srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java

   1 package fr.orsay.lri.varna.applications.fragseq;
   2
   3 import java.awt.datatransfer.DataFlavor;
   4 import java.io.File;
   5 import java.io.FileNotFoundException;
   6 import java.util.ArrayList;
   7 import java.util.Collection;
   8 import java.util.Date;
   9 import java.util.Random;
  10 import java.util.regex.Pattern;
  11
  12 import javax.swing.tree.DefaultMutableTreeNode;
  13
  14 import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
  15 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  16 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  17 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  18 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  19 import fr.orsay.lri.varna.factories.RNAFactory;
  20 import fr.orsay.lri.varna.models.rna.RNA;
  21
  22 public class FragSeqFileModel implements Comparable<FragSeqFileModel> {
  23         private ArrayList<FragSeqModel> _models = new ArrayList<FragSeqModel>();
  24           protected Date _lastModified;
  25           protected boolean _outOfSync = false;
  26           protected String _caption = "";
  27           protected String _path = "";
  28           protected String _folder = "";
  29           protected boolean _cached = false;
  30
  31
  32           public static Date lastModif(String path)
  33           {
  34                  return new Date(new File(path).lastModified()) ;
  35           }
  36
  37           public FragSeqFileModel(String folder, String path)
  38           {
  39                 this(folder,path,lastModif(path));
  40           }
  41
  42
  43           private static Random _rnd = new Random();
  44
  45           public FragSeqFileModel(String folder, String path,Date lastModified)
  46           {
  47                   _lastModified = lastModified;
  48                   _outOfSync = false;
  49                   _folder =folder;
  50                   _path = path;
  51                   String[] s = path.split(Pattern.quote(File.separator));
  52                   if (s.length>0)
  53                     _caption = s[s.length-1];
  54           }
  55
  56           public void load()
  57           {
  58                   ArrayList<RNA> rnas = null;
  59                   try {
  60                           rnas = createRNAs();
  61                         for (RNA r: rnas)
  62                         {
  63                                 this.addModel(new FragSeqRNASecStrModel(r));
  64                                   int nb =_rnd.nextInt(5);
  65                                   for(int i=0;i<nb;i++)
  66                                   {
  67                                           FragSeqAnnotationDataModel data = new FragSeqAnnotationDataModel(r.getID(),""+i+"-"+r.getID());
  68                                           FragSeqAnnotationDataModel.addRandomAnnotations(r,data);
  69                                           addModel(data);
  70                                   }
  71                         }
  72                 } catch (ExceptionUnmatchedClosingParentheses e) {
  73                         // TODO Auto-generated catch block
  74                         e.printStackTrace();
  75                 } catch (FileNotFoundException e) {
  76                         // TODO Auto-generated catch block
  77                         e.printStackTrace();
  78                 } catch (ExceptionFileFormatOrSyntax e) {
  79                         // TODO Auto-generated catch block
  80                         e.printStackTrace();
  81                 } catch (ExceptionExportFailed e) {
  82                         // TODO Auto-generated catch block
  83                         e.printStackTrace();
  84                 } catch (ExceptionPermissionDenied e) {
  85                         // TODO Auto-generated catch block
  86                         e.printStackTrace();
  87                 } catch (ExceptionLoadingFailed e) {
  88                         // TODO Auto-generated catch block
  89                         e.printStackTrace();
  90                 }
  91                   _cached = true;
  92           }
  93
  94           public boolean hasChanged()
  95           {
  96                   return _outOfSync;
  97           }
  98
  99           public boolean checkForModifications()
 100           {
 101                 if (!lastModif(_path).equals(_lastModified) && !_outOfSync)
 102                 {
 103                         _outOfSync = true;
 104                           return true;
 105                 }
 106                 return false;
 107           }
 108
 109
 110           public String toString()
 111           {
 112                   return _caption + (this._outOfSync?"*":"");
 113           }
 114
 115
 116           public String getCaption()
 117           {
 118                   return _caption;
 119           }
 120
 121           public String getFolder()
 122           {
 123                   return _folder;
 124           }
 125
 126           public String getPath()
 127           {
 128                   return _path;
 129           }
 130
 131
 132         public int compareTo(FragSeqFileModel o) {
 133                 return _caption.compareTo(o._caption);
 134         }
 135
 136         public ArrayList<FragSeqModel> getModels()
 137         {
 138                 if (!_cached)
 139                 {  load();  }
 140                 return _models;
 141         }
 142         public void addModel(FragSeqModel f)
 143         {
 144                 _models.add(f);
 145         }
 146
 147
 148         private ArrayList<RNA> createRNAs() throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed
 149           {
 150                   Collection<RNA> r = RNAFactory.loadSecStr(_path);
 151                   for (RNA r2 : r)
 152                   {
 153                           r2.drawRNARadiate();
 154                   }
 155                   return new ArrayList<RNA>(r);
 156           }
 157
 158 }