X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FModeleColorMap.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FModeleColorMap.java;h=9570ad4448bb1309fa50ac97aa5f9f0e1a877f90;hb=665d2c2f4c1310e6985b93b7c2c8a8eec2fa9086;hp=0000000000000000000000000000000000000000;hpb=0e684f72690bd6532272a39ab6c188a27559fd09;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/models/rna/ModeleColorMap.java b/src2/fr/orsay/lri/varna/models/rna/ModeleColorMap.java
new file mode 100644
index 0000000..9570ad4
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/models/rna/ModeleColorMap.java
@@ -0,0 +1,357 @@
+package fr.orsay.lri.varna.models.rna;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.StreamTokenizer;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Formatter;
+import java.util.Vector;
+
+public class ModeleColorMap implements Cloneable, Serializable{
+  /**
+	 * 
+	 */
+	private static final long serialVersionUID = 4055062096061553106L;
+private Vector<Color> _map;
+  private Vector<Double> _values;
+  
+  public static final Color DEFAULT_COLOR = Color.GREEN; 
+  
+  public enum NamedColorMapTypes {
+	  RED ("red",ModeleColorMap.redColorMap()),
+	  BLUE ("blue",ModeleColorMap.blueColorMap()),
+	  GREEN ("green",ModeleColorMap.greenColorMap()),
+	  HEAT ("heat",ModeleColorMap.heatColorMap()),
+	  ENERGY ("energy",ModeleColorMap.energyColorMap()),
+	  ROCKNROLL ("rocknroll",ModeleColorMap.rockNRollColorMap()),
+	  VIENNA ("vienna",ModeleColorMap.viennaColorMap()),
+	  BW ("bw",ModeleColorMap.bwColorMap());
+	  
+	  String _id;
+	  ModeleColorMap _cm;
+	  
+	  private NamedColorMapTypes(String id, ModeleColorMap cm)
+	  {
+		_id = id;
+		_cm = cm;
+	  }
+	  
+	  public String getId()
+	  {
+		  return _id;
+	  }
+	  public ModeleColorMap getColorMap()
+	  {
+		  return _cm;
+	  }
+	  public String toString()
+	  {
+		return _id; 
+	  }
+  }
+  
+  
+  public ModeleColorMap()
+  {
+    this(new Vector<Color>(),new Vector<Double>());
+  }
+
+  
+  public ModeleColorMap(Vector<Color> map,
+		  Vector<Double> values)
+  {
+	  _map = map;
+	  _values = values;
+  }
+  
+  public void addColor(double val, Color col)
+  {
+	  int offset = Arrays.binarySearch(_values.toArray(), val) ;
+	  if (offset<0)
+	  {
+		  int inspoint = (-offset)-1;
+		  _map.insertElementAt(col, inspoint);		  
+		  _values.insertElementAt(val,inspoint);		  
+	  }
+  }
+
+  public double getMinValue()
+  {
+	  if (_values.size()>0)
+	    return _values.get(0);
+	  return 0.0;
+  }
+ 
+  public double getMaxValue()
+  {
+	  if (_values.size()>0)
+	    return _values.get(_values.size()-1);
+	  return 0.0;
+  }
+ 
+  
+  public Color getMinColor()
+  {
+	  if (_map.size()>0)
+	    return _map.get(0);
+	  return DEFAULT_COLOR;
+  }
+
+  public Color getMaxColor()
+  {
+	  if (_map.size()>0)
+	    return _map.get(_map.size()-1);
+	  return DEFAULT_COLOR;
+  }
+ 
+
+  public int getNumColors()
+  {
+	  return (_map.size());
+  }
+ 
+  public Color getColorAt(int i)
+  {
+	  return (_map.get(i));
+  }
+
+  public Double getValueAt(int i)
+  {
+	  return (_values.get(i));
+  }
+  
+  public Color getColorForValue(double val)
+  {
+	  Color result; 
+	  if (val<=getMinValue())
+	  {	  result = getMinColor(); }
+	  else if (val>=getMaxValue())
+	  {
+		  result = getMaxColor();
+	  }
+	  else
+	  {
+	  int offset = Arrays.binarySearch(_values.toArray(), val) ;
+	  if (offset>=0)
+	  {
+		  result =  _map.get(offset);
+	  }
+	  else
+	  {
+		  int inspoint = (-offset)-1;
+		  Color c1 = _map.get(inspoint);
+		  double v1 = _values.get(inspoint);
+		  if (inspoint>0)
+		  {
+			  Color c2 = _map.get(inspoint-1);
+			  double v2 = _values.get(inspoint-1);
+			  double blendCoeff = (v2-val)/(v2-v1);
+			  result =  new Color((int)(blendCoeff*c1.getRed()+(1.0-blendCoeff)*c2.getRed()),
+				  (int)(blendCoeff*c1.getGreen()+(1.0-blendCoeff)*c2.getGreen()),
+				  (int)(blendCoeff*c1.getBlue()+(1.0-blendCoeff)*c2.getBlue()));
+			 
+		  }
+		  else
+		  {
+			result = c1;  
+		  }
+	  }
+	  }
+	  return result;
+  }
+  
+  public static ModeleColorMap energyColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(1.0,new Color(128,50,50).brighter());
+	  cm.addColor(0.9,new Color(255,50,50).brighter());
+	  cm.addColor(0.65,new Color(255,255,50).brighter());
+	  cm.addColor(0.55,new Color(20,255,50).brighter());
+	  cm.addColor(0.2,new Color(50,50,255).brighter());
+	  cm.addColor(0.0,new Color(50,50,128).brighter());
+	  return cm;
+  }
+  
+  public static ModeleColorMap viennaColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,new Color(0,80,220));
+	  cm.addColor(0.1,new Color(0,139,220));
+	  cm.addColor(0.2,new Color(0,220,218));
+	  cm.addColor(0.3,new Color(0,220,123));
+	  cm.addColor(0.4,new Color(0,220,49));
+	  cm.addColor(0.5,new Color(34,220,0));
+	  cm.addColor(0.6,new Color(109,220,0));
+	  cm.addColor(0.7,new Color(199,220,0));
+	  cm.addColor(0.8,new Color(220,165,0));
+	  cm.addColor(0.9,new Color(220,86,0));
+	  cm.addColor(1.0,new Color(220,0,0));
+	  return cm;
+  }
+  
+  public static ModeleColorMap bwColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,Color.white);
+	  cm.addColor(1.0,Color.gray.darker());
+	  return cm;
+  }
+
+  public static ModeleColorMap greenColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,Color.gray.brighter().brighter());
+	  cm.addColor(1.0,Color.green.darker());
+	  return cm;
+  }
+  
+  public static ModeleColorMap blueColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,Color.gray.brighter().brighter());
+	  cm.addColor(1.0,Color.blue);
+	  return cm;
+  }
+  
+  public static ModeleColorMap redColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,Color.gray.brighter().brighter());
+	  cm.addColor(1.0,Color.red);
+	  return cm;
+  }
+
+  public static ModeleColorMap heatColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,Color.yellow);
+	  cm.addColor(1.0,Color.red);
+	  return cm;
+  }
+  
+  public static ModeleColorMap rockNRollColorMap()
+  {
+	  ModeleColorMap cm = new ModeleColorMap();
+	  cm.addColor(0.0,Color.red.brighter());
+	  cm.addColor(1.0,Color.black);
+	  cm.addColor(2.0,Color.green.brighter());
+	  return cm;	  
+  }
+
+  
+  public static ModeleColorMap defaultColorMap()
+  {
+	  return energyColorMap();
+  }
+  
+  public static ModeleColorMap parseColorMap(String s)
+  {
+	  String[] data = s.split("[;,]");
+	  if (data.length==1)
+	  {
+		  String name = data[0].toLowerCase();
+		  for (NamedColorMapTypes p : NamedColorMapTypes.values())
+		  {
+			  if (name.equals(p.getId().toLowerCase()))
+			  {
+				  return p.getColorMap();
+			  }
+		  }
+		  return ModeleColorMap.defaultColorMap();
+	  }
+	  else
+	  {
+		  ModeleColorMap cm = new ModeleColorMap();
+		  
+		  for(int i=0;i<data.length;i++)
+		  {
+			  String[] data2 = data[i].split(":");
+			  if (data2.length==2)
+			  {
+				  try{
+					  Double val = Double.parseDouble(data2[0]);
+					  Color col = Color.decode(data2[1]);
+					  cm.addColor(val, col);
+				  }
+				  catch(Exception e)
+				  {  
+				  }
+			  }
+		  }
+		  if (cm.getNumColors()>1)
+			  return cm;
+	  }
+	  return ModeleColorMap.defaultColorMap();
+  }
+  
+  public void setMinValue(double newMin)
+  {
+	  rescale(newMin,getMaxValue());
+  }
+
+  public void setMaxValue(double newMax)
+  {
+	  rescale(getMinValue(),newMax);
+  }
+
+  public void rescale(double newMin, double newMax)
+  {
+	  double minBck = getMinValue();
+	  double maxBck = getMaxValue();
+	  double spanBck = maxBck-minBck;
+	  if (newMax!=newMin)
+	  {
+	      newMax = Math.max(newMax,newMin+1.0);
+		  for (int i=0;i<_values.size();i++)
+		  {
+			  double valBck = _values.get(i);
+			  _values.set(i, newMin+(newMax-newMin)*(valBck-minBck)/(spanBck));
+		  }
+	  }
+  }
+  
+  public ModeleColorMap clone()
+  {
+	  ModeleColorMap cm = new ModeleColorMap(); 
+	  cm._map = (Vector<Color>) _map.clone();
+	  cm._values = (Vector<Double>)_values.clone();
+	  return cm;
+  }
+  
+  public boolean equals(ModeleColorMap cm)
+  {
+	  if ( getNumColors()!=cm.getNumColors())
+		  return false;
+	  for (int i=0;i<getNumColors();i++)
+	  {
+		  if ((!getColorAt(i).equals(cm.getColorAt(i))) || (!getValueAt(i).equals(cm.getValueAt(i))) )
+				  return false;
+	  }
+	  return true;
+		  
+  }
+  
+  public String getParamEncoding()
+  {
+	  String result = "";
+	  Formatter f = new Formatter();
+	  for(int i=0;i<getNumColors();i++)
+	  {
+		  if (i!=0)
+			  f.format(",");
+		  f.format("%.2f:#%02X%02X%02X", _values.get(i),_map.get(i).getRed(),_map.get(i).getGreen(),_map.get(i).getBlue());
+	  }
+	  return f.out().toString();
+  }
+  
+
+  
+  public String toString()
+  {
+	  return getParamEncoding();
+  }
+}
+