-package jalview.io;\r
-\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-\r
-public class HTMLOutput\r
-{\r
- SequenceRenderer sr = new SequenceRenderer();\r
-\r
- public HTMLOutput(AlignmentI alignment, ColourSchemeI cs)\r
- {\r
- Color color;\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Save as HTML");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(null);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
- try{\r
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
- out.println("<HTML>");\r
- out.println("<style type=\"text/css\">");\r
- out.println("<!--");\r
- out.println("td {font-family: \"Courier New\", Courier, mono; font-size: medium;}");\r
- out.println("-->");\r
- out.println("</style>");\r
- out.println("<BODY>");\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
-\r
- //////////////\r
- for (int i = 0; i < alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = alignment.getSequenceAt(i);\r
- out.println("<tr><td>"+seq.getName()+" </td>");\r
- for (int res = 0; res < seq.getLength(); res++)\r
- {\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
- Integer.toHexString(color.getRed());\r
-\r
- out.println("<td bgcolor=\"#"\r
- + Integer.toHexString(color.getRed())\r
- + Integer.toHexString(color.getGreen())\r
- + Integer.toHexString(color.getBlue())\r
- +"\"><center>"+seq.getCharAt(res)+"</center></td>");\r
- }\r
-\r
- out.println("</tr>");\r
- }\r
- //////////////\r
- out.println("</td></tr></table>");\r
- out.println("</table>\n</body>\n</html>");\r
-\r
- out.close();\r
- }\r
- catch(Exception ex){}\r
- }\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public class HTMLOutput
+{
+ AlignViewport av;
+ SequenceRenderer sr;
+ FeatureRenderer fr;
+ Color color;
+
+ public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr1)
+ {
+ this.av = av;
+ this.sr = sr;
+
+ fr = new FeatureRenderer(av);
+ 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("Save as HTML");
+ chooser.setToolTipText("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)
+ {
+ r = Integer.toHexString(color.getRed());
+
+ if (r.length() < 2)
+ {
+ r = "0" + r;
+ }
+
+ g = Integer.toHexString(color.getGreen());
+
+ if (g.length() < 2)
+ {
+ g = "0" + g;
+ }
+
+ b = Integer.toHexString(color.getBlue());
+
+ if (b.length() < 2)
+ {
+ b = "0" + b;
+ }
+
+ out.println("<td bgcolor=\"#" + r + g + b + "\">" +
+ 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