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.util.ArrayList;
  24 import java.util.Vector;
  25 import java.util.regex.Matcher;
  26 import java.util.regex.Pattern;
  27
  28 import jalview.analysis.SecStrConsensus;
  29 import jalview.analysis.SecStrConsensus.SimpleBP;
  30 import jalview.datamodel.AlignmentAnnotation;
  31 import jalview.datamodel.Annotation;
  32 import jalview.datamodel.SecondaryStructureAnnotation;
  33 import jalview.datamodel.Sequence;
  34 import jalview.datamodel.SequenceFeature;
  35 import jalview.datamodel.SequenceI;
  36
  37 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  38 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  39 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  40 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  41 import fr.orsay.lri.varna.factories.RNAFactory;
  42 import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
  43 import fr.orsay.lri.varna.models.rna.RNA;
  44 import fr.orsay.lri.varna.utils.RNAMLParser;
  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         @SuppressWarnings("unchecked")
  76         public void parse() throws FileNotFoundException,
  77                         ExceptionPermissionDenied, ExceptionLoadingFailed,
  78                         ExceptionFileFormatOrSyntax {
  79
  80                 result = RNAFactory.loadSecStrRNAML(getReader());
  81
  82                 ArrayList<ArrayList> allarray = new ArrayList();
  83                 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
  84                 ArrayList strucinarray = new ArrayList();
  85                 SequenceI[] seqs = new SequenceI[result.size()];
  86                 namefile = inFile.getName();
  87
  88                 for (int i = 0; i < result.size(); i++) {
  89
  90                         RNA current = result.get(i);
  91                         String rna = current.getStructDBN(true);
  92                         String seq = current.getSeq();
  93                         int begin = 1;
  94                         int end = 1000;
  95                         id = i;
  96                         System.out.println("id=" + i);
  97                         name = this.safeName(namefile, i);
  98                         seqs[i] = new Sequence(name, seq, begin, end);
  99
 100                         seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
 101                         String[] annot = new String[rna.length()];
 102                         Annotation[] ann = new Annotation[rna.length()];
 103
 104                         for (int j = 0; j < rna.length(); j++) {
 105                                 annot[j] = "" + rna.charAt(j);
 106
 107                         }
 108                         for (int k = 0; k < rna.length(); k++) {
 109                                 ann[k] = new Annotation(annot[k], "",
 110                                                 jalview.schemes.ResidueProperties.getRNASecStrucState(
 111                                                                 annot[k]).charAt(0), 0f);
 112                         }
 113
 114                         AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
 115                                         current.getID(), ann);
 116
 117                         seqs[i].addAlignmentAnnotation(align);
 118                         seqs[i].setRNA(result.get(i));
 119
 120                         char[] struc = align.getRNAStruc().toCharArray();
 121
 122                         allarray.add(strucinarray);
 123
 124                         this.annotations.addElement(align);
 125                         BP.add(align.bps);
 126
 127                 }
 128                 this.setSeqs(seqs);
 129                 int[] tab = SecStrConsensus.extractConsensus(BP);
 130
 131
 132         }
 133
 134         public void parse(BufferedReader r) throws ExceptionPermissionDenied,
 135                         ExceptionLoadingFailed, ExceptionFileFormatOrSyntax {
 136
 137                 result = RNAFactory.loadSecStrRNAML(r);
 138
 139                 ArrayList<ArrayList> allarray = new ArrayList();
 140                 ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
 141                 ArrayList strucinarray = new ArrayList();
 142                 SequenceI[] seqs = new SequenceI[result.size()];
 143                 namefile = inFile.getName();
 144
 145                 for (int i = 0; i < result.size(); i++) {
 146
 147                         RNA current = result.get(i);
 148                         String rna = current.getStructDBN(true);
 149
 150                         String seq = current.getSeq();
 151                         int begin = 1;
 152                         int end = 1000;
 153                         id = i;
 154                         name = this.safeName(namefile, i);
 155                         seqs[i] = new Sequence(name, seq, begin, end);
 156
 157                         seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
 158                         String[] annot = new String[rna.length()];
 159                         Annotation[] ann = new Annotation[rna.length()];
 160
 161                         for (int j = 0; j < rna.length(); j++) {
 162                                 annot[j] = "" + rna.charAt(j);
 163
 164                         }
 165                         for (int k = 0; k < rna.length(); k++) {
 166                                 ann[k] = new Annotation(annot[k], "",
 167                                                 jalview.schemes.ResidueProperties.getRNASecStrucState(
 168                                                                 annot[k]).charAt(0), 0f);
 169                         }
 170
 171                         AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
 172                                         current.getID(), ann);
 173
 174                         seqs[i].addAlignmentAnnotation(align);
 175                         seqs[i].setRNA(result.get(i));
 176
 177                         char[] struc = align.getRNAStruc().toCharArray();
 178                         for (int y = 0; y < struc.length; y++) {
 179                                 strucinarray.add(struc[y]);
 180                                 // System.out.println("structy"+struc[y]);
 181                         }
 182                         // System.out.println("Sequence"+i+"\t : "+strucinarray.toString());
 183                         allarray.add(strucinarray);
 184
 185                         this.annotations.addElement(align);
 186                         System.out.println(rna);
 187                         BP.add(align.bps);
 188                         System.out.println(align.bps.size());
 189                 }
 190                 this.setSeqs(seqs);
 191                 int[] tab = SecStrConsensus.extractConsensus(BP);
 192
 193
 194         }
 195
 196
 197
 198         public static String print(SequenceI[] s) {
 199                 return "not yet implemented";
 200         }
 201
 202         public String print() {
 203                 System.out.print("print :");
 204                 return print(getSeqsAsArray());
 205         }
 206
 207         public ArrayList getRNA() {
 208                 return result;
 209         }
 210
 211         public Vector getAnnot() {
 212                 return annotations;
 213         }
 214
 215         // public static void main(String[] args) {
 216         // Pattern p= Pattern.compile("(.+)[.][^.]+");
 217         // Matcher m = p.matcher("toto.xml.zip");
 218         // System.out.println(m.matches());
 219         // System.out.println(m.group(1));
 220         // }
 221         public String safeName(String namefile, int id) {
 222
 223                 Pattern p = Pattern.compile("(.*)[.][^.]+");
 224                 Matcher m = p.matcher(namefile);
 225                 name = m.group(1) + "_" + id;
 226
 227                 return name;
 228
 229         }
 230
 231 }