2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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25 import jalview.datamodel.*;
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26 import jalview.gui.*;
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28 public class HTMLOutput
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31 SequenceRenderer sr;
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35 public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)
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40 fr = new FeatureRenderer(ap);
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41 fr.transferSettings(fr1);
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43 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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45 "LAST_DIRECTORY"), new String[]
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48 {"HTML files"}, "HTML files");
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50 chooser.setFileView(new JalviewFileView());
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51 chooser.setDialogTitle("Save as HTML");
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52 chooser.setToolTipText("Save");
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54 int value = chooser.showSaveDialog(null);
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56 if (value == JalviewFileChooser.APPROVE_OPTION)
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58 String choice = chooser.getSelectedFile().getPath();
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59 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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60 chooser.getSelectedFile().getParent());
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64 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
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66 out.println("<HTML>");
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67 out.println("<style type=\"text/css\">");
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68 out.println("<!--");
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69 out.print("td {font-family: \"" + av.getFont().getFamily() +
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70 "\", \"" + av.getFont().getName() + "\", mono; " +
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71 "font-size: " + av.getFont().getSize() + "px; ");
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73 if (av.getFont().getStyle() == Font.BOLD)
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75 out.print("font-weight: BOLD; ");
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78 if (av.getFont().getStyle() == Font.ITALIC)
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80 out.print("font-style: italic; ");
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83 out.println("text-align: center; }");
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86 out.println("</style>");
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87 out.println("<BODY>");
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89 if (av.getWrapAlignment())
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91 drawWrappedAlignment(out);
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95 drawUnwrappedAlignment(out);
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98 out.println("\n</body>\n</html>");
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100 jalview.util.BrowserLauncher.openURL("file:///" + choice);
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102 catch (Exception ex)
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104 ex.printStackTrace();
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109 void drawUnwrappedAlignment(PrintWriter out)
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111 out.println("<table border=\"1\"><tr><td>\n");
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113 "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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117 AlignmentI alignment = av.getAlignment();
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119 // draws the top row, the measure rule
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120 out.println("<tr><td colspan=\"6\"></td>");
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124 for (i = 10; i < (alignment.getWidth() - 10); i += 10)
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126 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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129 out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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131 out.println("</tr>");
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133 for (i = 0; i < alignment.getHeight(); i++)
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135 seq = alignment.getSequenceAt(i);
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137 String id = seq.getDisplayId(av.getShowJVSuffix());
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139 out.println("<tr><td nowrap>" + id +
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140 " </td>");
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142 for (int res = 0; res < seq.getLength(); res++)
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144 if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
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146 color = sr.getResidueBoxColour(seq, res);
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148 color = fr.findFeatureColour(color, seq, res);
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152 color = Color.white;
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155 if (color.getRGB() < -1)
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157 out.println("<td bgcolor=\"#" +
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158 jalview.util.Format.getHexString(color) + "\">" +
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159 seq.getCharAt(res) + "</td>");
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163 out.println("<td>" + seq.getCharAt(res) + "</td>");
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167 out.println("</tr>");
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171 out.println("</table>");
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172 out.println("</td></tr></table>");
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175 void drawWrappedAlignment(PrintWriter out)
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177 ////////////////////////////////////
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178 /// How many sequences and residues can we fit on a printable page?
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179 AlignmentI al = av.getAlignment();
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185 out.println("<table border=\"1\"><tr><td>\n");
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187 "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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189 for (int startRes = 0; startRes < al.getWidth();
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190 startRes += av.getWrappedWidth())
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192 int endRes = startRes + av.getWrappedWidth();
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194 if (endRes > al.getWidth())
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196 endRes = al.getWidth();
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199 if (av.getScaleAboveWrapped())
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201 out.println("<tr>");
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203 if (av.getScaleLeftWrapped())
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205 out.println("<td colspan=\"7\"> </td>");
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209 out.println("<td colspan=\"6\"> </td>");
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212 for (int i = startRes + 10; i < endRes; i += 10)
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214 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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217 out.println("</tr>");
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220 int startPos, endPos;
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221 for (int s = 0; s < al.getHeight(); s++)
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223 out.println("<tr>");
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224 seq = al.getSequenceAt(s);
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226 startPos = seq.findPosition(startRes);
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227 endPos = seq.findPosition(endRes) - 1;
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229 String id = seq.getDisplayId(av.getShowJVSuffix());
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231 out.println("<td nowrap>" + id +
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232 " </td>");
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234 if (av.getScaleLeftWrapped())
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236 if (startPos > seq.getEnd() || endPos == 0)
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238 out.println("<td nowrap> </td>");
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242 out.println("<td nowrap>" + startPos +
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243 " </td>");
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247 for (int res = startRes; res < endRes; res++)
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249 if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
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251 color = sr.getResidueBoxColour(seq, res);
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253 color = fr.findFeatureColour(color, seq, res);
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257 color = Color.white;
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260 if (color.getRGB() < -1)
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262 out.println("<td bgcolor=\"#" +
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263 jalview.util.Format.getHexString(color) + "\">" +
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264 seq.getCharAt(res) + "</td>");
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268 out.println("<td>" + seq.getCharAt(res) + "</td>");
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273 if (av.getScaleRightWrapped() &&
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274 endRes < startRes + av.getWrappedWidth())
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276 out.println("<td colspan=\"" +
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277 (startRes + av.getWrappedWidth() - endRes) + "\">"
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278 + " </td>");
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281 if (av.getScaleRightWrapped() && startPos < endPos)
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283 out.println("<td nowrap> " + endPos +
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284 " </td>");
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287 out.println("</tr>");
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290 if (endRes < al.getWidth())
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292 out.println("<tr><td height=\"5\"></td></tr>");
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296 out.println("</table>");
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297 out.println("</table>");
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300 public static String getImageMapHTML()
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305 + "<script language=\"JavaScript\">\n"
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306 + "var ns4 = document.layers;\n"
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307 + "var ns6 = document.getElementById && !document.all;\n"
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308 + "var ie4 = document.all;\n"
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310 + "offsetY = 20;\n"
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311 + "var toolTipSTYLE=\"\";\n"
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312 + "function initToolTips()\n"
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314 + " if(ns4||ns6||ie4)\n"
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316 + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
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317 + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
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318 + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
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319 + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
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322 + " toolTipSTYLE.visibility = \"visible\";\n"
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323 + " toolTipSTYLE.display = \"none\";\n"
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325 + " document.onmousemove = moveToMouseLoc;\n"
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328 + "function toolTip(msg, fg, bg)\n"
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330 + " if(toolTip.arguments.length < 1) // hide\n"
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332 + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
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333 + " else toolTipSTYLE.display = \"none\";\n"
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335 + " else // show\n"
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337 + " if(!fg) fg = \"#555555\";\n"
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338 + " if(!bg) bg = \"#FFFFFF\";\n"
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339 + " var content =\n"
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340 + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
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341 + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
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343 " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
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344 + " '\" size=\"-2\"> ' + msg +\n"
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345 + " ' </font></td></table></td></table>';\n"
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348 + " toolTipSTYLE.document.write(content);\n"
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349 + " toolTipSTYLE.document.close();\n"
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350 + " toolTipSTYLE.visibility = \"visible\";\n"
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355 " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
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356 + " toolTipSTYLE.display='block'\n"
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360 + " document.all(\"toolTipLayer\").innerHTML=content;\n"
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361 + " toolTipSTYLE.display='block'\n"
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365 + "function moveToMouseLoc(e)\n"
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367 + " if(ns4||ns6)\n"
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369 + " x = e.pageX;\n"
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370 + " y = e.pageY;\n"
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374 + " x = event.x + document.body.scrollLeft;\n"
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375 + " y = event.y + document.body.scrollTop;\n"
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377 + " toolTipSTYLE.left = x + offsetX;\n"
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378 + " toolTipSTYLE.top = y + offsetY;\n"
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379 + " return true;\n"
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384 + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
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385 + "<script language=\"JavaScript\"><!--\n"
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386 + "initToolTips(); //--></script>\n");
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