/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
/**
* PredFile.java
* JalviewX / Vamsas Project
* JPred.seq.concise reader
*/
-
package jalview.io;
-import jalview.datamodel.*;
-import jalview.util.*;
-
import java.io.*;
import java.util.*;
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
public class JPredFile
extends AlignFile
{
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;
}
- public Hashtable getScores() {
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getScores()
+ {
return Scores;
}
- public Hashtable getSymscores() {
- return Symscores;
- }
- public JPredFile(String inStr)
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getSymscores()
{
- super(inStr);
+ return Symscores;
}
+ /**
+ * DOCUMENT ME!
+ */
public void initData()
{
-
super.initData();
Scores = new Hashtable();
ids = null;
conf = null;
}
- public JPredFile(String inFile, String type)
- throws IOException
- {
-
- super(inFile, type);
- }
-
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
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) {
+ if (numSymbols == 0)
+ {
continue;
}
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";
+ String ascore = "dead";
+
try
{
// store elements as floats...
- while (symbols.hasMoreTokens()) {
+ 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.setElementAt(
+ (Object) ( (Float) scores.elementAt(j)).toString(), j);
}
- scores.addElement((Object) ascore);
- while (symbols.hasMoreTokens()) {
- {
- ascore = symbols.nextToken();
- scores.addElement( (Object) ascore);
- }
+
+ scores.addElement( (Object) ascore);
+
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+ scores.addElement( (Object) ascore);
}
+
Scores.put(id, scores);
}
}
// 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());
+ 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++)
{
- // Sequence or a prediction string (rendered as sequence)
+ newseq.append(symbols.nextToken());
+ }
- StringBuffer newseq = new StringBuffer();
+ if (id.indexOf(";") > -1)
+ {
+ seq_entries.addElement(newseq);
+
+ int i = 1;
+ String name = id.substring(id.indexOf(";") + 1);
- for (int i = 0; i < numSymbols; i++) {
- newseq.append(symbols.nextToken());
+ while (ids.lastIndexOf(name) > -1)
+ {
+ name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
}
- 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;
- }
- ids.addElement(name);
+ ids.addElement(name);
- noSeqs++;
- }
- else
+ noSeqs++;
+ }
+ else
+ {
+ if (id.equals("JNETPRED"))
{
- 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));
+ 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!");
+ }*/
-
- 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() + ")");
- }
+ 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");
+ ids.elementAt(i).toString() +
+ ") has an unexpected number of columns");
}
- if (newSeq.getName().startsWith("QUERY") && QuerySeqPosition==-1) {
+
+ if (newSeq.getName().startsWith("QUERY") &&
+ (QuerySeqPosition == -1))
+ {
QuerySeqPosition = seqs.size();
}
seqs.addElement(newSeq);
-
}
}
* print
*
* @return String
- */
+ */
+ public String print()
+ {
+ return "Not Supported";
+ }
- public String print()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args)
+ {
+ try
{
- return "Not Supported";
- }
+ JPredFile blc = new JPredFile(args[0], "File");
- 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)).getSequence()
- + "\n");
- }
- }
- catch (java.io.IOException e)
+ for (int i = 0; i < blc.seqs.size(); i++)
{
- System.err.println("Exception " + e);
- e.printStackTrace();
+ 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();
+ }
}
- /*
- 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
+ Vector annotSeqs = null;
+ /**
+ * removeNonSequences
+ */
+ public void removeNonSequences()
+ {
+ if (annotSeqs != null)
{
- BLCFile blc = new BLCFile(args[0], "File");
- DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
- for (int i = 0; i < blc.seqs.size(); i++)
+ 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"))
{
- s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
+ annotSeqs.addElement(sq);
+ seqs.removeElementAt(--j);
}
- 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)
+ for (; i < j; i++)
{
- System.out.println("Exception " + e);
+ 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)
+ {
+ System.out.println("Exception " + e);
+ }
+ }
+
+ }
+ */
git://source.jalview.org / jalview.git / blobdiff