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

   1 package fr.orsay.lri.varna.applications.fragseq;
   2
   3 import java.awt.Color;
   4 import java.awt.datatransfer.DataFlavor;
   5 import java.util.Hashtable;
   6 import java.util.Random;
   7
   8 import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
   9 import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType;
  10 import fr.orsay.lri.varna.models.rna.ModeleBase;
  11 import fr.orsay.lri.varna.models.rna.RNA;
  12
  13 public class FragSeqAnnotationDataModel extends FragSeqModel {
  14   private String _id;
  15   private String _name;
  16   private Hashtable<Integer, ChemProbModel> _values = new Hashtable<Integer, ChemProbModel>();
  17
  18
  19   public FragSeqAnnotationDataModel(String id, String name)
  20   {
  21         _id = id;
  22         _name = name;
  23   }
  24
  25   public FragSeqAnnotationDataModel()
  26   {
  27         this(Long.toHexString(Double.doubleToLongBits(Math.random())),Long.toHexString(Double.doubleToLongBits(Math.random())));
  28   }
  29
  30   public void addValue(ChemProbModel cpm)
  31   {
  32           _values.put(cpm._baseNumber1,cpm);
  33   }
  34
  35   static Random _rnd = new Random();
  36
  37   public static void addRandomAnnotations(RNA r,FragSeqAnnotationDataModel data){
  38           int nb = r.getSize()/5+_rnd.nextInt(r.getSize()/3);
  39           Color[] colors = {Color.orange,Color.black,Color.blue.darker(),Color.green.darker(), Color.gray};
  40           ChemProbAnnotationType[] types  = ChemProbAnnotationType.values();
  41           for(int i=0;i<nb;i++)
  42           {
  43                   int index = _rnd.nextInt(r.getSize()-1);
  44                   int number1 = r.getBaseNumber(index);
  45                   int number2 = r.getBaseNumber(index+1);
  46                   ChemProbModel cpm = data.new ChemProbModel(number1,number2,colors[_rnd.nextInt(colors.length)],2*_rnd.nextDouble(),types[_rnd.nextInt(types.length)],true);
  47                   data.addValue(cpm);
  48           }
  49   }
  50
  51
  52   public String toString()
  53   {
  54           return _name;
  55   }
  56
  57   public String getID()
  58   {
  59           return _id;
  60   }
  61
  62   public void applyTo(RNA r)
  63   {
  64         r.clearChemProbAnnotations();
  65         for (ChemProbModel c : _values.values())
  66         {
  67                 c.applyTo(r);
  68         }
  69   }
  70
  71
  72   public class ChemProbModel
  73   {
  74                 private Color _color;
  75                 private double _intensity;
  76                 private ChemProbAnnotationType _type;
  77                 private boolean _out;
  78                 private int _baseNumber1;
  79                 private int _baseNumber2;
  80
  81                 public ChemProbModel (int baseNumber1,int baseNumber2, Color color, double intensity, ChemProbAnnotationType type, boolean out)
  82                 {
  83                         _color= color;
  84                         _intensity = intensity;
  85                         _type= type;
  86                         _out= out;
  87                         _baseNumber1 = baseNumber1;
  88                         _baseNumber2 = baseNumber2;
  89                 }
  90
  91                 public void applyTo(RNA r)
  92                 {
  93                         System.out.println(this);
  94                         int i = r.getIndexFromBaseNumber(_baseNumber1);
  95                         int j = r.getIndexFromBaseNumber(_baseNumber2);
  96                         if (i!=-1 && j!=-1)
  97                         {
  98                                 ModeleBase mb1 = r.getBaseAt(i);
  99                                 ModeleBase mb2 = r.getBaseAt(j);
 100                                 r.addChemProbAnnotation(new ChemProbAnnotation(mb1, mb2, _type, _intensity,_color, _out));
 101                         }
 102                 }
 103
 104                 public String toString()
 105                 {
 106                         return ""+_baseNumber1+": col="+_color+" int="+_intensity+" type="+_type+" out="+_out;
 107                 }
 108   }
 109
 110   public static DataFlavor Flavor = new DataFlavor(FragSeqAnnotationDataModel.class, "RNA Chem Prob Data");
 111
 112 }