src/jalview/io/RnamlFile.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.io;
  19
  20 import java.io.BufferedReader;
  21 import java.io.FileNotFoundException;
  22 import java.io.FileReader;
  23 import java.io.IOException;
  24 import java.util.ArrayList;
  25 import java.util.Vector;
  26 import java.util.regex.Matcher;
  27 import java.util.regex.Pattern;
  28
  29 import jalview.analysis.SecStrConsensus;
  30 import jalview.analysis.SecStrConsensus.SimpleBP;
  31 import jalview.datamodel.AlignmentAnnotation;
  32 import jalview.datamodel.Annotation;
  33 import jalview.datamodel.Sequence;
  34 import jalview.datamodel.SequenceI;
  35
  36 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  37 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  38 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  39 import fr.orsay.lri.varna.factories.RNAFactory;
  40 import fr.orsay.lri.varna.models.rna.RNA;
  41
  42 /**
  43  * @author jimp
  44  *
  45  */
  46 public class RnamlFile extends AlignFile {
  47         public int id;
  48         public String namefile;
  49         public String name;
  50         protected ArrayList<RNA> result;
  51
  52         public RnamlFile() {
  53                 super();
  54
  55         }
  56
  57         public RnamlFile(String inFile, String type) throws Exception {
  58                 super(inFile, type);
  59
  60         }
  61
  62         public RnamlFile(FileParse source) throws Exception {
  63                 super(source);
  64
  65         }
  66
  67         public BufferedReader CreateReader() throws FileNotFoundException {
  68                 FileReader fr = null;
  69                 fr = new FileReader(inFile);
  70
  71                 BufferedReader r = new BufferedReader(fr);
  72                 return r;
  73         }
  74
  75         /* (non-Javadoc)
  76          * @see jalview.io.AlignFile#parse()
  77          */
  78         public void parse() throws IOException
  79         {
  80         // rather than lose exception semantics whilst parsing RNAML with VARNA we
  81         // wrap the routine and catch all exceptions before passing them up the
  82         // chain as an IOException
  83           try {
  84             _parse();
  85           } catch (Exception x)
  86           {
  87             error=true;
  88             errormessage="Problem parsing data as RNAML ("+x.getMessage()+")";
  89             throw new IOException("Couldn't parse the datasource as RNAML",x);
  90           }
  91         }
  92         @SuppressWarnings("unchecked")
  93         public void _parse() throws FileNotFoundException,
  94                         ExceptionPermissionDenied, ExceptionLoadingFailed,
  95                         ExceptionFileFormatOrSyntax {
  96
  97                 result = RNAFactory.loadSecStrRNAML(getReader());
  98
  99                 ArrayList<ArrayList> allarray = new ArrayList();
 100                 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
 101                 ArrayList strucinarray = new ArrayList();
 102                 SequenceI[] seqs = new SequenceI[result.size()];
 103                 namefile = inFile.getName();
 104
 105                 for (int i = 0; i < result.size(); i++) {
 106
 107                         RNA current = result.get(i);
 108                         String rna = current.getStructDBN(true);
 109                         String seq = current.getSeq();
 110                         int begin = 1;
 111                         int end = 1000;
 112                         id = i;
 113                         System.out.println("id=" + i);
 114                         name = this.safeName(namefile, i);
 115                         seqs[i] = new Sequence(name, seq, begin, end);
 116
 117                         seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
 118                         String[] annot = new String[rna.length()];
 119                         Annotation[] ann = new Annotation[rna.length()];
 120
 121                         for (int j = 0; j < rna.length(); j++) {
 122                                 annot[j] = "" + rna.charAt(j);
 123
 124                         }
 125                         for (int k = 0; k < rna.length(); k++) {
 126                                 ann[k] = new Annotation(annot[k], "",
 127                                                 jalview.schemes.ResidueProperties.getRNASecStrucState(
 128                                                                 annot[k]).charAt(0), 0f);
 129                         }
 130
 131                         AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
 132                                         current.getID(), ann);
 133
 134                         seqs[i].addAlignmentAnnotation(align);
 135                         seqs[i].setRNA(result.get(i));
 136
 137                         char[] struc = align.getRNAStruc().toCharArray();
 138
 139                         allarray.add(strucinarray);
 140
 141                         this.annotations.addElement(align);
 142                         BP.add(align.bps);
 143
 144                 }
 145                 this.setSeqs(seqs);
 146                 int[] tab = SecStrConsensus.extractConsensus(BP);
 147
 148
 149         }
 150
 151         public void parse(BufferedReader r) throws ExceptionPermissionDenied,
 152                         ExceptionLoadingFailed, ExceptionFileFormatOrSyntax {
 153
 154                 result = RNAFactory.loadSecStrRNAML(r);
 155
 156                 ArrayList<ArrayList> allarray = new ArrayList();
 157                 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
 158                 ArrayList strucinarray = new ArrayList();
 159                 SequenceI[] seqs = new SequenceI[result.size()];
 160                 namefile = inFile.getName();
 161
 162                 for (int i = 0; i < result.size(); i++) {
 163
 164                         RNA current = result.get(i);
 165                         String rna = current.getStructDBN(true);
 166
 167                         String seq = current.getSeq();
 168                         int begin = 1;
 169                         int end = 1000;
 170                         id = i;
 171                         name = this.safeName(namefile, i);
 172                         seqs[i] = new Sequence(name, seq, begin, end);
 173
 174                         seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
 175                         String[] annot = new String[rna.length()];
 176                         Annotation[] ann = new Annotation[rna.length()];
 177
 178                         for (int j = 0; j < rna.length(); j++) {
 179                                 annot[j] = "" + rna.charAt(j);
 180
 181                         }
 182                         for (int k = 0; k < rna.length(); k++) {
 183                                 ann[k] = new Annotation(annot[k], "",
 184                                                 jalview.schemes.ResidueProperties.getRNASecStrucState(
 185                                                                 annot[k]).charAt(0), 0f);
 186                         }
 187
 188                         AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
 189                                         current.getID(), ann);
 190
 191                         seqs[i].addAlignmentAnnotation(align);
 192                         seqs[i].setRNA(result.get(i));
 193
 194                         char[] struc = align.getRNAStruc().toCharArray();
 195                         for (int y = 0; y < struc.length; y++) {
 196                                 strucinarray.add(struc[y]);
 197                                 // System.out.println("structy"+struc[y]);
 198                         }
 199                         // System.out.println("Sequence"+i+"\t : "+strucinarray.toString());
 200                         allarray.add(strucinarray);
 201
 202                         this.annotations.addElement(align);
 203                         System.out.println(rna);
 204                         BP.add(align.bps);
 205                         System.out.println(align.bps.size());
 206                 }
 207                 this.setSeqs(seqs);
 208                 int[] tab = SecStrConsensus.extractConsensus(BP);
 209
 210
 211         }
 212
 213
 214
 215         public static String print(SequenceI[] s) {
 216                 return "not yet implemented";
 217         }
 218
 219         public String print() {
 220                 System.out.print("print :");
 221                 return print(getSeqsAsArray());
 222         }
 223
 224         public ArrayList getRNA() {
 225                 return result;
 226         }
 227
 228         public Vector getAnnot() {
 229                 return annotations;
 230         }
 231
 232         // public static void main(String[] args) {
 233         // Pattern p= Pattern.compile("(.+)[.][^.]+");
 234         // Matcher m = p.matcher("toto.xml.zip");
 235         // System.out.println(m.matches());
 236         // System.out.println(m.group(1));
 237         // }
 238         public String safeName(String namefile, int id) {
 239
 240                 Pattern p = Pattern.compile("(.*)[.][^.]+");
 241                 Matcher m = p.matcher(namefile);
 242                 name = m.group(1) + "_" + id;
 243
 244                 return name;
 245
 246         }
 247
 248 }