2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.SequenceI;
26 import jalview.gui.AlignViewport;
27 import jalview.gui.AlignmentPanel;
28 import jalview.gui.FeatureRenderer;
29 import jalview.gui.SequenceRenderer;
30 import jalview.util.BrowserLauncher;
31 import jalview.util.Comparison;
32 import jalview.util.Format;
33 import jalview.util.MessageManager;
35 import java.awt.Color;
37 import java.io.PrintWriter;
39 public class HTMLOutput
45 jalview.renderer.seqfeatures.FeatureRenderer fr;
49 public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
55 fr = new FeatureRenderer(ap);
56 fr.transferSettings(fr1);
58 JalviewFileChooser chooser = new JalviewFileChooser(
59 Cache.getProperty("LAST_DIRECTORY"), new String[]
60 { "html" }, new String[]
61 { "HTML files" }, "HTML files");
63 chooser.setFileView(new JalviewFileView());
64 chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
65 chooser.setToolTipText(MessageManager.getString("action.save"));
67 int value = chooser.showSaveDialog(null);
69 if (value == JalviewFileChooser.APPROVE_OPTION)
71 String choice = chooser.getSelectedFile().getPath();
72 Cache.setProperty("LAST_DIRECTORY", chooser
73 .getSelectedFile().getParent());
77 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
79 out.println("<HTML>");
80 out.println("<style type=\"text/css\">");
82 out.print("td {font-family: \"" + av.getFont().getFamily()
83 + "\", \"" + av.getFont().getName() + "\", mono; "
84 + "font-size: " + av.getFont().getSize() + "px; ");
86 if (av.getFont().getStyle() == Font.BOLD)
88 out.print("font-weight: BOLD; ");
91 if (av.getFont().getStyle() == Font.ITALIC)
93 out.print("font-style: italic; ");
96 out.println("text-align: center; }");
99 out.println("</style>");
100 out.println("<BODY>");
102 if (av.getWrapAlignment())
104 drawWrappedAlignment(out);
108 drawUnwrappedAlignment(out);
111 out.println("\n</body>\n</html>");
113 BrowserLauncher.openURL("file:///" + choice);
114 } catch (Exception ex)
116 ex.printStackTrace();
121 void drawUnwrappedAlignment(PrintWriter out)
123 out.println("<table border=\"1\"><tr><td>\n");
124 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
128 AlignmentI alignment = av.getAlignment();
130 // draws the top row, the measure rule
131 out.println("<tr><td colspan=\"6\"></td>");
135 for (i = 10; i < (alignment.getWidth() - 10); i += 10)
137 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
140 out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
142 out.println("</tr>");
144 for (i = 0; i < alignment.getHeight(); i++)
146 seq = alignment.getSequenceAt(i);
148 String id = seq.getDisplayId(av.getShowJVSuffix());
150 out.println("<tr><td nowrap>" + id + " </td>");
152 for (int res = 0; res < seq.getLength(); res++)
154 if (!Comparison.isGap(seq.getCharAt(res)))
156 color = sr.getResidueBoxColour(seq, res);
158 color = fr.findFeatureColour(color, seq, res);
165 if (color.getRGB() < -1)
167 out.println("<td bgcolor=\"#" + Format.getHexString(color)
168 + "\">" + seq.getCharAt(res) + "</td>");
172 out.println("<td>" + seq.getCharAt(res) + "</td>");
176 out.println("</tr>");
180 out.println("</table>");
181 out.println("</td></tr></table>");
184 void drawWrappedAlignment(PrintWriter out)
186 // //////////////////////////////////
187 // / How many sequences and residues can we fit on a printable page?
188 AlignmentI al = av.getAlignment();
194 out.println("<table border=\"1\"><tr><td>\n");
195 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
197 for (int startRes = 0; startRes < al.getWidth(); startRes += av
200 int endRes = startRes + av.getWrappedWidth();
202 if (endRes > al.getWidth())
204 endRes = al.getWidth();
207 if (av.getScaleAboveWrapped())
211 if (av.getScaleLeftWrapped())
213 out.println("<td colspan=\"7\"> </td>");
217 out.println("<td colspan=\"6\"> </td>");
220 for (int i = startRes + 10; i < endRes; i += 10)
222 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
225 out.println("</tr>");
228 int startPos, endPos;
229 for (int s = 0; s < al.getHeight(); s++)
232 seq = al.getSequenceAt(s);
234 startPos = seq.findPosition(startRes);
235 endPos = seq.findPosition(endRes) - 1;
237 String id = seq.getDisplayId(av.getShowJVSuffix());
239 out.println("<td nowrap>" + id + " </td>");
241 if (av.getScaleLeftWrapped())
243 if (startPos > seq.getEnd() || endPos == 0)
245 out.println("<td nowrap> </td>");
249 out.println("<td nowrap>" + startPos + " </td>");
253 for (int res = startRes; res < endRes; res++)
255 if (!Comparison.isGap(seq.getCharAt(res)))
257 color = sr.getResidueBoxColour(seq, res);
259 color = fr.findFeatureColour(color, seq, res);
266 if (color.getRGB() < -1)
268 out.println("<td bgcolor=\"#" + Format.getHexString(color)
269 + "\">" + seq.getCharAt(res) + "</td>");
273 out.println("<td>" + seq.getCharAt(res) + "</td>");
278 if (av.getScaleRightWrapped()
279 && endRes < startRes + av.getWrappedWidth())
281 out.println("<td colspan=\""
282 + (startRes + av.getWrappedWidth() - endRes) + "\">"
283 + " </td>");
286 if (av.getScaleRightWrapped() && startPos < endPos)
288 out.println("<td nowrap> " + endPos + " </td>");
291 out.println("</tr>");
294 if (endRes < al.getWidth())
296 out.println("<tr><td height=\"5\"></td></tr>");
300 out.println("</table>");
301 out.println("</table>");
304 public static String getImageMapHTML()
309 + "<script language=\"JavaScript\">\n"
310 + "var ns4 = document.layers;\n"
311 + "var ns6 = document.getElementById && !document.all;\n"
312 + "var ie4 = document.all;\n"
315 + "var toolTipSTYLE=\"\";\n"
316 + "function initToolTips()\n"
318 + " if(ns4||ns6||ie4)\n"
320 + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
321 + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
322 + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
323 + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
326 + " toolTipSTYLE.visibility = \"visible\";\n"
327 + " toolTipSTYLE.display = \"none\";\n"
329 + " document.onmousemove = moveToMouseLoc;\n"
332 + "function toolTip(msg, fg, bg)\n"
334 + " if(toolTip.arguments.length < 1) // hide\n"
336 + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
337 + " else toolTipSTYLE.display = \"none\";\n"
341 + " if(!fg) fg = \"#555555\";\n"
342 + " if(!bg) bg = \"#FFFFFF\";\n"
344 + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
345 + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
346 + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
347 + " '\" size=\"-2\"> ' + msg +\n"
348 + " ' </font></td></table></td></table>';\n"
351 + " toolTipSTYLE.document.write(content);\n"
352 + " toolTipSTYLE.document.close();\n"
353 + " toolTipSTYLE.visibility = \"visible\";\n"
357 + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
358 + " toolTipSTYLE.display='block'\n"
362 + " document.all(\"toolTipLayer\").innerHTML=content;\n"
363 + " toolTipSTYLE.display='block'\n"
367 + "function moveToMouseLoc(e)\n"
376 + " x = event.x + document.body.scrollLeft;\n"
377 + " y = event.y + document.body.scrollTop;\n"
379 + " toolTipSTYLE.left = x + offsetX;\n"
380 + " toolTipSTYLE.top = y + offsetY;\n"
386 + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
387 + "<script language=\"JavaScript\"><!--\n"
388 + "initToolTips(); //--></script>\n");