X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=30cd18190fd881541e735d9a8106d0f34db39b5e;hb=ad52f1ddcaefa09c6a3e85329b28dad155613f49;hp=3f308be12c4c47406e231a6713230dcc7a30e6dd;hpb=558597672640984d936ea22409a674293192a09c;p=jalview.git diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 3f308be..30cd181 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,21 +1,21 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* 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 -* 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 @@ -29,330 +29,338 @@ import java.util.*; import jalview.datamodel.*; - /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ -public class JPredFile extends AlignFile +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); - } + 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; - /** - * DOCUMENT ME! - * - * @param QuerySeqPosition DOCUMENT ME! - */ - public void setQuerySeqPosition(int QuerySeqPosition) - { - this.QuerySeqPosition = 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! - * - * @return DOCUMENT ME! - */ - public int getQuerySeqPosition() - { - return QuerySeqPosition; - } + /** + * DOCUMENT ME! + * + * @param QuerySeqPosition DOCUMENT ME! + */ + public void setQuerySeqPosition(int QuerySeqPosition) + { + this.QuerySeqPosition = QuerySeqPosition; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Hashtable getScores() - { - return Scores; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getQuerySeqPosition() + { + return QuerySeqPosition; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Hashtable getSymscores() - { - return Symscores; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Hashtable getScores() + { + return Scores; + } - /** - * DOCUMENT ME! - */ - public void initData() - { - super.initData(); - Scores = new Hashtable(); - ids = null; - conf = null; - } + /** + * 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 + /** + * 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) { - // JBPNote log.System.out.println("all read in "); - String line; - QuerySeqPosition = -1; - noSeqs = 0; + // 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"; - Vector seq_entries = new Vector(); - Vector ids = new Vector(); - Hashtable Symscores = new Hashtable(); + try + { + // store elements as floats... + while (symbols.hasMoreTokens()) + { + ascore = symbols.nextToken(); + + Float score = new Float(ascore); + scores.addElement( (Object) score); + } - while ((line = nextLine()) != null) + Scores.put(id, scores); + } + catch (Exception e) { - // 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; - } - - 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)); - } - } + // 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); } - /* leave it to the parser user to actually check this. - if (noSeqs < 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++) { - throw new IOException( - "JpredFile Parser: No sequence in the prediction!"); - }*/ + conf.setElementAt(symbols.nextToken(), i); + } + } + else + { + // Sequence or a prediction string (rendered as sequence) + StringBuffer newseq = new StringBuffer(); - maxLength = seq_entries.elementAt(0).toString().length(); + for (int i = 0; i < numSymbols; i++) + { + newseq.append(symbols.nextToken()); + } - for (int i = 0; i < ids.size(); i++) + if (id.indexOf(";") > -1) { - // 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); + 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!"); + }*/ - /** - * print - * - * @return String - */ - public String print() + maxLength = seq_entries.elementAt(0).toString().length(); + + for (int i = 0; i < ids.size(); i++) { - return "Not Supported"; + // 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); } + } - /** - * DOCUMENT ME! - * - * @param args DOCUMENT ME! - */ - public static void main(String[] args) + /** + * print + * + * @return String + */ + public String print() + { + return "Not Supported"; + } + + /** + * DOCUMENT ME! + * + * @param args DOCUMENT ME! + */ + public static void main(String[] args) + { + try { - 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(); - } + 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; + } + + Vector annotSeqs = null; /** * removeNonSequences */ public void removeNonSequences() { - if (annotSeqs!=null) + if (annotSeqs != null) + { return; + } annotSeqs = new Vector(); Vector newseqs = new Vector(); - int i=0; - int j=seqs.size(); - for (; i