+ public void makePNGImageMap(File imgMapFile, String imageName)\r
+ {\r
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
+ //////////////////////////////////////////////\r
+ int idWidth = getVisibleIdWidth();\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+ // Gen image map\r
+ //////////////////////////////////\r
+ if (imgMapFile != null)\r
+ {\r
+ try\r
+ {\r
+ int s, sSize = av.alignment.getHeight(),\r
+ res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;\r
+ StringBuffer text = new StringBuffer();\r
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
+ out.println("<img src=\"" + imageName +\r
+ "\" border=\"0\" usemap=\"#Map\" >"\r
+ + "<map name=\"Map\">");\r
+\r
+ for (s = 0; s < sSize; s++)\r
+ {\r
+ sy = s * av.charHeight + scaleHeight;\r
+\r
+ SequenceI seq = av.alignment.getSequenceAt(s);\r
+ SequenceFeature[] features = seq.getDatasetSequence().\r
+ getSequenceFeatures();\r
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
+ for (res = 0; res < alwidth; res++)\r
+ {\r
+ text = new StringBuffer();\r
+ Object obj = null;\r
+ if (av.alignment.isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +\r
+ "");\r
+ }\r
+ else\r
+ {\r
+ obj = ResidueProperties.aa2Triplet.get(\r
+ seq.getCharAt(res) + "");\r
+ }\r
+\r
+ if (obj == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ String triplet = obj.toString();\r
+ int alIndex = seq.findPosition(res);\r
+ gSize = groups.length;\r
+ for (g = 0; g < gSize; g++)\r
+ {\r
+ if (text.length() < 1)\r
+ {\r
+ text.append("<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet);\r
+ }\r