+ }\r
+ }\r
+\r
+ public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
+ int sRes, int eRes,\r
+ int y,\r
+ float min, float max,\r
+ int graphHeight)\r
+ {\r
+ if(sRes>aa.annotations.length)\r
+ return;\r
+\r
+\r
+\r
+ int x = 0;\r
+\r
+ //Adjustment for fastpaint to left\r
+ if(eRes<av.endRes)\r
+ eRes++;\r
+\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
+\r
+ if(sRes==0)\r
+ {\r
+ sRes++;\r
+ x+=av.charWidth;\r
+ }\r
+\r
+ int y1=y, y2=y;\r
+ float range = max - min;\r
+\r
+ ////Draw origin\r
+ if(min<0)\r
+ y2 = y - (int)((0-min / range)*graphHeight);\r
+\r
+ g.setColor(Color.gray);\r
+ g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
+\r
+\r
+ for (int j = sRes; j < eRes; j++)\r
+ {\r
+ if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
+ {\r
+ x+=av.charWidth;\r
+ continue;\r
+ }\r
+ g.setColor(aa.annotations[j].colour);\r
+ y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
+ y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
+ g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
+ x += av.charWidth;\r
+ }\r
+\r
+\r
+ if(aa.threshold!=null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ }\r
+\r
+ }\r
+\r
+ public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
+ int sRes, int eRes,\r
+ float min, float max,\r
+ int y)\r
+ {\r
+ if(sRes>aa.annotations.length)\r
+ return;\r
+\r
+\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
+ int x=0, y1, y2;\r
+\r
+ float range = max - min;\r
+\r
+ y1 = y2 = y;\r
+\r
+ if(min<0)\r
+ y2 = y -(int)( (0-min / (range))*aa.graphHeight);\r
+\r
+ g.setColor(Color.gray);\r
+\r
+ g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
+\r
+ for (int j = sRes; j < eRes; j++)\r
+ {\r
+\r
+ if (aa.annotations[j] == null)\r
+ {\r
+ x += av.charWidth;\r
+ continue;\r
+ }\r
+\r
+ g.setColor(aa.annotations[j].colour);\r
+ y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
+\r
+ if(y1-y2>0)\r
+ g.fillRect(x, y2, av.charWidth, y1-y2 );\r
+ else\r
+ g.fillRect(x, y1, av.charWidth, y2-y1 );\r
+\r
+ x += av.charWidth;\r
+ }\r
+\r
+\r
+ if(aa.threshold!=null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ }\r
+\r
+\r