X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=ab2c00ad3b7cb5076cb965892e50ab8790524a76;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=a038cacb4746d9e8e3e3b62a0eba851a3e12fa08;hpb=3a4b644986de0b69dfe6a8b016a53eab295440dd;p=jalview.git diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index a038cac..ab2c00a 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,20 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ /** * PredFile.java @@ -23,10 +25,18 @@ */ package jalview.io; -import java.io.*; -import java.util.*; +import java.util.Locale; -import jalview.datamodel.*; +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 @@ -52,24 +62,28 @@ public class JPredFile extends AlignFile Hashtable Scores; // Hash of names and score vectors Hashtable Symscores; // indexes of symbol annotation properties in sequenceI - // vector + + // vector private int QuerySeqPosition; /** * Creates a new JPredFile object. * + * BH allows File or String + * * @param inFile - * DOCUMENT ME! - * @param type - * DOCUMENT ME! + * DOCUMENT ME! + * @param sourceType + * DOCUMENT ME! * * @throws IOException - * DOCUMENT ME! + * DOCUMENT ME! */ - public JPredFile(String inFile, String type) throws IOException + public JPredFile(Object inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } public JPredFile(FileParse source) throws IOException @@ -81,7 +95,7 @@ public class JPredFile extends AlignFile * DOCUMENT ME! * * @param QuerySeqPosition - * DOCUMENT ME! + * DOCUMENT ME! */ public void setQuerySeqPosition(int QuerySeqPosition) { @@ -121,6 +135,7 @@ public class JPredFile extends AlignFile /** * DOCUMENT ME! */ + @Override public void initData() { super.initData(); @@ -132,6 +147,7 @@ public class JPredFile extends AlignFile /** * parse a JPred concise file into a sequence-alignment like object. */ + @Override public void parse() throws IOException { // JBPNote log.System.out.println("all read in "); @@ -195,8 +211,8 @@ public class JPredFile extends AlignFile { ascore = symbols.nextToken(); - Float score = new Float(ascore); - scores.addElement((Object) score); + Float score = Float.valueOf(ascore); + scores.addElement(score); } Scores.put(id, scores); @@ -207,16 +223,16 @@ public class JPredFile extends AlignFile for (int j = 0; j < i; j++) { - scores.setElementAt((Object) ((Float) scores.elementAt(j)) - .toString(), j); + scores.setElementAt(((Float) scores.elementAt(j)).toString(), + j); } - scores.addElement((Object) ascore); + scores.addElement(ascore); while (symbols.hasMoreTokens()) { ascore = symbols.nextToken(); - scores.addElement((Object) ascore); + scores.addElement(ascore); } Scores.put(id, scores); @@ -256,7 +272,9 @@ public class JPredFile extends AlignFile } if (QuerySeqPosition == -1) + { QuerySeqPosition = ids.size(); + } ids.addElement(name); noSeqs++; } @@ -269,7 +287,7 @@ public class JPredFile extends AlignFile seq_entries.addElement(newseq.toString()); ids.addElement(id); - Symscores.put((Object) id, (Object) new Integer(ids.size() - 1)); + Symscores.put(id, Integer.valueOf(ids.size() - 1)); } } } @@ -285,18 +303,19 @@ public class JPredFile extends AlignFile { // 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()); + 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"); + 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;")) + if ((newSeq.getName().startsWith("QUERY") + || newSeq.getName().startsWith("align;")) && (QuerySeqPosition == -1)) { QuerySeqPosition = seqs.size(); @@ -304,10 +323,11 @@ public class JPredFile extends AlignFile seqs.addElement(newSeq); } - if (seqs.size() > 0 && QuerySeqPosition>-1) + if (seqs.size() > 0 && QuerySeqPosition > -1) { // 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 is given and prediction contains a QUERY or align;sequence_id + // line) Alignment tal = new Alignment(this.getSeqsAsArray()); try { @@ -316,10 +336,12 @@ public class JPredFile extends AlignFile } catch (Exception e) { tal = null; - IOException ex = new IOException( - "Couldn't parse concise annotation for prediction profile.\n" - + e); - e.printStackTrace(); // java 1.1 does not have : ex.setStackTrace(e.getStackTrace()); + 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(); @@ -336,28 +358,28 @@ public class JPredFile extends AlignFile * * @return String */ - public String print() + @Override + public String print(SequenceI[] sqs, boolean jvsuffix) { return "Not Supported"; } /** - * DOCUMENT ME! * * @param args - * DOCUMENT ME! + * @j2sIgnore */ public static void main(String[] args) { try { - JPredFile blc = new JPredFile(args[0], "File"); + JPredFile jpred = new JPredFile(args[0], DataSourceType.FILE); - for (int i = 0; i < blc.seqs.size(); i++) + for (int i = 0; i < jpred.seqs.size(); i++) { - System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() + System.out.println(((Sequence) jpred.seqs.elementAt(i)).getName() + "\n" - + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString() + + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString() + "\n"); } } catch (java.io.IOException e) @@ -388,8 +410,8 @@ public class JPredFile extends AlignFile } // check that no stray annotations have been added at the end. { - SequenceI sq = (SequenceI) seqs.elementAt(j - 1); - if (sq.getName().toUpperCase().startsWith("JPRED")) + SequenceI sq = seqs.elementAt(j - 1); + if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED")) { annotSeqs.addElement(sq); seqs.removeElementAt(--j); @@ -408,8 +430,8 @@ public class JPredFile extends AlignFile /* * 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("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) + " "); @@ -420,12 +442,11 @@ public class JPredFile extends AlignFile * * 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); + * 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); } } - * } + * System.out.println("Exception " + e); } } } */