X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=cadf1535555db4ded65a52c50ea3a29d3003d587;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=754b539eead65bcb98709fd2470a42850e67fb2c;hpb=950f8f47f9eff65f5f39501789b03f03591f1819;p=jalview.git diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 754b539..cadf153 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,270 +1,388 @@ -/** - * PredFile.java - * 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 - public JPredFile(String inStr) - { - super(inStr); - } - - public void initData() - { - - super.initData(); - Scores = new Hashtable(); - } - - public JPredFile(String inFile, String type) - throws IOException - { - - super(inFile, type); - } - - /** - * parse a JPred concise file into a sequence-alignment like object. - */ - - public void parse() - throws IOException - { - - String line; - - 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 = ""; - String seq = ""; - 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.set(j, - (Object) ( (Float) scores.get(j)).toString()); - } - scores.addElement((Object) ascore); - while (symbols.hasMoreTokens()) { - { - ascore = symbols.nextToken(); - scores.addElement( (Object) ascore); - } - } - Scores.put(id, scores); - } - } else - if (id.equals("jnetconf")) - { - 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(); - - 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)+"_"+1; - } - 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)); - } - } - } - - - 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() + ")"); - } - - if (maxLength != seq_entries.elementAt(i).toString().length()) - { - throw new IOException("JPredConcise: Entry (" + - ids.elementAt(i).toString() - + ") has an unexpected number of columns"); - } - seqs.addElement(newSeq); - - } - } - - /** - * print - * - * @return String - */ - - public String print() - { - return "Not Supported"; - } - - 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) - { - System.out.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 - { - 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); - } - } - - } - */ +/* +* 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 +*/ + +/** + * PredFile.java + * JalviewX / Vamsas Project + * JPred.seq.concise reader + */ +package jalview.io; + +import jalview.datamodel.*; + +import java.io.*; + +import java.util.*; + + +/** + * 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 inStr DOCUMENT ME! + */ + public JPredFile(String inStr) + { + super(inStr); + } + + /** + * 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.set(j, + (Object) ((Float) scores.get(j)).toString()); + } + + 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.set(i, (Object) symbols.nextToken()); + } + } + 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)); + } + } + } + + 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() + ")"); + } + + 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); + } + } + + /** + * 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)).getSequence() + + "\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 + { + 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); + } + } + + } + */