X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Fannotations%2FChemProbAnnotation.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Fannotations%2FChemProbAnnotation.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=83c215862796b3e1f121b315137e0cfb9bdeac0e;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/models/annotations/ChemProbAnnotation.java b/src2/fr/orsay/lri/varna/models/annotations/ChemProbAnnotation.java
deleted file mode 100644
index 83c2158..0000000
--- a/src2/fr/orsay/lri/varna/models/annotations/ChemProbAnnotation.java
+++ /dev/null
@@ -1,260 +0,0 @@
-package fr.orsay.lri.varna.models.annotations;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-
-import javax.xml.transform.sax.TransformerHandler;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.AttributesImpl;
-
-import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.utils.XMLUtils;
-
-
-public class ChemProbAnnotation implements Serializable {
-
-	public static final String HEADER_TEXT = "ChemProbAnnotation";
-
-	/**
-	 * 
-	 */
-	private static final long serialVersionUID = 5833315460145031242L;
-
-
-	public enum ChemProbAnnotationType 
-	{
-		TRIANGLE,
-		ARROW,
-		PIN,
-		DOT;
-	};
-	
-	public static double DEFAULT_INTENSITY = 1.0;
-	public static ChemProbAnnotationType DEFAULT_TYPE = ChemProbAnnotationType.ARROW;
-	public static Color DEFAULT_COLOR = Color.blue.darker();
-
-	private ModeleBase _mbfst;
-	private ModeleBase _mbsnd;
-	private Color _color;
-	private double _intensity;
-	private ChemProbAnnotationType _type;
-	private boolean _outward;
-	
-	public static String XML_ELEMENT_NAME = "ChemProbAnnotation";
-	public static String XML_VAR_INDEX5_NAME = "Index5";
-	public static String XML_VAR_INDEX3_NAME = "Index3";
-	public static String XML_VAR_COLOR_NAME = "Color";
-	public static String XML_VAR_INTENSITY_NAME = "Intensity";
-	public static String XML_VAR_TYPE_NAME = "Type";
-	public static String XML_VAR_OUTWARD_NAME = "Outward";
-
-	public void toXML(TransformerHandler hd) throws SAXException
-	{
-		AttributesImpl atts = new AttributesImpl();
-		atts.addAttribute("","",XML_VAR_INDEX5_NAME,"CDATA",""+_mbfst.getIndex());
-		atts.addAttribute("","",XML_VAR_INDEX3_NAME,"CDATA",""+_mbsnd.getIndex());
-		atts.addAttribute("","",XML_VAR_COLOR_NAME,"CDATA",XMLUtils.toHTMLNotation(_color));
-		atts.addAttribute("","",XML_VAR_INTENSITY_NAME,"CDATA",""+_intensity);
-		atts.addAttribute("","",XML_VAR_TYPE_NAME,"CDATA",""+_type);
-		atts.addAttribute("","",XML_VAR_OUTWARD_NAME,"CDATA",""+_outward);
-		hd.startElement("","",XML_ELEMENT_NAME,atts);
-		hd.endElement("","",XML_ELEMENT_NAME);
-	}
-
-	
-	public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, String styleDesc) {
-		this(mbfst,mbsnd);
-		applyStyle(styleDesc);
-	}
-
-	public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd) {
-		this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,ChemProbAnnotation.DEFAULT_INTENSITY);
-	}
-
-	public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, double intensity) {
-		this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,intensity);
-	}
-
-	public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type) {
-		this(mbfst,mbsnd,type,ChemProbAnnotation.DEFAULT_INTENSITY);
-	}
-	
-	public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity) {
-		this(mbfst,mbsnd, type, intensity, DEFAULT_COLOR, true);
-	}
-
-	public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity, Color color, boolean out) {
-		if (mbfst.getIndex()>mbsnd.getIndex())
-		{
-			ModeleBase tmp = mbsnd;
-			mbsnd = mbfst;
-			mbfst = tmp;
-		}
-		_mbfst = mbfst;
-		_mbsnd = mbsnd;
-		_type = type;
-		_intensity = intensity;
-		_color = color;
-		_outward = out;
-	}
-
-	public boolean isOut()
-	{
-		return _outward; 
-	}
-	
-	public void setOut(boolean b)
-	{
-		_outward = b;
-	}
-
-	public Color getColor()
-	{
-		return _color; 
-	}
-
-	public double getIntensity()
-	{
-		return _intensity; 
-	}
-	
-	public ChemProbAnnotationType getType()
-	{
-		return _type; 
-	}
-	
-	public void setColor(Color c){
-		_color = c;
-	}
-
-	public void setIntensity(double d){
-		_intensity = d;
-	}
-	
-	public Point2D.Double getAnchorPosition()
-	{
-		Point2D.Double result = new Point2D.Double(
-				(_mbfst.getCoords().x+_mbsnd.getCoords().x)/2.0,
-				(_mbfst.getCoords().y+_mbsnd.getCoords().y)/2.0);
-		return result;
-	}
-	
-	public Point2D.Double getDirVector()
-	{
-		Point2D.Double norm = getNormalVector();
-		Point2D.Double result = new Point2D.Double(-norm.y,norm.x);
-		Point2D.Double anchor = getAnchorPosition();
-		Point2D.Double center = new Point2D.Double(
-				(_mbfst.getCenter().x+_mbsnd.getCenter().x)/2.0,
-				(_mbfst.getCenter().y+_mbsnd.getCenter().y)/2.0);
-		Point2D.Double vradius = new Point2D.Double(
-				(center.x-anchor.x)/2.0,
-				(center.y-anchor.y)/2.0);
-		if (_outward)
-		{
-		  if (result.x*vradius.x+result.y*vradius.y>0)
-		  {
-			return new Point2D.Double(-result.x,-result.y);
-		  }
-		}
-		else
-		{
-			  if (result.x*vradius.x+result.y*vradius.y<0)
-			  {
-				return new Point2D.Double(-result.x,-result.y);
-			  }			
-		}
-		return result;		
-	}
-	public Point2D.Double getNormalVector()
-	{
-		Point2D.Double tmp;
-		if (_mbfst==_mbsnd)
-		{
-			tmp = new Point2D.Double(
-					(-(_mbsnd.getCenter().y-_mbsnd.getCoords().y)),
-					((_mbsnd.getCenter().x-_mbsnd.getCoords().x)));			
-		}
-		else
-		{
-			tmp = new Point2D.Double(
-				(_mbsnd.getCoords().x-_mbfst.getCoords().x)/2.0,
-				(_mbsnd.getCoords().y-_mbfst.getCoords().y)/2.0);
-		}
-		
-		double norm = tmp.distance(0, 0);
-		Point2D.Double result = new Point2D.Double(tmp.x/norm,tmp.y/norm);
-		return result;				
-	}
-	
-	public static ChemProbAnnotationType annotTypeFromString(String value)
-	{
-		if (value.toLowerCase().equals("arrow"))
-		{return ChemProbAnnotationType.ARROW;}
-		else if (value.toLowerCase().equals("triangle"))
-		{return ChemProbAnnotationType.TRIANGLE;}
-		else if (value.toLowerCase().equals("pin"))
-		{return ChemProbAnnotationType.PIN;}
-		else if (value.toLowerCase().equals("dot"))
-		{return ChemProbAnnotationType.DOT;}
-		else
-		{return ChemProbAnnotationType.ARROW;}
-	}
-	
-	
-	public void applyStyle(String styleDesc)
-	{
-		String[] chemProbs = styleDesc.split(",");
-		for (int i = 0; i < chemProbs.length; i++) {
-			String thisStyle = chemProbs[i];
-			String[] data = thisStyle.split("=");
-			if (data.length==2)
-			{
-				String name = data[0];
-				String value = data[1];
-				if (name.toLowerCase().equals("color"))
-				{
-					Color c = Color.decode(value);
-					if (c==null)
-					{ c = _color; }
-					setColor(c);
-				}
-				else if (name.toLowerCase().equals("intensity"))
-				{
-					_intensity = Double.parseDouble(value);
-				}
-				else if (name.toLowerCase().equals("dir"))
-				{
-					_outward = value.toLowerCase().equals("out");
-				}
-				else if (name.toLowerCase().equals("glyph"))
-				{
-					_type= annotTypeFromString(value);
-				}
-			}
-		}
-	}
-	
-	public void setType(ChemProbAnnotationType s)
-	{
-		_type = s;
-	}
-
-	public ChemProbAnnotation clone()
-	{
-		ChemProbAnnotation result = new ChemProbAnnotation(this._mbfst,this._mbsnd);
-		result._intensity = _intensity;
-		result._type = _type;
-		result._color= _color;
-		result._outward = _outward;
-		return result;
-	}
-	
-	public String toString()
-	{
-		return "Chem. prob. "+this._type+" Base#"+this._mbfst.getBaseNumber()+"-"+this._mbsnd.getBaseNumber();
-	}
-	
-}