JAL-3032 adds Java 8 functionality (2/2)

[jalview.git] / src2 / fr / orsay / lri / varna / applications / fragseq / FragSeqAnnotationDataModel.java

diff --git a/src2/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java b/src2/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java
new file mode 100644 (file)
index 0000000..15c0522
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java
@@ -0,0 +1,112 @@
+package fr.orsay.lri.varna.applications.fragseq;
+
+import java.awt.Color;
+import java.awt.datatransfer.DataFlavor;
+import java.util.Hashtable;
+import java.util.Random;
+
+import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
+import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class FragSeqAnnotationDataModel extends FragSeqModel {
+  private String _id;
+  private String _name;
+  private Hashtable<Integer, ChemProbModel> _values = new Hashtable<Integer, ChemProbModel>();  
+  
+  
+  public FragSeqAnnotationDataModel(String id, String name)
+  {
+       _id = id;
+       _name = name;
+  }
+
+  public FragSeqAnnotationDataModel()
+  {
+       this(Long.toHexString(Double.doubleToLongBits(Math.random())),Long.toHexString(Double.doubleToLongBits(Math.random())));
+  }
+
+  public void addValue(ChemProbModel cpm)
+  {
+         _values.put(cpm._baseNumber1,cpm);
+  }
+
+  static Random _rnd = new Random();
+  
+  public static void addRandomAnnotations(RNA r,FragSeqAnnotationDataModel data){
+         int nb = r.getSize()/5+_rnd.nextInt(r.getSize()/3);
+         Color[] colors = {Color.orange,Color.black,Color.blue.darker(),Color.green.darker(), Color.gray};
+         ChemProbAnnotationType[] types  = ChemProbAnnotationType.values();
+         for(int i=0;i<nb;i++)
+         {
+                 int index = _rnd.nextInt(r.getSize()-1);
+                 int number1 = r.getBaseNumber(index);
+                 int number2 = r.getBaseNumber(index+1);
+                 ChemProbModel cpm = data.new ChemProbModel(number1,number2,colors[_rnd.nextInt(colors.length)],2*_rnd.nextDouble(),types[_rnd.nextInt(types.length)],true);
+                 data.addValue(cpm);
+         }
+  }
+
+  
+  public String toString()
+  {
+         return _name;
+  }
+  
+  public String getID()
+  {
+         return _id;
+  }
+
+  public void applyTo(RNA r)
+  {
+       r.clearChemProbAnnotations();
+       for (ChemProbModel c : _values.values())
+       {
+               c.applyTo(r);
+       }
+  }
+
+  
+  public class ChemProbModel
+  {
+               private Color _color;
+               private double _intensity;
+               private ChemProbAnnotationType _type;
+               private boolean _out;
+               private int _baseNumber1;
+               private int _baseNumber2;
+               
+               public ChemProbModel (int baseNumber1,int baseNumber2, Color color, double intensity, ChemProbAnnotationType type, boolean out)
+               {
+                       _color= color;
+                       _intensity = intensity;
+                       _type= type;
+                       _out= out;
+                       _baseNumber1 = baseNumber1;
+                       _baseNumber2 = baseNumber2;
+               }
+
+               public void applyTo(RNA r)
+               {
+                       System.out.println(this);
+                       int i = r.getIndexFromBaseNumber(_baseNumber1);
+                       int j = r.getIndexFromBaseNumber(_baseNumber2);
+                       if (i!=-1 && j!=-1)
+                       {
+                               ModeleBase mb1 = r.getBaseAt(i);
+                               ModeleBase mb2 = r.getBaseAt(j);
+                               r.addChemProbAnnotation(new ChemProbAnnotation(mb1, mb2, _type, _intensity,_color, _out));
+                       }
+               }
+               
+               public String toString()
+               {
+                       return ""+_baseNumber1+": col="+_color+" int="+_intensity+" type="+_type+" out="+_out;
+               }
+  }
+  
+  public static DataFlavor Flavor = new DataFlavor(FragSeqAnnotationDataModel.class, "RNA Chem Prob Data");
+
+}