import java.awt.*;\r
import java.util.*;\r
\r
-public class FeatureRenderer implements RendererI {\r
+public class FeatureRenderer\r
+{\r
+ AlignViewport av;\r
+\r
+ SequenceGroup currentSequenceGroup = null;\r
+ SequenceGroup [] allGroups = null;\r
+ Color resBoxColour;\r
+ Graphics graphics;\r
+\r
+ public FeatureRenderer(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
+\r
+ public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
+ {\r
+ Vector features = seq.getSequenceFeatures();\r
+ Enumeration e = features.elements();\r
+ while( e.hasMoreElements() )\r
+ {\r
+ SequenceFeature sf = (SequenceFeature)e.nextElement();\r
+ if(sf.getStart()>seq.getEnd())\r
+ continue;\r
+\r
+ int fstart = seq.findIndex(sf.getStart())-1;\r
+ int fend = seq.findIndex(sf.getEnd())-1;\r
+\r
+ if( (fstart<=end && fend>=start) )\r
+ {\r
+ if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
+ fstart = 0;// but the feature end is still valid!!\r
+\r
+ if(fstart==fend)\r
+ {\r
+ g.setColor(Color.red);\r
+ g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
+ g.setColor(Color.white);\r
+\r
+ char s = seq.getSequence().charAt(fstart);\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s))/2;\r
+ int pady = height/5;\r
+ g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
\r
-\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
- Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
- return c;\r
- }\r
-\r
- 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
-\r
- int i = start;\r
- int length = seq.getLength();\r
-\r
- Color currentColor = Color.black;\r
-\r
-\r
- int prev = -1;\r
- int fstart = 0;\r
- char prevc = '-';\r
-\r
- g.setColor(Color.magenta);\r
-\r
- while (i <= end && i < length) {\r
- char c = seq.getCharAt(i);\r
- if (c != '-') {\r
-\r
- if (prevc != c) {\r
-\r
- if (prevc == 'F') {\r
- g.setColor(Color.green);\r
- } else if (prevc == 'R') {\r
- g.setColor(Color.cyan);\r
- } else if (prevc == 'M') {\r
- g.setColor(Color.magenta);\r
- } else if (prevc == 'P') {\r
- g.setColor(Color.yellow);\r
- }\r
- g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2);\r
-\r
- prevc = c;\r
- fstart = i;\r
- }\r
- } else if (prevc != '-') {\r
- if (prevc == 'F') {\r
- g.setColor(Color.green);\r
- } else if (prevc == 'R') {\r
- g.setColor(Color.cyan);\r
- } else if (prevc == 'M') {\r
- g.setColor(Color.magenta);\r
- } else if (prevc == 'P') {\r
- g.setColor(Color.yellow);\r
- }\r
- g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2);\r
-\r
- prevc = c;\r
- } else {\r
- fstart = -1;\r
+ }\r
+ else\r
+ {\r
+ for (int i = fstart; i <= fend; i++)\r
+ {\r
+ char s = seq.getSequence().charAt(i);\r
+ if( jalview.util.Comparison.isGap(s) )\r
+ continue;\r
+\r
+ g.setColor(Color.blue);\r
+ g.fillRect( (i-start) * width, y1, width, height);\r
+\r
+ g.setColor(Color.white);\r
+\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + width * (i-start),\r
+ y1 + height - pady);\r
}\r
- i++;\r
- }\r
-\r
- if (fstart != -1) {\r
- if (prevc == 'F') {\r
- g.setColor(Color.green);\r
- } else if (prevc == 'R') {\r
- g.setColor(Color.cyan);\r
- } else if (prevc == 'M') {\r
- g.setColor(Color.magenta);\r
- } else if (prevc == 'P') {\r
- g.setColor(Color.yellow);\r
}\r
+ }\r
\r
- //g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2);\r
-\r
- }\r
}\r
+ }\r
\r
}\r