X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=30cd18190fd881541e735d9a8106d0f34db39b5e;hb=ad52f1ddcaefa09c6a3e85329b28dad155613f49;hp=08f7d176333556640fe6267fa9c9d53fdce9e010;hpb=1b239902a068acb9cb65ace621a15c6f3984b77b;p=jalview.git diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 08f7d17..30cd181 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,3 +1,22 @@ +/* + * 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 @@ -5,12 +24,17 @@ */ 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 { @@ -19,73 +43,108 @@ public class JPredFile 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. */ public void parse() throws IOException { -System.out.println("all read in "); + // 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) { + if (numSymbols == 0) + { continue; } @@ -95,123 +154,137 @@ System.out.println("all read in "); 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); } } else if (id.equals("jnetconf")) { - System.out.println("here"); + // 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); - for (int i = 0; i < numSymbols; i++) { - newseq.append(symbols.nextToken()); + int i = 1; + String name = id.substring(id.indexOf(";") + 1); + + 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); - } } @@ -219,75 +292,116 @@ System.out.println("all read in "); * 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.out.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); + } + } + + } + */