-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-public class HTMLOutput {\r
- AlignViewport av;\r
- SequenceRenderer sr;\r
- Color color;\r
-\r
- public HTMLOutput(AlignViewport av) {\r
- this.av = av;\r
- sr = new SequenceRenderer(av);\r
-\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "html" },\r
- new String[] { "HTML files" }, "HTML files");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save as HTML");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(null);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION) {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- try {\r
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
- choice));\r
- out.println("<HTML>");\r
- out.println("<style type=\"text/css\">");\r
- out.println("<!--");\r
- out.print("td {font-family: \"" + av.getFont().getFamily() +\r
- "\", \"" + av.getFont().getName() + "\", mono; " +\r
- "font-size: " + av.getFont().getSize() + "px; ");\r
-\r
- if (av.getFont().getStyle() == Font.BOLD) {\r
- out.print("font-weight: BOLD; ");\r
- }\r
-\r
- if (av.getFont().getStyle() == Font.ITALIC) {\r
- out.print("font-style: italic; ");\r
- }\r
-\r
- out.println("text-align: center; }");\r
-\r
- out.println("-->");\r
- out.println("</style>");\r
- out.println("<BODY>");\r
-\r
- if (av.getWrapAlignment()) {\r
- drawWrappedAlignment(out);\r
- } else {\r
- drawUnwrappedAlignment(out);\r
- }\r
-\r
- out.println("\n</body>\n</html>");\r
- out.close();\r
- jalview.util.BrowserLauncher.openURL("file:///" + choice);\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- void drawUnwrappedAlignment(PrintWriter out) {\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println(\r
- "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- //////////////\r
- SequenceGroup[] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- AlignmentI alignment = av.getAlignment();\r
- String r;\r
- String g;\r
- String b;\r
-\r
- // draws the top row, the measure rule\r
- out.println("<tr><td colspan=\"6\"></td>");\r
-\r
- int i = 0;\r
-\r
- for (i = 10; i < (alignment.getWidth() - 10); i += 10)\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-\r
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- "<br>|</td>");\r
- out.println("</tr>");\r
-\r
- for (i = 0; i < alignment.getHeight(); i++) {\r
- seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups(seq);\r
-\r
- if (av.getShowFullId()) {\r
- out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
- " </td>");\r
- } else {\r
- out.println("<tr><td nowrap>" + seq.getName() +\r
- " </td>");\r
- }\r
-\r
- for (int res = 0; res < seq.getLength(); res++) {\r
- cs = av.getGlobalColourScheme();\r
-\r
- if (groups != null) {\r
- for (int k = 0; k < groups.length; k++)\r
- if ((groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res)) {\r
- cs = groups[k].cs;\r
-\r
- break;\r
- }\r
- }\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if (color.getRGB() < -1) {\r
- out.println("<td bgcolor=\"#" +\r
- jalview.util.Format.getHexString(color) + "\">" +\r
- seq.getCharAt(res) + "</td>");\r
- } else {\r
- out.println("<td>" + seq.getCharAt(res) + "</td>");\r
- }\r
- }\r
-\r
- out.println("</tr>");\r
- }\r
-\r
- //////////////\r
- out.println("</table>");\r
- out.println("</td></tr></table>");\r
- }\r
-\r
- void drawWrappedAlignment(PrintWriter out) {\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- AlignmentI al = av.getAlignment();\r
- SequenceGroup[] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- String r;\r
- String g;\r
- String b;\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println(\r
- "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- for (int startRes = 0; startRes < al.getWidth();\r
- startRes += av.getChunkWidth()) {\r
- int endRes = startRes + av.getChunkWidth();\r
-\r
- if (endRes > al.getWidth()) {\r
- endRes = al.getWidth();\r
- }\r
-\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\r
-\r
- for (int i = startRes + 10; i < endRes; i += 10)\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- // "<br>|</td>");\r
- out.println("</tr>");\r
-\r
- for (int s = 0; s < al.getHeight(); s++) {\r
- out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups(seq);\r
-\r
- if (av.getShowFullId()) {\r
- out.println("<td nowrap>" + seq.getDisplayId() +\r
- " </td>");\r
- } else {\r
- out.println("<td nowrap>" + seq.getName() +\r
- " </td>");\r
- }\r
-\r
- for (int res = startRes; res < endRes; res++) {\r
- cs = av.getGlobalColourScheme();\r
-\r
- if (groups != null) {\r
- for (int k = 0; k < groups.length; k++)\r
- if ((groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res)) {\r
- cs = groups[k].cs;\r
-\r
- break;\r
- }\r
- }\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if (color.getRGB() < -1) {\r
- r = Integer.toHexString(color.getRed());\r
-\r
- if (r.length() < 2) {\r
- r = "0" + r;\r
- }\r
-\r
- g = Integer.toHexString(color.getGreen());\r
-\r
- if (g.length() < 2) {\r
- g = "0" + g;\r
- }\r
-\r
- b = Integer.toHexString(color.getBlue());\r
-\r
- if (b.length() < 2) {\r
- b = "0" + b;\r
- }\r
-\r
- out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
- seq.getCharAt(res) + "</td>");\r
- } else {\r
- out.println("<td>" + seq.getCharAt(res) + "</td>");\r
- }\r
- }\r
-\r
- out.println("</tr>");\r
- }\r
-\r
- if (endRes < al.getWidth()) {\r
- out.println("<tr><td height=\"5\"></td></tr>");\r
- }\r
- }\r
-\r
- out.println("</table>");\r
- out.println("</table>");\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.PrintWriter;
+
+public class HTMLOutput
+{
+ AlignViewport av;
+
+ SequenceRenderer sr;
+
+ jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+ Color color;
+
+ public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+ FeatureRenderer fr1)
+ {
+ this.av = ap.av;
+ this.sr = sr;
+
+ fr = new FeatureRenderer(ap);
+ fr.transferSettings(fr1);
+
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
+
+ try
+ {
+ PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+ choice));
+ out.println("<HTML>");
+ out.println("<style type=\"text/css\">");
+ out.println("<!--");
+ out.print("td {font-family: \"" + av.getFont().getFamily()
+ + "\", \"" + av.getFont().getName() + "\", mono; "
+ + "font-size: " + av.getFont().getSize() + "px; ");
+
+ if (av.getFont().getStyle() == Font.BOLD)
+ {
+ out.print("font-weight: BOLD; ");
+ }
+
+ if (av.getFont().getStyle() == Font.ITALIC)
+ {
+ out.print("font-style: italic; ");
+ }
+
+ out.println("text-align: center; }");
+
+ out.println("-->");
+ out.println("</style>");
+ out.println("<BODY>");
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedAlignment(out);
+ }
+ else
+ {
+ drawUnwrappedAlignment(out);
+ }
+
+ out.println("\n</body>\n</html>");
+ out.close();
+ jalview.util.BrowserLauncher.openURL("file:///" + choice);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ void drawUnwrappedAlignment(PrintWriter out)
+ {
+ out.println("<table border=\"1\"><tr><td>\n");
+ out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
+
+ // ////////////
+ SequenceI seq;
+ AlignmentI alignment = av.getAlignment();
+
+ // draws the top row, the measure rule
+ out.println("<tr><td colspan=\"6\"></td>");
+
+ int i = 0;
+
+ for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+ {
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+ }
+
+ out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
+ + "<br>|</td>");
+ out.println("</tr>");
+
+ for (i = 0; i < alignment.getHeight(); i++)
+ {
+ seq = alignment.getSequenceAt(i);
+
+ String id = seq.getDisplayId(av.getShowJVSuffix());
+
+ out.println("<tr><td nowrap>" + id + " </td>");
+
+ for (int res = 0; res < seq.getLength(); res++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+ {
+ color = sr.getResidueBoxColour(seq, res);
+
+ color = fr.findFeatureColour(color, seq, res);
+ }
+ else
+ {
+ color = Color.white;
+ }
+
+ if (color.getRGB() < -1)
+ {
+ out.println("<td bgcolor=\"#"
+ + jalview.util.Format.getHexString(color) + "\">"
+ + seq.getCharAt(res) + "</td>");
+ }
+ else
+ {
+ out.println("<td>" + seq.getCharAt(res) + "</td>");
+ }
+ }
+
+ out.println("</tr>");
+ }
+
+ // ////////////
+ out.println("</table>");
+ out.println("</td></tr></table>");
+ }
+
+ void drawWrappedAlignment(PrintWriter out)
+ {
+ // //////////////////////////////////
+ // / How many sequences and residues can we fit on a printable page?
+ AlignmentI al = av.getAlignment();
+ SequenceI seq;
+ String r;
+ String g;
+ String b;
+
+ out.println("<table border=\"1\"><tr><td>\n");
+ out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
+
+ for (int startRes = 0; startRes < al.getWidth(); startRes += av
+ .getWrappedWidth())
+ {
+ int endRes = startRes + av.getWrappedWidth();
+
+ if (endRes > al.getWidth())
+ {
+ endRes = al.getWidth();
+ }
+
+ if (av.getScaleAboveWrapped())
+ {
+ out.println("<tr>");
+
+ if (av.getScaleLeftWrapped())
+ {
+ out.println("<td colspan=\"7\"> </td>");
+ }
+ else
+ {
+ out.println("<td colspan=\"6\"> </td>");
+ }
+
+ for (int i = startRes + 10; i < endRes; i += 10)
+ {
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+ }
+
+ out.println("</tr>");
+ }
+
+ int startPos, endPos;
+ for (int s = 0; s < al.getHeight(); s++)
+ {
+ out.println("<tr>");
+ seq = al.getSequenceAt(s);
+
+ startPos = seq.findPosition(startRes);
+ endPos = seq.findPosition(endRes) - 1;
+
+ String id = seq.getDisplayId(av.getShowJVSuffix());
+
+ out.println("<td nowrap>" + id + " </td>");
+
+ if (av.getScaleLeftWrapped())
+ {
+ if (startPos > seq.getEnd() || endPos == 0)
+ {
+ out.println("<td nowrap> </td>");
+ }
+ else
+ {
+ out.println("<td nowrap>" + startPos + " </td>");
+ }
+ }
+
+ for (int res = startRes; res < endRes; res++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+ {
+ color = sr.getResidueBoxColour(seq, res);
+
+ color = fr.findFeatureColour(color, seq, res);
+ }
+ else
+ {
+ color = Color.white;
+ }
+
+ if (color.getRGB() < -1)
+ {
+ out.println("<td bgcolor=\"#"
+ + jalview.util.Format.getHexString(color) + "\">"
+ + seq.getCharAt(res) + "</td>");
+ }
+ else
+ {
+ out.println("<td>" + seq.getCharAt(res) + "</td>");
+ }
+
+ }
+
+ if (av.getScaleRightWrapped()
+ && endRes < startRes + av.getWrappedWidth())
+ {
+ out.println("<td colspan=\""
+ + (startRes + av.getWrappedWidth() - endRes) + "\">"
+ + " </td>");
+ }
+
+ if (av.getScaleRightWrapped() && startPos < endPos)
+ {
+ out.println("<td nowrap> " + endPos + " </td>");
+ }
+
+ out.println("</tr>");
+ }
+
+ if (endRes < al.getWidth())
+ {
+ out.println("<tr><td height=\"5\"></td></tr>");
+ }
+ }
+
+ out.println("</table>");
+ out.println("</table>");
+ }
+
+ public static String getImageMapHTML()
+ {
+ return new String(
+ "<html>\n"
+ + "<head>\n"
+ + "<script language=\"JavaScript\">\n"
+ + "var ns4 = document.layers;\n"
+ + "var ns6 = document.getElementById && !document.all;\n"
+ + "var ie4 = document.all;\n"
+ + "offsetX = 0;\n"
+ + "offsetY = 20;\n"
+ + "var toolTipSTYLE=\"\";\n"
+ + "function initToolTips()\n"
+ + "{\n"
+ + " if(ns4||ns6||ie4)\n"
+ + " {\n"
+ + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+ + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+ + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+ + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+ + " else\n"
+ + " {\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n"
+ + " toolTipSTYLE.display = \"none\";\n"
+ + " }\n"
+ + " document.onmousemove = moveToMouseLoc;\n"
+ + " }\n"
+ + "}\n"
+ + "function toolTip(msg, fg, bg)\n"
+ + "{\n"
+ + " if(toolTip.arguments.length < 1) // hide\n"
+ + " {\n"
+ + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+ + " else toolTipSTYLE.display = \"none\";\n"
+ + " }\n"
+ + " else // show\n"
+ + " {\n"
+ + " if(!fg) fg = \"#555555\";\n"
+ + " if(!bg) bg = \"#FFFFFF\";\n"
+ + " var content =\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+ + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+ + " '\" size=\"-2\"> ' + msg +\n"
+ + " ' </font></td></table></td></table>';\n"
+ + " if(ns4)\n"
+ + " {\n"
+ + " toolTipSTYLE.document.write(content);\n"
+ + " toolTipSTYLE.document.close();\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n"
+ + " }\n"
+ + " if(ns6)\n"
+ + " {\n"
+ + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+ + " toolTipSTYLE.display='block'\n"
+ + " }\n"
+ + " if(ie4)\n"
+ + " {\n"
+ + " document.all(\"toolTipLayer\").innerHTML=content;\n"
+ + " toolTipSTYLE.display='block'\n"
+ + " }\n"
+ + " }\n"
+ + "}\n"
+ + "function moveToMouseLoc(e)\n"
+ + "{\n"
+ + " if(ns4||ns6)\n"
+ + " {\n"
+ + " x = e.pageX;\n"
+ + " y = e.pageY;\n"
+ + " }\n"
+ + " else\n"
+ + " {\n"
+ + " x = event.x + document.body.scrollLeft;\n"
+ + " y = event.y + document.body.scrollTop;\n"
+ + " }\n"
+ + " toolTipSTYLE.left = x + offsetX;\n"
+ + " toolTipSTYLE.top = y + offsetY;\n"
+ + " return true;\n"
+ + "}\n"
+ + "</script>\n"
+ + "</head>\n"
+ + "<body>\n"
+ + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+ + "<script language=\"JavaScript\"><!--\n"
+ + "initToolTips(); //--></script>\n");
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff