X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=5bc615ec0af0d76c4966daee69633db919f79875;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=12be9de5f536530b3e7ab28c6d649e8b159f2c2d;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 12be9de..5bc615e 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,300 +1,444 @@ /* -* 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 (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview 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 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ /** * 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 - private int QuerySeqPosition; - - public JPredFile(String inStr) { - super(inStr); - } - - public JPredFile(String inFile, String type) throws IOException { - super(inFile, type); - } - - public void setQuerySeqPosition(int QuerySeqPosition) { - this.QuerySeqPosition = QuerySeqPosition; - } - - public int getQuerySeqPosition() { - return QuerySeqPosition; - } - - public Hashtable getScores() { - return Scores; - } - - public Hashtable getSymscores() { - return Symscores; - } - - 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) + "_" + 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"); - } - - if (newSeq.getName().startsWith("QUERY") && - (QuerySeqPosition == -1)) { - QuerySeqPosition = seqs.size(); - } - - 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.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 + */ +package jalview.io; + +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; + +import java.io.IOException; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; + +/** + * Parser for the JPred/JNet concise format. This is a series of CSV lines, each + * line is either a sequence (QUERY), a sequence profile (align;), or jnet + * prediction annotation (anything else). Automagic translation happens for + * annotation called 'JNETPRED' (translated to Secondary Structure Prediction), + * or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are + * differentiated from symbolic by being parseable into a float vector. They are + * put in Scores. Symscores gets the others. JNetAnnotationMaker translates the + * data parsed by this object into annotation on an alignment. It is + * automatically called but can be used to transfer the annotation onto a + * sequence in another alignment (and insert gaps where necessary) + * + * @author jprocter + * @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 JPredFile(FileParse source) throws IOException + { + super(source); + } + + /** + * 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() { - BLCFile blc = new BLCFile(args[0], "File"); - DrawableSequence[] s = new DrawableSequence[blc.seqs.size()]; - for (int i = 0; i < blc.seqs.size(); i++) + 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( + MessageManager + .formatMessage( + "exception.jpredconcide_entry_has_unexpected_number_of_columns", + new String[] { ids.elementAt(i).toString() })); + } + + if ((newSeq.getName().startsWith("QUERY") || newSeq.getName() + .startsWith("align;")) && (QuerySeqPosition == -1)) + { + QuerySeqPosition = seqs.size(); + } + + seqs.addElement(newSeq); + } + if (seqs.size() > 0 && QuerySeqPosition > -1) { - s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); + // try to make annotation for a prediction only input (default if no + // alignment is given and prediction contains a QUERY or align;sequence_id + // line) + Alignment tal = new Alignment(this.getSeqsAsArray()); + try + { + JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition, + true); + } catch (Exception e) + { + tal = null; + IOException ex = new IOException( + MessageManager + .formatMessage( + "exception.couldnt_parse_concise_annotation_for_prediction", + new String[] { e.getMessage() })); + e.printStackTrace(); // java 1.1 does not have : + // ex.setStackTrace(e.getStackTrace()); + throw ex; + } + this.annotations = new Vector(); + AlignmentAnnotation[] aan = tal.getAlignmentAnnotation(); + for (int aai = 0; aan != null && aai < aan.length; aai++) + { + annotations.addElement(aan[aai]); + } } - String out = BLCFile.print(s); + } - AlignFrame af = new AlignFrame(null, s); - af.resize(700, 500); - af.show(); - System.out.println(out); + /** + * print + * + * @return String + */ + public String print() + { + return "Not Supported"; } - catch (java.io.IOException e) + + /** + * 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(); not java 1.1 compatible! + } + } + + Vector annotSeqs = null; + + /** + * removeNonSequences + */ + public void removeNonSequences() { - System.out.println("Exception " + e); + 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; } - } +} - } - */ +/* + * 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); } } } + */