores;
+ }
- /**
- * 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)
+ /**
+ * DOCUMENT ME!
+ */
+ public void initData()
{
- // Concise format allows no comments or non comma-formatted data
- StringTokenizer str = new StringTokenizer(line, ":");
- String id = "";
- if (!str.hasMoreTokens())
- {
- continue;
- }
+ super.initData();
+ Scores = new Hashtable();
+ ids = null;
+ conf = null;
+ }
- 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();
+ /**
+ * 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;
- if (numSymbols==0) {
- continue;
- }
+ Vector seq_entries = new Vector();
+ Vector ids = new Vector();
+ Hashtable Symscores = new Hashtable();
- if (seqsym.length() != (2 * numSymbols))
- {
- // Set of scalars for some property
- if (Scores.containsKey(id))
+ while ((line = nextLine()) != null)
{
- 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.set(j,
- (Object) ( (Float) scores.get(j)).toString());
- }
- scores.addElement((Object) ascore);
- while (symbols.hasMoreTokens()) {
+ // Concise format allows no comments or non comma-formatted data
+ StringTokenizer str = new StringTokenizer(line, ":");
+ String id = "";
+
+ if (!str.hasMoreTokens())
{
- ascore = symbols.nextToken();
- scores.addElement( (Object) ascore);
+ continue;
}
- }
- 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.set(i, (Object) symbols.nextToken());
- }
- }
- else
- {
- // Sequence or a prediction string (rendered as sequence)
- StringBuffer newseq = new StringBuffer();
+ id = str.nextToken();
+
+ String seqsym = str.nextToken();
+ StringTokenizer symbols = new StringTokenizer(seqsym, ",");
- for (int i = 0; i < numSymbols; i++) {
- newseq.append(symbols.nextToken());
- }
+ // decide if we have more than just alphanumeric symbols
+ int numSymbols = symbols.countTokens();
- 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)+"_"+1;
+ if (numSymbols == 0)
+ {
+ continue;
}
- ids.addElement(name);
-
- noSeqs++;
- }
- else
- {
- if (id.equals("JNETPRED")) {
- id = "Predicted Secondary Structure";
+
+ 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);
+ }
}
- seq_entries.addElement( newseq.toString() );
- ids.addElement(id);
- Symscores.put((Object) id, (Object) new Integer(ids.size()-1));
- }
- }
- }
+ 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;
+ }
+
+ 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();
- 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 (!Symscores.containsKey(ids.elementAt(i))
- && !isValidProteinSequence(newSeq.getSequence()))
- {
- throw new IOException(
- "JPredConcise: Not a valid protein sequence - ("
- + ids.elementAt(i).toString() + ")");
- }
+ 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") && QuerySeqPosition==-1) {
- QuerySeqPosition = seqs.size();
- }
- seqs.addElement(newSeq);
+ 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") &&
+ (QuerySeqPosition == -1))
+ {
+ QuerySeqPosition = seqs.size();
+ }
- /**
- * print
- *
- * @return String
- */
+ seqs.addElement(newSeq);
+ }
+ }
+ /**
+ * print
+ *
+ * @return String
+ */
public String print()
{
- return "Not Supported";
+ 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++)
+ try
{
- System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName()
- + "\n" +
- ( (Sequence) blc.seqs.elementAt(i)).getSequence()
- + "\n");
+ 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)
+ 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.
{
- System.err.println("Exception " + e);
- e.printStackTrace();
+ 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;
}
+}
- /*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
- out.append(s[0].sequence.substring(i, i + 1) + " ");
- out.append(s[1].sequence.substring(i, i + 1) + " ");
- out.append(s[1].score[0].elementAt(i) + " ");
- out.append(s[1].score[1].elementAt(i) + " ");
- out.append(s[1].score[2].elementAt(i) + " ");
- out.append(s[1].score[3].elementAt(i) + " ");
-
- out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
- public static void main(String[] args)
- {
- try
- {
- BLCFile blc = new BLCFile(args[0], "File");
- DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
- for (int i = 0; i < blc.seqs.size(); i++)
- {
- s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
- }
- String out = BLCFile.print(s);
- AlignFrame af = new AlignFrame(null, s);
- af.resize(700, 500);
- af.show();
- System.out.println(out);
- }
- catch (java.io.IOException e)
+/*
+ StringBuffer out = new StringBuffer();
+
+ out.append("START PRED\n");
+ for (int i = 0; i < s[0].sequence.length(); i++)
+ {
+ out.append(s[0].sequence.substring(i, i + 1) + " ");
+ out.append(s[1].sequence.substring(i, i + 1) + " ");
+ out.append(s[1].score[0].elementAt(i) + " ");
+ out.append(s[1].score[1].elementAt(i) + " ");
+ out.append(s[1].score[2].elementAt(i) + " ");
+ out.append(s[1].score[3].elementAt(i) + " ");
+
+ out.append("\n");
+ }
+ out.append("END PRED\n");
+ return out.toString();
+ }
+
+ public static void main(String[] args)
+ {
+ try
+ {
+ BLCFile blc = new BLCFile(args[0], "File");
+ DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
+ for (int i = 0; i < blc.seqs.size(); i++)
{
- System.out.println("Exception " + e);
+ s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
}
- }
+ String out = BLCFile.print(s);
- }
- */
+ AlignFrame af = new AlignFrame(null, s);
+ af.resize(700, 500);
+ af.show();
+ System.out.println(out);
+ }
+ catch (java.io.IOException e)
+ {
+ System.out.println("Exception " + e);
+ }
+ }
+
+ }
+ */
git://source.jalview.org / jalview.git / blobdiff