--- /dev/null
+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();
+ }
+}
+
git://source.jalview.org / jalview.git / blobdiff