src/jalview/io/RnamlFile.java

   1 package jalview.io;
   2
   3
   4
   5
   6
   7 import jalview.datamodel.AlignmentAnnotation;
   8 import jalview.datamodel.Annotation;
   9 import jalview.datamodel.SecondaryStructureAnnotation;
  10 import jalview.datamodel.Sequence;
  11 import jalview.datamodel.SequenceFeature;
  12 import jalview.datamodel.SequenceI;
  13
  14 import java.io.BufferedReader;
  15 import java.io.FileNotFoundException;
  16 import java.io.IOException;
  17 import java.io.Reader;
  18 import java.io.FileReader;
  19 import java.lang.reflect.Array;
  20 import java.util.ArrayList;
  21 import java.util.Collections;
  22 import java.util.Hashtable;
  23 import java.util.List;
  24 import java.util.Vector;
  25
  26 import javax.xml.parsers.ParserConfigurationException;
  27 import javax.xml.parsers.SAXParser;
  28 import javax.xml.parsers.SAXParserFactory;
  29
  30 import org.xml.sax.InputSource;
  31 import org.xml.sax.SAXException;
  32
  33 import com.stevesoft.pat.Regex;
  34
  35 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  36 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  37 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  38 import fr.orsay.lri.varna.factories.RNAFactory;
  39 import fr.orsay.lri.varna.models.rna.RNA;
  40 import fr.orsay.lri.varna.utils.RNAMLParser;
  41
  42
  43
  44
  45 public class RnamlFile extends AlignFile
  46 {
  47          public String id;
  48
  49          public RnamlFile()
  50           {
  51                  super();
  52
  53           }
  54
  55          public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
  56           {
  57             super(inFile, type);
  58
  59           }
  60
  61           public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
  62           {
  63             super(source);
  64
  65           }
  66
  67
  68
  69
  70           public void parse() throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax, FileNotFoundException
  71           {
  72                   System.out.println("this is a rnaml file");
  73
  74
  75                   FileReader fr = null;
  76                   fr = new FileReader(inFile);
  77
  78                   BufferedReader r = new BufferedReader (fr);
  79
  80                   Hashtable seqhash = new Hashtable();
  81                   Vector headers = new Vector();
  82                   //ArrayList<String> seq =new ArrayList();
  83                   System.out.println(r);
  84                   ArrayList<RNA> result = RNAFactory.loadSecStrRNAML(r);
  85
  86                   System.out.println("this is the secondary scructure:" +result.toArray());
  87                   System.out.println("this is the secondary scructure:" +result.toString());
  88                   System.out.println("this is the secondary scructure:" +result.size());
  89                         for(int i=0;i<result.size();i++)
  90                         {
  91                   System.out.println(result.get(0).getSeq());
  92                   System.out.println(result.get(0).getStructBPSEQ());
  93                   System.out.println(result.get(0).getStructDBN(true));
  94                   String rna1 =result.get(0).getStructDBN(true);
  95                   System.out.println(result.get(0).getAnnotations());
  96                   String seq = result.get(0).getSeq();
  97                   System.out.println(type); //the type is "File"
  98                   System.out.println(inFile );//inFile is the path
  99                   int begin=0;
 100                   int end = seq.length()-1;
 101                   SequenceI[] seqs = new SequenceI[1];
 102                   id = safeName(getDataName());
 103                   seqs[0] = new Sequence(id, seq, begin, end);
 104                   SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 105                   seqs[0].addSequenceFeature(feat);
 106                   this.setSeqs(seqs);
 107
 108                   String[] annot=new String[10000] ;
 109                   Annotation[] ann = new Annotation[1000];
 110                   for(int j=0;j<rna1.length();j++)
 111                         {
 112                   annot[j] =rna1.substring(j,j+1);
 113                   System.out.println(annot[j]);
 114                         }
 115
 116                   for(int k=0;k<rna1.length();k++)
 117                 {
 118                           ann[k] = new Annotation(annot[k], "", ' ', 0f);
 119
 120                           ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
 121
 122                 }
 123                   AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
 124                   seqs[0].addAlignmentAnnotation(align);
 125                   this.annotations.addElement(align);
 126                 }
 127
 128
 129
 130
 131
 132
 133
 134
 135
 136
 137 //                                      for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
 138 //                                      {
 139 //                                              // Retrieving parsed data
 140 //                                              seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
 141 //                                              System.out.println(seq);
 142 //                                              String seqAsStr = "";
 143 //                                              for(String s:seq)
 144 //                                              {
 145 //                                                      // Only consider last character, e.g. in case of modified nucleotide
 146 //                                                      seqAsStr += s.charAt(s.length()-1);
 147 //                                              }
 148 //                                              int begin=0;
 149 //                                              int end = seqAsStr.length()-1;
 150 //                                              SequenceI[] seqs = new SequenceI[1];
 151 //                                              id = safeName(getDataName());
 152 //                                              seqs[0] = new Sequence(id, seqAsStr, begin, end);
 153 //                                              SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 154 //
 155 //                          seqs[0].addSequenceFeature(feat);
 156 //                                              this.setSeqs(seqs);
 157
 158                                                 //String pos = annot.substring(1, 2);
 159                                                 //System.out.println(annot);
 160                                                 //System.out.println(pos);
 161
 162                                            // ann[1] = new Annotation(pos, "", ' ', 0f);
 163                                            // ann[1].secondaryStructure = 'A';
 164                                             //System.out.println(ann[1]);
 165
 166                                            // toto.annotations=ann;
 167
 168
 169
 170 ////                                             Annotation[] els = new Annotation[seq.size()];
 171 //
 172 //                                              //System.err.println(""+seq.size());
 173 //                                          Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
 174 //                                          String[] annot = new String[10000];
 175 //
 176 //                                              //Annotation[] ann = new Annotation[allbpsTmp.size()];
 177 //                                              for (int i = 0; i < allbpsTmp.size(); i++) {
 178 //                                              RNAMLParser.BPTemp bp = allbpsTmp.get(i);
 179 //                                              //System.err.println("toto ="+bp);
 180 //                                              int bp5 = bp.pos5;
 181 //                                              annot[bp5]= "(";
 182 //                                              //annot[bp5]= '(';
 183 //                                              System.out.println(annot[bp5]);
 184 //                                              //System.out.println("bp5 ="+bp5);
 185 //                                              int bp3 = bp.pos3;
 186 //
 187 //                                              annot[bp3]= ")";
 188 //                                              System.out.println(annot[bp3]);
 189 //                                              //System.out.println(annot.get(bp3));
 190 //
 191 //                                              //String pos1 = annot.substring(bp5, bp5+1);
 192 //                                              //String pos2 = annot.substring(bp3, bp3+1);
 193 //                                              //ann[i] = new Annotation(pos1, "", ' ', 0f);
 194 //                                              //ann[i+1] = new Annotation(pos2, "", ' ', 0f);
 195 //                                              //System.out.println(pos1);
 196 //
 197 //                                              //System.out.println("bp3 ="+bp3);
 198 //                                              //ModeleBP newStyle = bp.createBPStyle(mb, part);
 199 //                                              }
 200 //                                              Annotation[] ann = new Annotation[annot.length+1];
 201 //                                              for(int i=0;i<annot.length;i++)
 202 //                                              {
 203 //                                                      if(annot[i]==null)
 204 //                                                      {
 205 //                                                              annot[i]=".";
 206 //                                                      }
 207 //
 208 //                                                      ann[i] = new Annotation(annot[i], "", ' ', 0f);
 209 //                                              //System.out.print(annot[i]);
 210 //                                              }
 211 //
 212 //                                              AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
 213 //                                              this.annotations.addElement(toto);
 214
 215                                                 // Creating empty structure of suitable size
 216 //                                              int[] str = new int[seq.size()];
 217 //                                              for (int i=0;i<str.length;i++)
 218 //                                              { str[i] = -1; }
 219 //                                              Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
 220 //                                              for (int i = 0; i < allbpsTmp.size(); i++) {
 221 //                                                      RNAMLParser.BPTemp bp = allbpsTmp.get(i);
 222 //                                                      //System.err.println("toto ="+bp);
 223 //                                                      int bp5 = bp.pos5;
 224 //                                                      //System.out.println("bp5 ="+bp5);
 225 //                                                      int bp3 = bp.pos3;
 226                                                         //System.out.println("bp3 ="+bp3);
 227                                                         //ModeleBP newStyle = bp.createBPStyle(mb, part);
 228 //                                              }
 229                                                 //Annotation ann;
 230                                             //ann = new Annotation(bp5, "", ' ', 0f);
 231
 232                                         //}
 233
 234
 235
 236 //                              return result;
 237
 238 }
 239
 240
 241           public static String print(SequenceI[] s)
 242           {
 243             return "not yet implemented";
 244           }
 245
 246           public String print()
 247           {
 248                 System.out.print("affiche :");
 249             return print(getSeqsAsArray());
 250           }
 251
 252           /**
 253            * make a friendly ID string.
 254            *
 255            * @param dataName
 256            * @return truncated dataName to after last '/'
 257            */
 258           private String safeName(String dataName)
 259           {
 260             int b = 0;
 261             while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )
 262             {
 263                 dataName = dataName.substring(b + 1).trim();
 264
 265             }
 266             int e = (dataName.length() - dataName.indexOf("."))+1;
 267             dataName = dataName.substring(1,e).trim();
 268             return dataName;
 269           }
 270
 271 }
 272