2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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27 import jalview.schemes.*;
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29 public class HTMLOutput
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32 SequenceRenderer sr;
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35 public HTMLOutput(AlignViewport av)
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38 sr = new SequenceRenderer(av);
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40 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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42 "LAST_DIRECTORY"), new String[]
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45 {"HTML files"}, "HTML files");
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47 chooser.setFileView(new JalviewFileView());
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48 chooser.setDialogTitle("Save as HTML");
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49 chooser.setToolTipText("Save");
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51 int value = chooser.showSaveDialog(null);
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53 if (value == JalviewFileChooser.APPROVE_OPTION)
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55 String choice = chooser.getSelectedFile().getPath();
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56 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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57 chooser.getSelectedFile().getParent());
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61 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
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63 out.println("<HTML>");
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64 out.println("<style type=\"text/css\">");
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65 out.println("<!--");
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66 out.print("td {font-family: \"" + av.getFont().getFamily() +
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67 "\", \"" + av.getFont().getName() + "\", mono; " +
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68 "font-size: " + av.getFont().getSize() + "px; ");
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70 if (av.getFont().getStyle() == Font.BOLD)
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72 out.print("font-weight: BOLD; ");
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75 if (av.getFont().getStyle() == Font.ITALIC)
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77 out.print("font-style: italic; ");
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80 out.println("text-align: center; }");
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83 out.println("</style>");
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84 out.println("<BODY>");
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86 if (av.getWrapAlignment())
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88 drawWrappedAlignment(out);
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92 drawUnwrappedAlignment(out);
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95 out.println("\n</body>\n</html>");
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97 jalview.util.BrowserLauncher.openURL("file:///" + choice);
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99 catch (Exception ex)
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101 ex.printStackTrace();
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106 void drawUnwrappedAlignment(PrintWriter out)
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108 out.println("<table border=\"1\"><tr><td>\n");
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110 "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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113 SequenceGroup[] groups;
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115 ColourSchemeI cs = null;
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116 AlignmentI alignment = av.getAlignment();
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121 // draws the top row, the measure rule
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122 out.println("<tr><td colspan=\"6\"></td>");
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126 for (i = 10; i < (alignment.getWidth() - 10); i += 10)
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128 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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131 out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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133 out.println("</tr>");
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135 for (i = 0; i < alignment.getHeight(); i++)
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137 seq = alignment.getSequenceAt(i);
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138 groups = alignment.findAllGroups(seq);
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140 if (av.getShowFullId())
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142 out.println("<tr><td nowrap>" + seq.getDisplayId() +
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143 " </td>");
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147 out.println("<tr><td nowrap>" + seq.getName() +
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148 " </td>");
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151 for (int res = 0; res < seq.getLength(); res++)
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153 cs = av.getGlobalColourScheme();
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155 if (groups != null)
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157 for (int k = 0; k < groups.length; k++)
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159 if ( (groups[k].getStartRes() <= res) &&
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160 (groups[k].getEndRes() >= res))
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169 color = sr.getResidueBoxColour(cs, seq, res);
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171 if (color.getRGB() < -1)
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173 out.println("<td bgcolor=\"#" +
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174 jalview.util.Format.getHexString(color) + "\">" +
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175 seq.getCharAt(res) + "</td>");
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179 out.println("<td>" + seq.getCharAt(res) + "</td>");
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183 out.println("</tr>");
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187 out.println("</table>");
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188 out.println("</td></tr></table>");
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191 void drawWrappedAlignment(PrintWriter out)
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193 ////////////////////////////////////
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194 /// How many sequences and residues can we fit on a printable page?
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195 AlignmentI al = av.getAlignment();
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196 SequenceGroup[] groups;
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198 ColourSchemeI cs = null;
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203 out.println("<table border=\"1\"><tr><td>\n");
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205 "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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207 for (int startRes = 0; startRes < al.getWidth();
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208 startRes += av.getWrappedWidth())
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210 int endRes = startRes + av.getWrappedWidth();
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212 if (endRes > al.getWidth())
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214 endRes = al.getWidth();
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217 out.println("<tr>");
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218 out.println("<td colspan=\"6\"> </td>");
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220 for (int i = startRes + 10; i < endRes; i += 10)
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222 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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225 // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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227 out.println("</tr>");
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229 for (int s = 0; s < al.getHeight(); s++)
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231 out.println("<tr>");
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232 seq = al.getSequenceAt(s);
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233 groups = al.findAllGroups(seq);
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235 if (av.getShowFullId())
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237 out.println("<td nowrap>" + seq.getDisplayId() +
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238 " </td>");
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242 out.println("<td nowrap>" + seq.getName() +
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243 " </td>");
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246 for (int res = startRes; res < endRes; res++)
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248 cs = av.getGlobalColourScheme();
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250 if (groups != null)
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252 for (int k = 0; k < groups.length; k++)
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254 if ( (groups[k].getStartRes() <= res) &&
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255 (groups[k].getEndRes() >= res))
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264 color = sr.getResidueBoxColour(cs, seq, res);
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266 if (color.getRGB() < -1)
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268 r = Integer.toHexString(color.getRed());
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270 if (r.length() < 2)
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275 g = Integer.toHexString(color.getGreen());
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277 if (g.length() < 2)
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282 b = Integer.toHexString(color.getBlue());
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284 if (b.length() < 2)
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289 out.println("<td bgcolor=\"#" + r + g + b + "\">" +
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290 seq.getCharAt(res) + "</td>");
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294 out.println("<td>" + seq.getCharAt(res) + "</td>");
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298 out.println("</tr>");
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301 if (endRes < al.getWidth())
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303 out.println("<tr><td height=\"5\"></td></tr>");
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307 out.println("</table>");
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308 out.println("</table>");
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311 public static String getImageMapHTML()
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316 +"<script language=\"JavaScript\">\n"
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317 +"var ns4 = document.layers;\n"
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318 +"var ns6 = document.getElementById && !document.all;\n"
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319 +"var ie4 = document.all;\n"
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322 +"var toolTipSTYLE=\"\";\n"
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323 +"function initToolTips()\n"
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325 +" if(ns4||ns6||ie4)\n"
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327 +" if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
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328 +" else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
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329 +" else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
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330 +" if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
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333 +" toolTipSTYLE.visibility = \"visible\";\n"
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334 +" toolTipSTYLE.display = \"none\";\n"
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336 +" document.onmousemove = moveToMouseLoc;\n"
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339 +"function toolTip(msg, fg, bg)\n"
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341 +" if(toolTip.arguments.length < 1) // hide\n"
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343 +" if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
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344 +" else toolTipSTYLE.display = \"none\";\n"
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348 +" if(!fg) fg = \"#555555\";\n"
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349 +" if(!bg) bg = \"#FFFFFF\";\n"
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350 +" var content =\n"
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351 +" '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
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352 +" '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
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353 +" '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
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354 +" '\" size=\"-2\"> ' + msg +\n"
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355 +" ' </font></td></table></td></table>';\n"
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358 +" toolTipSTYLE.document.write(content);\n"
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359 +" toolTipSTYLE.document.close();\n"
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360 +" toolTipSTYLE.visibility = \"visible\";\n"
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364 +" document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
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365 +" toolTipSTYLE.display='block'\n"
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369 +" document.all(\"toolTipLayer\").innerHTML=content;\n"
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370 +" toolTipSTYLE.display='block'\n"
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374 +"function moveToMouseLoc(e)\n"
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383 +" x = event.x + document.body.scrollLeft;\n"
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384 +" y = event.y + document.body.scrollTop;\n"
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386 +" toolTipSTYLE.left = x + offsetX;\n"
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387 +" toolTipSTYLE.top = y + offsetY;\n"
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393 +"<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
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394 +"<script language=\"JavaScript\"><!--\n"
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395 +"initToolTips(); //--></script>\n");
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