X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2Ffragseq%2FFragSeqAnnotationDataModel.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2Ffragseq%2FFragSeqAnnotationDataModel.java;h=15c0522f443fb0a2d1ccd14bf53e00e15644ba16;hb=65740880573a48adc758bec3939ece9d9ae104dd;hp=0000000000000000000000000000000000000000;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java b/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java
new file mode 100644
index 0000000..15c0522
--- /dev/null
+++ b/srcjar/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");
+
+}