X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Fannotations%2FHighlightRegionAnnotation.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Fannotations%2FHighlightRegionAnnotation.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=1e671bd8accff7660a42840712382c787c28e71c;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;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
deleted file mode 100644
index 1e671bd..0000000
--- a/srcjar/fr/orsay/lri/varna/models/annotations/HighlightRegionAnnotation.java
+++ /dev/null
@@ -1,376 +0,0 @@
-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;
-	}
-	
-}