+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+ {\r
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+ }\r
+\r
+ setStatusMessage(sequence, res, seq);\r
+\r
+ // use aa to see if the mouse pointer is on a\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ tooltipText.setLength(6); // Cuts the buffer back to <html>\r
+\r
+ SequenceFeature[] features = findFeaturesAtRes(\r
+ sequence.getDatasetSequence(), sequence.findPosition(res));\r
+\r
+ if(features!=null)\r
+ {\r
+ for (int i = 0; i < features.length; i++)\r
+ {\r
+ if (features[i].getType().equals("disulfide bond"))\r
+ {\r
+ if (features[i].getBegin() == sequence.findPosition(res)\r
+ || features[i].getEnd() == sequence.findPosition(res))\r
+ {\r
+ if (tooltipText.length() > 6)\r
+ tooltipText.append("<br>");\r
+ tooltipText.append("disulfide bond " + features[i].getBegin() + ":" +\r
+ features[i].getEnd());\r
+ if (features[i].links != null)\r
+ tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (tooltipText.length() > 6)\r
+ tooltipText.append("<br>");\r
+\r
+ tooltipText.append(features[i].getType() + " " +\r
+ features[i].begin);\r
+ if (features[i].begin != features[i].end)\r
+ tooltipText.append(" " + features[i].end);\r
+\r
+ if (features[i].getDescription() != null\r
+ && !features[i].description.equals(features[i].getType()))\r
+ {\r
+ tmpString = features[i].getDescription();\r
+ int startTag=tmpString.toUpperCase().indexOf("<HTML>");\r
+ if(startTag>-1)\r
+ {\r
+ tmpString = tmpString.substring(startTag + 6);\r
+ }\r
+ int endTag=tmpString.toUpperCase().indexOf("</BODY>");\r
+ if(endTag>-1)\r
+ {\r
+ tmpString = tmpString.substring(0, endTag);\r
+ }\r
+ endTag = tmpString.toUpperCase().indexOf("</HTML>");\r
+ if(endTag>-1)\r
+ {\r
+ tmpString = tmpString.substring(0, endTag);\r
+ }\r
+\r
+ if(startTag>-1)\r
+ {\r
+ tooltipText.append("; " + tmpString);\r
+ }\r
+ else\r
+ {\r
+ if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)\r
+ {\r
+ //The description does not specify html is to\r
+ //be used, so we must remove < > symbols\r
+ tmpString = tmpString.replaceAll("<", "<");\r
+ tmpString = tmpString.replaceAll(">", ">");\r
+\r
+ tooltipText.append("; ");\r
+ tooltipText.append(tmpString);\r
+\r
+ }\r
+ else\r
+ tooltipText.append("; "+tmpString);\r
+ }\r
+ }\r
+ if (features[i].getValue("status") != null )\r
+ {\r
+ String status = features[i].getValue("status").toString();\r
+ if(status.length()>0)\r
+ tooltipText.append("; (" + features[i].getValue("status") + ")");\r
+ }\r