X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Fannotations%2FHighlightRegionAnnotation.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Fannotations%2FHighlightRegionAnnotation.java;h=1e671bd8accff7660a42840712382c787c28e71c;hb=e95c5f895775891d55d9f23d5da64f8ce6bd07bb;hp=0000000000000000000000000000000000000000;hpb=74f21ca6ca8fa17d53708e457d191e15904f8310;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/models/annotations/HighlightRegionAnnotation.java b/srcjar/fr/orsay/lri/varna/models/annotations/HighlightRegionAnnotation.java
new file mode 100644
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--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/annotations/HighlightRegionAnnotation.java
@@ -0,0 +1,376 @@
+package fr.orsay.lri.varna.models.annotations;
+
+import java.awt.Color;
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.LinkedList;
+
+import javax.xml.transform.sax.TransformerHandler;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.AttributesImpl;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.controlers.ControleurClicMovement;
+import fr.orsay.lri.varna.models.VARNAConfigLoader;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.RNA;
+import fr.orsay.lri.varna.models.rna.VARNAPoint;
+import fr.orsay.lri.varna.utils.XMLUtils;
+import fr.orsay.lri.varna.views.VueHighlightRegionEdit;
+import fr.orsay.lri.varna.views.VueUI;
+
+public class HighlightRegionAnnotation implements Serializable {
+	
+	public static final String HEADER_TEXT = "HighlightRegionAnnotation";
+
+	private static final long serialVersionUID = 7087014168028684775L;
+	public static final Color DEFAULT_OUTLINE_COLOR = Color.decode("#6ed86e");
+	public static final Color DEFAULT_FILL_COLOR = Color.decode("#bcffdd");
+	public static final double DEFAULT_RADIUS = 16.0;
+	
+	private Color _outlineColor = DEFAULT_OUTLINE_COLOR;
+	private Color _fillColor = DEFAULT_FILL_COLOR;
+	private double _radius = DEFAULT_RADIUS;
+	private ArrayList<ModeleBase> _bases;
+	
+	public static String XML_ELEMENT_NAME = "region";
+	public static String XML_VAR_OUTLINE_NAME = "outline";
+	public static String XML_VAR_FILL_NAME = "fill";
+	public static String XML_VAR_RADIUS_NAME = "radius";
+
+	public void toXML(TransformerHandler hd) throws SAXException
+	{
+		AttributesImpl atts = new AttributesImpl();
+		atts.addAttribute("","",XML_VAR_OUTLINE_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_outlineColor));
+		atts.addAttribute("","",XML_VAR_FILL_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_fillColor));
+		atts.addAttribute("","",XML_VAR_RADIUS_NAME,"CDATA",""+_radius);
+		hd.startElement("","",XML_ELEMENT_NAME,atts);
+		XMLUtils.toXML(hd, _bases);
+		hd.endElement("","",XML_ELEMENT_NAME);
+	}
+
+  public HighlightRegionAnnotation(RNA r, int startIndex, int stopIndex)
+  {
+	  this(r.getBasesBetween(startIndex, stopIndex));
+  }
+
+  public HighlightRegionAnnotation()
+  {
+	  this(new ArrayList<ModeleBase>());
+  }
+
+  public HighlightRegionAnnotation(ArrayList<ModeleBase> b)
+  {
+	  this(b,DEFAULT_FILL_COLOR,DEFAULT_OUTLINE_COLOR,DEFAULT_RADIUS);
+  }
+ 
+  
+  public HighlightRegionAnnotation(ArrayList<ModeleBase> b,Color fill, Color outline, double radius)
+  {
+	  _bases = b;
+	  _fillColor = fill;
+	  _outlineColor = outline;
+	  _radius = radius;
+  }
+  
+	public HighlightRegionAnnotation clone()
+	{
+		return new HighlightRegionAnnotation(_bases,_fillColor,_outlineColor,_radius);
+	}
+	
+  public int getMinIndex()
+  {
+	  int min = Integer.MAX_VALUE;
+	  for (ModeleBase mb : _bases)
+	  {
+		  min = Math.min(min, mb.getIndex());
+	  }
+	  return min;
+  }
+
+  public int getMaxIndex()
+  {
+	  int max = Integer.MIN_VALUE;
+	  for (ModeleBase mb : _bases)
+	  {
+		  max = Math.max(max, mb.getIndex());
+	  }
+	  return max;
+  }
+
+  
+  public void setOutlineColor(Color c)
+  {
+	  _outlineColor = c;  
+  }
+
+  public ArrayList<ModeleBase> getBases()
+  {
+	  return _bases;
+  }
+
+  public void setBases(ArrayList<ModeleBase> b)
+  {
+	  _bases = b;
+  }
+  
+  public void setFillColor(Color c)
+  {
+	  _fillColor = c;  
+  }
+
+  public Color getFillColor()
+  {
+	  return _fillColor;  
+  }
+ 
+  public Color getOutlineColor()
+  {
+	  return _outlineColor;  
+  }
+
+  public double getRadius()
+  {
+	  return _radius;  
+  }
+
+  public void setRadius(double v)
+  {
+	  _radius = v;  
+  }
+  
+  public static final int NUM_STEPS_ROUNDED_CORNERS = 16;
+  
+  private Point2D.Double symImage(Point2D.Double p, Point2D.Double center)
+  {
+	  return new Point2D.Double(2.*center.x-p.x, 2.*center.y-p.y);
+  }
+  
+  private LinkedList<Point2D.Double> buildRoundedCorner(Point2D.Double p1, Point2D.Double p2, Point2D.Double anotherPoint)
+  {
+		LinkedList<Point2D.Double> result = new LinkedList<Point2D.Double>();
+		Point2D.Double m = new Point2D.Double((p1.x+p2.x)/2.0,(p1.y+p2.y)/2.0);
+		double rad = p1.distance(p2)/2.;
+		double angle = Math.atan2(p1.y-m.y, p1.x-m.x);
+		
+		double incr = Math.PI/((double)NUM_STEPS_ROUNDED_CORNERS+1);
+		
+		Point2D.Double pdir = new Point2D.Double(m.x+rad*Math.cos(angle+Math.PI/2.),m.y+rad*Math.sin(angle+Math.PI/2.));
+		if (pdir.distance(anotherPoint)<p1.distance(anotherPoint))
+		{ incr = -incr; }
+		
+		for(int k=1;k<=NUM_STEPS_ROUNDED_CORNERS;k++)
+		{
+			double angle2 = angle+k*incr;
+			Point2D.Double interForward = new Point2D.Double(m.x+rad*Math.cos(angle2),m.y+rad*Math.sin(angle2));
+			result.addLast(interForward);
+		}
+		return result;
+  }
+  
+  
+	public GeneralPath getShape(Point2D.Double[] realCoords,Point2D.Double[] realCenters, double scaleFactor)
+	{
+		GeneralPath p = new GeneralPath();
+		LinkedList<Point2D.Double> pointList = new LinkedList<Point2D.Double>();
+		for (int i = 0;i<getBases().size();i++)
+		{ 
+			int j1 = getBases().get(i).getIndex();
+			{
+				int j0 = j1-1;
+				int j2 = j1+1;
+				Point2D.Double p0 = new Point2D.Double(0., 0.);
+				Point2D.Double p1 = new Point2D.Double(0., 0.);			
+				Point2D.Double p2 = new Point2D.Double(0., 0.);
+				if (i==0)
+				{
+					// Single point
+					if (i==getBases().size()-1)
+					{
+						p1 = realCoords[j1];			
+						p0 = new Point2D.Double(p1.x+scaleFactor *getRadius(), p1.y);
+						p2 = new Point2D.Double(p1.x-scaleFactor *getRadius(), p1.y);
+					}
+					else
+					{
+						p1 = realCoords[j1];			
+						p2 = realCoords[j2];
+						p0 = symImage(p2, p1);
+					}
+				}
+				else if (i==getBases().size()-1)
+				{
+					p0 = realCoords[j0];
+					p1 = realCoords[j1];				
+					p2 = symImage(p0, p1);;					
+				}
+				else
+				{
+					p0 = realCoords[j0];
+					p1 = realCoords[j1];			
+					p2 = realCoords[j2];
+				}
+
+				double dist1 = p2.distance(p1);
+				Point2D.Double v1 = new Point2D.Double((p2.x-p1.x)/dist1,(p2.y-p1.y)/dist1);
+				Point2D.Double vn1 = new Point2D.Double(v1.y,-v1.x);
+				double dist2 = p1.distance(p0);
+				Point2D.Double v2 = new Point2D.Double((p1.x-p0.x)/dist2,(p1.y-p0.y)/dist2);
+				Point2D.Double vn2 = new Point2D.Double(v2.y,-v2.x);
+				double h = (new Point2D.Double(vn2.x-vn1.x,vn2.y-vn1.y).distance(new Point2D.Double(0,0))/2.0);
+				Point2D.Double vn = new Point2D.Double((vn1.x+vn2.x)/2.0,(vn1.y+vn2.y)/2.0);
+				double D = vn.distance(new Point2D.Double(0.0,0.0));
+				vn.x/= D;
+				vn.y/= D;
+				double nnorm = (D+h*h/D);
+				
+				double nnormF = nnorm;
+				double nnormB = nnorm;
+				
+				
+				Point2D.Double interForward = new Point2D.Double(p1.x + nnormF*scaleFactor *getRadius()*vn.x, 
+						p1.y + nnormF*scaleFactor *getRadius()*vn.y);
+				Point2D.Double interBackward = new Point2D.Double(p1.x - nnormB*scaleFactor *getRadius()*vn.x, 
+						p1.y - nnormB*scaleFactor *getRadius()*vn.y);
+
+
+				if (pointList.size()>0)
+				{
+					Point2D.Double prev1 = pointList.getLast();			
+					Point2D.Double prev2 = pointList.getFirst();
+
+					if ((interForward.distance(prev1)+interBackward.distance(prev2))<(interForward.distance(prev2)+interBackward.distance(prev1)))
+					{
+						pointList.addLast(interForward);
+						pointList.addFirst(interBackward);
+					}
+					else
+					{
+						pointList.addFirst(interForward);
+						pointList.addLast(interBackward);
+					}
+				}
+				else
+				{
+					pointList.addLast(interForward);
+					pointList.addFirst(interBackward);
+				}
+			}
+		}
+		if (getBases().size()==1)
+		{
+			int midl = pointList.size()/2;
+			Point2D.Double mid = pointList.get(midl);
+			Point2D.Double apoint = new Point2D.Double(mid.x+1.,mid.y);
+			LinkedList<Point2D.Double> pointListStart = buildRoundedCorner(pointList.get(midl-1), pointList.get(midl), apoint);
+			pointList.addAll(midl, pointListStart);
+			mid = pointList.get(midl);
+			apoint = new Point2D.Double(mid.x+1.,mid.y);
+			LinkedList<Point2D.Double> pointListEnd = buildRoundedCorner(pointList.get(pointList.size()-1),pointList.get(0), apoint);
+			pointList.addAll(0,pointListEnd);			
+		}
+		else if (getBases().size()>1)
+		{
+			int midl = pointList.size()/2;
+			Point2D.Double apoint = symImage(pointList.get(midl),pointList.get(midl-1));
+			LinkedList<Point2D.Double> pointListStart = buildRoundedCorner(pointList.get(midl-1), pointList.get(midl), apoint);
+			pointList.addAll(midl, pointListStart);
+			apoint = symImage(realCoords[getBases().get(getBases().size()-1).getIndex()],
+					realCoords[getBases().get(getBases().size()-2).getIndex()]);
+			LinkedList<Point2D.Double> pointListEnd = buildRoundedCorner(pointList.get(pointList.size()-1),pointList.get(0), apoint);
+			pointList.addAll(0,pointListEnd);
+		}
+		
+
+		if (pointList.size()>0)
+		{
+			Point2D.Double point = pointList.get(0);
+			p.moveTo((float)point.x, (float)point.y);
+
+			for (int i=1;i<pointList.size();i++)
+			{
+				point = pointList.get(i);
+				p.lineTo((float)point.x, (float)point.y);				
+			}
+			p.closePath();
+		}
+		return p;
+	}
+
+	
+	public static HighlightRegionAnnotation parseHighlightRegionAnnotation(String txt, VARNAPanel vp)
+	{
+		try
+		{
+		String[] parts = txt.split(":");
+		String[] coords = parts[0].split("-");
+		int from = Integer.parseInt(coords[0]);
+		int to = Integer.parseInt(coords[1]);
+		int  i = vp.getRNA().getIndexFromBaseNumber(from);
+		int  j = vp.getRNA().getIndexFromBaseNumber(to);
+		Color fill = HighlightRegionAnnotation.DEFAULT_FILL_COLOR;
+		Color outline = HighlightRegionAnnotation.DEFAULT_OUTLINE_COLOR;
+		double radius = HighlightRegionAnnotation.DEFAULT_RADIUS;
+		ArrayList<ModeleBase> bases = vp.getRNA().getBasesBetween(i, j);
+		if (parts.length>1)
+		{
+		try
+		{
+			String[] options = parts[1].split(",");
+			for (int k = 0; k < options.length; k++) 
+			{
+				//System.out.println(options[k]);
+				try
+				{
+					String[] data = options[k].split("=");
+					String lhs = data[0].toLowerCase();
+					String rhs = data[1];
+					if (lhs.equals("fill"))
+					{
+						fill = VARNAConfigLoader.getSafeColor(rhs, fill);
+					}
+					else if (lhs.equals("outline"))
+					{
+						outline = VARNAConfigLoader.getSafeColor(rhs, outline);
+					}
+					else if (lhs.equals("radius"))
+					{
+						radius = Double.parseDouble(rhs);
+					}	
+				}
+				catch(Exception e)
+				{
+				}				
+			}
+		}
+		catch(Exception e)
+		{
+			e.printStackTrace();
+		}
+		}
+		return new HighlightRegionAnnotation(bases,fill,outline,radius);
+		}
+	catch(Exception e)
+	{
+		e.printStackTrace();
+	}
+	return null;
+	}
+	
+	public String toString()
+	{
+		//String result = "HighlightRegionAnnotation[";
+		//result += "fill:"+_fillColor.toString();
+		//result += ",outline:"+_outlineColor.toString();
+		//result += ",radius:"+_radius;
+		//return result+"]";
+		String result = "Highlighted region "+getMinIndex()+"-"+getMaxIndex();
+		return result;
+	}
+	
+}