+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ // This is because MacOSX creates a mouseMoved\r
+ // If control is down, other platforms will not.\r
+ mouseDragged(evt);\r
+ }\r
+\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
+\r
+\r
+ if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())\r
+ return;\r
+\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+\r
+ if (res > sequence.getLength())\r
+ {\r
+ return;\r
+ }\r
+\r
+ 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
+\r
+ if (features[i].links != null)\r
+ tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
+\r
+ }\r
+\r
+ // else if(features[i].begin==0 && features[i].end==0)\r
+ {\r
+ // seqSpecific.append(features[i].featureGroup+": "\r
+ // + features[i].getType()+" "\r
+ // +features[i].getDescription()+"<br>");\r
+\r
+ }\r
+ }\r
+\r
+ if(tooltipText.length()==6) // <html></html>\r
+ {\r
+ setToolTipText(null);\r
+ }\r
+ else\r
+ {\r
+ tooltipText.append("</html>");\r
+ setToolTipText(tooltipText.toString());\r
+ }\r
+ }\r
+ else\r
+ setToolTipText(null);\r
+ }\r
+ }\r
+\r
+ void setStatusMessage(SequenceI sequence, int res, int seq)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+\r
+ Object obj = null;\r
+ if (av.alignment.isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
+ "");\r
+ if (obj != null)\r
+ text.append(" Nucleotide: ");\r
+ }\r
+ else\r
+ {\r
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ if (obj != null)\r
+ text.append(" Residue: ");\r
+ }\r
+\r
+ if (obj != null)\r
+ {\r
+\r
+ if (obj != "")\r
+ {\r
+ text.append(obj + " (" + sequence.findPosition(res) +\r
+ ")");\r
+ }\r
+ }\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (mouseWheelPressed)\r
+ {\r
+ int oldWidth = av.charWidth;\r
+\r
+ //Which is bigger, left-right or up-down?\r
+ if (Math.abs(evt.getY() - lastMousePress.getY())\r
+ > Math.abs(evt.getX() - lastMousePress.getX()))\r
+ {\r
+ int fontSize = av.font.getSize();\r
+\r
+ if (evt.getY() < lastMousePress.getY())\r
+ {\r
+ fontSize--;\r
+ }\r
+ else if (evt.getY() > lastMousePress.getY())\r
+ {\r
+ fontSize++;\r
+ }\r
+\r
+ if(fontSize<1)\r
+ fontSize = 1;\r
+\r
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
+ av.charWidth = oldWidth;\r
+ ap.fontChanged();\r
+ }\r
+ else\r
+ {\r
+ if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)\r
+ {\r
+ av.charWidth--;\r
+ }\r
+ else if (evt.getX() > lastMousePress.getX())\r
+ {\r
+ av.charWidth++;\r
+ }\r
+\r
+ ap.repaint();\r
+ }\r