src/jalview/gui/GraphRenderer.java

   1 package jalview.gui;\r
   2 \r
   3 import jalview.datamodel.*;\r
   4 import jalview.schemes.*;\r
   5 import jalview.util.*;\r
   6 \r
   7 import java.awt.*;\r
   8 import java.awt.geom.*;\r
   9 import java.util.*;\r
  10 \r
  11 public class GraphRenderer implements RendererI {\r
  12     protected Color   color = Color.black;\r
  13     protected Color   maroon = new Color(200,0,50);\r
  14 \r
  15     public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
  16         Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
  17         return c;\r
  18     }\r
  19 \r
  20     public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText,Vector pid, int seqnum,AlignViewport av) {\r
  21 \r
  22         int i      = start;\r
  23         int length = seq.getLength();\r
  24 \r
  25         Color currentColor = Color.white;\r
  26 \r
  27         g.setColor(Color.black);\r
  28 \r
  29         int prev = -1;\r
  30 \r
  31         while (i <= end && i < length) {\r
  32             char c = seq.getCharAt(i);\r
  33 \r
  34             if (c != '-') {\r
  35             Vector values = (Vector)pid.elementAt(i-start);\r
  36             int val = ((Integer)values.elementAt(seqnum)).intValue();\r
  37 \r
  38             int frac = (int)(100*val/(av.getPIDWindow()+1));\r
  39 \r
  40 //          if (frac > 95) {\r
  41  //               g.setColor(maroon);\r
  42   //          } else if (frac > 90) {\r
  43 //              g.setColor(Color.red);\r
  44 //          } else if (frac > 80) {\r
  45 //              g.setColor(Color.orange);\r
  46 //          } else if (frac > 70) {\r
  47 //              g.setColor(Color.pink);\r
  48 //          } else if (frac > 50) {\r
  49 //              g.setColor(Color.yellow);\r
  50 //          } else if (frac > 30) {\r
  51 //              g.setColor(Color.lightGray);\r
  52 //          }\r
  53 \r
  54             int baseline = av.getPIDBaseline();\r
  55 \r
  56             frac -= baseline;\r
  57 \r
  58             if (frac < 0) {\r
  59               frac = 0;\r
  60             }\r
  61             if (baseline == 100) {\r
  62                 baseline = 99;\r
  63             }\r
  64 \r
  65              Graphics2D g2d = (Graphics2D)g;\r
  66 \r
  67              g2d.setColor(new Color(255*frac/(100-baseline),50*frac/(100-baseline),50*frac/(100-baseline)));\r
  68 \r
  69              //g.setColor(new Color(255*frac/(100-baseline),50*frac/(100-baseline),255-50*frac/(100-baseline)));\r
  70              //g.fillRect(x1+(int)(width*(i-start)),y1+height - (int)(frac*height/(100-baseline)),\r
  71                            //width,                      (int)(frac*height/(100-baseline)));\r
  72 \r
  73              int[] xpoints = new int[4];\r
  74              int[] ypoints = new int[4];\r
  75 \r
  76              if (prev == -1) {\r
  77                prev = y1 + height - (int)(frac*height/(100-baseline));\r
  78              }\r
  79 \r
  80              //   1----2\r
  81              //   |    |\r
  82              //   4----3\r
  83 \r
  84              xpoints[0] = (x1+ (int)(width*(i-start)));\r
  85              ypoints[0] = prev;\r
  86 \r
  87              xpoints[1] = (x1 + (int)(width*(i-start+1)));\r
  88              ypoints[1] = y1 + height - (int)(frac*height/(100-baseline));\r
  89 \r
  90              xpoints[3] = (x1 + (int)(width*(i-start)));;\r
  91              ypoints[3] = y1 + height;\r
  92 \r
  93              xpoints[2] = (x1  + (int)(width*(i-start+1)));\r
  94              ypoints[2] = y1 + height;\r
  95 \r
  96              Polygon poly = new Polygon();\r
  97 \r
  98              poly.xpoints = xpoints;\r
  99              poly.ypoints = ypoints;\r
 100              poly.npoints = 4;\r
 101 \r
 102              g2d.fill(poly);\r
 103 \r
 104              if (width > 5) {\r
 105                  g.setColor(Color.black);\r
 106                  g.drawString(seq.getSequence().substring(i,i+1),x1+(int)(width*(i-start)),y1+height);\r
 107              } else {\r
 108                  g.setColor(Color.black);\r
 109 \r
 110                  if (prev != -1) {\r
 111 \r
 112               g.drawLine(x1+(int)(width*(i-start)-width/2),  prev,\r
 113                          x1+(int)(width*(i-start+1)-width/2),y1+height - (int)(frac*height/(100-baseline)));\r
 114               } else {\r
 115               g.drawLine(x1+(int)(width*(i-start)),  y1+height - (int)(frac*height/(100-baseline)),\r
 116                          x1+(int)(width*(i-start+1)),y1+height - (int)(frac*height/(100-baseline)));\r
 117               }\r
 118 \r
 119             }\r
 120             prev = ypoints[1];\r
 121             }  else {\r
 122               prev = -1;\r
 123             }\r
 124             i++;\r
 125         }\r
 126     }\r
 127 \r
 128 }\r