+ while (yPos < endRes)\r
+ {\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+ if (column > row.annotations.length-1)\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ else\r
+ column = yPos;\r
+\r
+ if ((row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
+\r
+ x = (yPos - startRes) * av.charWidth;\r
+\r
+ if (activeRow == i)\r
+ {\r
+ g.setColor(Color.red);\r
+\r
+ if (av.getColumnSelection() != null)\r
+ {\r
+ for (int n = 0; n < av.getColumnSelection().size(); n++)\r
+ {\r
+ int v = av.getColumnSelection().columnAt(n);\r
+\r
+ if (v == column)\r
+ {\r
+ g.fillRect((column - startRes) * av.charWidth, y,\r
+ av.charWidth, row.height);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
+ {\r
+\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[column].colour);\r
+\r
+ if (column == 0 || row.graph>0)\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ else if (((row.annotations[column - 1] == null)\r
+ ||\r
+ (!row.annotations[column].displayCharacter.equals(\r
+ row.annotations[column - 1].displayCharacter))))\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ }\r
+\r
+ if (row.hasIcons)\r
+ {\r
+ if (!validRes ||\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
+ {\r
+ switch (lastSS)\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX, 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[] { x - 4, x - 4, x },\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 8 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
+\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ x - lastSSX, 2);\r
+\r
+ break;\r
+ }\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS = row.annotations[column].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS = ' ';\r
+ }\r
+\r
+ lastSSX = x;\r
+ }\r
+ }\r
+\r
+ yPos++;\r
+ }\r