src2/fr/orsay/lri/varna/models/annotations/ChemProbAnnotation.java

   1 package fr.orsay.lri.varna.models.annotations;
   2
   3 import java.awt.Color;
   4 import java.awt.geom.Point2D;
   5 import java.io.Serializable;
   6
   7 import javax.xml.transform.sax.TransformerHandler;
   8
   9 import org.xml.sax.SAXException;
  10 import org.xml.sax.helpers.AttributesImpl;
  11
  12 import fr.orsay.lri.varna.models.rna.ModeleBase;
  13 import fr.orsay.lri.varna.utils.XMLUtils;
  14
  15
  16 public class ChemProbAnnotation implements Serializable {
  17
  18         public static final String HEADER_TEXT = "ChemProbAnnotation";
  19
  20         /**
  21          *
  22          */
  23         private static final long serialVersionUID = 5833315460145031242L;
  24
  25
  26         public enum ChemProbAnnotationType
  27         {
  28                 TRIANGLE,
  29                 ARROW,
  30                 PIN,
  31                 DOT;
  32         };
  33
  34         public static double DEFAULT_INTENSITY = 1.0;
  35         public static ChemProbAnnotationType DEFAULT_TYPE = ChemProbAnnotationType.ARROW;
  36         public static Color DEFAULT_COLOR = Color.blue.darker();
  37
  38         private ModeleBase _mbfst;
  39         private ModeleBase _mbsnd;
  40         private Color _color;
  41         private double _intensity;
  42         private ChemProbAnnotationType _type;
  43         private boolean _outward;
  44
  45         public static String XML_ELEMENT_NAME = "ChemProbAnnotation";
  46         public static String XML_VAR_INDEX5_NAME = "Index5";
  47         public static String XML_VAR_INDEX3_NAME = "Index3";
  48         public static String XML_VAR_COLOR_NAME = "Color";
  49         public static String XML_VAR_INTENSITY_NAME = "Intensity";
  50         public static String XML_VAR_TYPE_NAME = "Type";
  51         public static String XML_VAR_OUTWARD_NAME = "Outward";
  52
  53         public void toXML(TransformerHandler hd) throws SAXException
  54         {
  55                 AttributesImpl atts = new AttributesImpl();
  56                 atts.addAttribute("","",XML_VAR_INDEX5_NAME,"CDATA",""+_mbfst.getIndex());
  57                 atts.addAttribute("","",XML_VAR_INDEX3_NAME,"CDATA",""+_mbsnd.getIndex());
  58                 atts.addAttribute("","",XML_VAR_COLOR_NAME,"CDATA",XMLUtils.toHTMLNotation(_color));
  59                 atts.addAttribute("","",XML_VAR_INTENSITY_NAME,"CDATA",""+_intensity);
  60                 atts.addAttribute("","",XML_VAR_TYPE_NAME,"CDATA",""+_type);
  61                 atts.addAttribute("","",XML_VAR_OUTWARD_NAME,"CDATA",""+_outward);
  62                 hd.startElement("","",XML_ELEMENT_NAME,atts);
  63                 hd.endElement("","",XML_ELEMENT_NAME);
  64         }
  65
  66
  67         public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, String styleDesc) {
  68                 this(mbfst,mbsnd);
  69                 applyStyle(styleDesc);
  70         }
  71
  72         public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd) {
  73                 this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,ChemProbAnnotation.DEFAULT_INTENSITY);
  74         }
  75
  76         public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, double intensity) {
  77                 this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,intensity);
  78         }
  79
  80         public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type) {
  81                 this(mbfst,mbsnd,type,ChemProbAnnotation.DEFAULT_INTENSITY);
  82         }
  83
  84         public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity) {
  85                 this(mbfst,mbsnd, type, intensity, DEFAULT_COLOR, true);
  86         }
  87
  88         public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity, Color color, boolean out) {
  89                 if (mbfst.getIndex()>mbsnd.getIndex())
  90                 {
  91                         ModeleBase tmp = mbsnd;
  92                         mbsnd = mbfst;
  93                         mbfst = tmp;
  94                 }
  95                 _mbfst = mbfst;
  96                 _mbsnd = mbsnd;
  97                 _type = type;
  98                 _intensity = intensity;
  99                 _color = color;
 100                 _outward = out;
 101         }
 102
 103         public boolean isOut()
 104         {
 105                 return _outward;
 106         }
 107
 108         public void setOut(boolean b)
 109         {
 110                 _outward = b;
 111         }
 112
 113         public Color getColor()
 114         {
 115                 return _color;
 116         }
 117
 118         public double getIntensity()
 119         {
 120                 return _intensity;
 121         }
 122
 123         public ChemProbAnnotationType getType()
 124         {
 125                 return _type;
 126         }
 127
 128         public void setColor(Color c){
 129                 _color = c;
 130         }
 131
 132         public void setIntensity(double d){
 133                 _intensity = d;
 134         }
 135
 136         public Point2D.Double getAnchorPosition()
 137         {
 138                 Point2D.Double result = new Point2D.Double(
 139                                 (_mbfst.getCoords().x+_mbsnd.getCoords().x)/2.0,
 140                                 (_mbfst.getCoords().y+_mbsnd.getCoords().y)/2.0);
 141                 return result;
 142         }
 143
 144         public Point2D.Double getDirVector()
 145         {
 146                 Point2D.Double norm = getNormalVector();
 147                 Point2D.Double result = new Point2D.Double(-norm.y,norm.x);
 148                 Point2D.Double anchor = getAnchorPosition();
 149                 Point2D.Double center = new Point2D.Double(
 150                                 (_mbfst.getCenter().x+_mbsnd.getCenter().x)/2.0,
 151                                 (_mbfst.getCenter().y+_mbsnd.getCenter().y)/2.0);
 152                 Point2D.Double vradius = new Point2D.Double(
 153                                 (center.x-anchor.x)/2.0,
 154                                 (center.y-anchor.y)/2.0);
 155                 if (_outward)
 156                 {
 157                   if (result.x*vradius.x+result.y*vradius.y>0)
 158                   {
 159                         return new Point2D.Double(-result.x,-result.y);
 160                   }
 161                 }
 162                 else
 163                 {
 164                           if (result.x*vradius.x+result.y*vradius.y<0)
 165                           {
 166                                 return new Point2D.Double(-result.x,-result.y);
 167                           }
 168                 }
 169                 return result;
 170         }
 171         public Point2D.Double getNormalVector()
 172         {
 173                 Point2D.Double tmp;
 174                 if (_mbfst==_mbsnd)
 175                 {
 176                         tmp = new Point2D.Double(
 177                                         (-(_mbsnd.getCenter().y-_mbsnd.getCoords().y)),
 178                                         ((_mbsnd.getCenter().x-_mbsnd.getCoords().x)));
 179                 }
 180                 else
 181                 {
 182                         tmp = new Point2D.Double(
 183                                 (_mbsnd.getCoords().x-_mbfst.getCoords().x)/2.0,
 184                                 (_mbsnd.getCoords().y-_mbfst.getCoords().y)/2.0);
 185                 }
 186
 187                 double norm = tmp.distance(0, 0);
 188                 Point2D.Double result = new Point2D.Double(tmp.x/norm,tmp.y/norm);
 189                 return result;
 190         }
 191
 192         public static ChemProbAnnotationType annotTypeFromString(String value)
 193         {
 194                 if (value.toLowerCase().equals("arrow"))
 195                 {return ChemProbAnnotationType.ARROW;}
 196                 else if (value.toLowerCase().equals("triangle"))
 197                 {return ChemProbAnnotationType.TRIANGLE;}
 198                 else if (value.toLowerCase().equals("pin"))
 199                 {return ChemProbAnnotationType.PIN;}
 200                 else if (value.toLowerCase().equals("dot"))
 201                 {return ChemProbAnnotationType.DOT;}
 202                 else
 203                 {return ChemProbAnnotationType.ARROW;}
 204         }
 205
 206
 207         public void applyStyle(String styleDesc)
 208         {
 209                 String[] chemProbs = styleDesc.split(",");
 210                 for (int i = 0; i < chemProbs.length; i++) {
 211                         String thisStyle = chemProbs[i];
 212                         String[] data = thisStyle.split("=");
 213                         if (data.length==2)
 214                         {
 215                                 String name = data[0];
 216                                 String value = data[1];
 217                                 if (name.toLowerCase().equals("color"))
 218                                 {
 219                                         Color c = Color.decode(value);
 220                                         if (c==null)
 221                                         { c = _color; }
 222                                         setColor(c);
 223                                 }
 224                                 else if (name.toLowerCase().equals("intensity"))
 225                                 {
 226                                         _intensity = Double.parseDouble(value);
 227                                 }
 228                                 else if (name.toLowerCase().equals("dir"))
 229                                 {
 230                                         _outward = value.toLowerCase().equals("out");
 231                                 }
 232                                 else if (name.toLowerCase().equals("glyph"))
 233                                 {
 234                                         _type= annotTypeFromString(value);
 235                                 }
 236                         }
 237                 }
 238         }
 239
 240         public void setType(ChemProbAnnotationType s)
 241         {
 242                 _type = s;
 243         }
 244
 245         public ChemProbAnnotation clone()
 246         {
 247                 ChemProbAnnotation result = new ChemProbAnnotation(this._mbfst,this._mbsnd);
 248                 result._intensity = _intensity;
 249                 result._type = _type;
 250                 result._color= _color;
 251                 result._outward = _outward;
 252                 return result;
 253         }
 254
 255         public String toString()
 256         {
 257                 return "Chem. prob. "+this._type+" Base#"+this._mbfst.getBaseNumber()+"-"+this._mbsnd.getBaseNumber();
 258         }
 259
 260 }