+/*\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.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
+import java.awt.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
+import jalview.schemes.*;\r
\r
public class HTMLOutput\r
{\r
AlignViewport av;\r
SequenceRenderer sr;\r
+ FeatureRenderer fr;\r
Color color;\r
\r
- public HTMLOutput(AlignViewport av)\r
+ public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr)\r
{\r
this.av = av;\r
- sr = new SequenceRenderer(av);\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ this.sr = sr;\r
+ this.fr = fr;\r
+\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"html"},\r
+ new String[]\r
+ {"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
- if(value == JFileChooser.APPROVE_OPTION)\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try{\r
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ try\r
+ {\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()+"\", \""+av.getFont().getName()+ "\", mono; "\r
- +"font-size: "+av.getFont().getSize()+"px; ");\r
-\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
+ out.print("font-weight: BOLD; ");\r
+ }\r
\r
if (av.getFont().getStyle() == Font.ITALIC)\r
- out.print("font-style: italic; ");\r
+ {\r
+ out.print("font-style: italic; ");\r
+ }\r
\r
out.println("text-align: center; }");\r
\r
out.println("</style>");\r
out.println("<BODY>");\r
\r
-\r
- if(av.getWrapAlignment())\r
- drawWrappedAlignment(out);\r
+ if (av.getWrapAlignment())\r
+ {\r
+ drawWrappedAlignment(out);\r
+ }\r
else\r
- drawUnwrappedAlignment(out);\r
+ {\r
+ drawUnwrappedAlignment(out);\r
+ }\r
\r
out.println("\n</body>\n</html>");\r
out.close();\r
- jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
+ jalview.util.BrowserLauncher.openURL("file:///" + choice);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
}\r
- catch(Exception ex){ex.printStackTrace();}\r
}\r
}\r
\r
void drawUnwrappedAlignment(PrintWriter out)\r
{\r
-\r
out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\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,g,b;\r
\r
- // draws the top row, the measure rule\r
+ // draws the top row, the measure rule\r
out.println("<tr><td colspan=\"6\"></td>");\r
- int i=0;\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+"<br>|</td>");\r
+ int i = 0;\r
+\r
+ for (i = 10; i < (alignment.getWidth() - 10); i += 10)\r
+ {\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+ }\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
{\r
seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups( seq );\r
- out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\r
+\r
+ String id = seq.getDisplayId(av.getShowJVSuffix());\r
+\r
+ out.println("<tr><td nowrap>" + id +\r
+ " </td>");\r
\r
\r
for (int res = 0; res < seq.getLength(); res++)\r
{\r
- cs = av.getGlobalColourScheme();\r
-\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
\r
+ color = sr.findSequenceColour(Color.white, seq, res);\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
+ color = fr.findFeatureColour(color, seq, res);\r
\r
- if(color.getRGB()<-1)\r
+ if (color.getRGB() < -1)\r
{\r
- r = Integer.toHexString(color.getRed());\r
- if(r.length()<2)\r
- r = "0"+r;\r
- g = Integer.toHexString(color.getGreen());\r
- if(g.length()<2)\r
- g = "0"+g;\r
- b = Integer.toHexString(color.getBlue());\r
- if(b.length()<2)\r
- b = "0"+b;\r
- out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
+ out.println("<td bgcolor=\"#" +\r
+ jalview.util.Format.getHexString(color) + "\">" +\r
+ seq.getCharAt(res) + "</td>");\r
}\r
else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
-\r
+ {\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
\r
void drawWrappedAlignment(PrintWriter out)\r
{\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,g,b;\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())\r
- {\r
-\r
- int endRes = startRes+av.getChunkWidth();\r
- if(endRes>al.getWidth())\r
- endRes = al.getWidth();\r
-\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\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
-\r
-\r
- for (int s = 0; s < al.getHeight(); s++)\r
- {\r
- out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups( seq );\r
- out.println("<td nowrap>"+seq.getDisplayId()+" </td>");\r
-\r
- for (int res = startRes; res < endRes; res++)\r
- {\r
- cs = av.getGlobalColourScheme();\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if(color.getRGB()<-1)\r
- {\r
- r = Integer.toHexString(color.getRed());\r
- if(r.length()<2)\r
- r = "0"+r;\r
- g = Integer.toHexString(color.getGreen());\r
- if(g.length()<2)\r
- g = "0"+g;\r
- b = Integer.toHexString(color.getBlue());\r
- if(b.length()<2)\r
- b = "0"+b;\r
- out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
- }\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
-\r
- }\r
-\r
- out.println("</tr>");\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ AlignmentI al = av.getAlignment();\r
+ SequenceI seq;\r
+ String r;\r
+ String g;\r
+ String b;\r
\r
- }\r
- if(endRes<al.getWidth())\r
- out.println("<tr><td height=\"5\"></td></tr>");\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.getWrappedWidth())\r
+ {\r
+ int endRes = startRes + av.getWrappedWidth();\r
+\r
+ if (endRes > al.getWidth())\r
+ {\r
+ endRes = al.getWidth();\r
+ }\r
\r
+ if(av.getScaleAboveWrapped())\r
+ {\r
+ out.println("<tr>");\r
\r
+ if (av.getScaleLeftWrapped())\r
+ out.println("<td colspan=\"7\"> </td>");\r
+ else\r
+ out.println("<td colspan=\"6\"> </td>");\r
\r
- }\r
\r
- out.println("</table>");\r
- out.println("</table>");\r
+ for (int i = startRes + 10; i < endRes; i += 10)\r
+ {\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+ }\r
+\r
+ out.println("</tr>");\r
+ }\r
+\r
+ int startPos, endPos;\r
+ for (int s = 0; s < al.getHeight(); s++)\r
+ {\r
+ out.println("<tr>");\r
+ seq = al.getSequenceAt(s);\r
+\r
+ startPos = seq.findPosition( startRes );\r
+ endPos = seq.findPosition( endRes )-1;\r
+\r
+ String id = seq.getDisplayId(av.getShowJVSuffix());\r
+\r
+ out.println("<td nowrap>" + id +\r
+ " </td>");\r
+\r
+\r
+ if(av.getScaleLeftWrapped())\r
+ {\r
+ if(startPos > seq.getEnd() || endPos==0)\r
+ out.println("<td nowrap> </td>");\r
+ else\r
+ out.println("<td nowrap>" + startPos +\r
+ " </td>");\r
+ }\r
+\r
+\r
+ for (int res = startRes; res < endRes; res++)\r
+ {\r
+ color = sr.findSequenceColour(Color.white, seq, res);\r
+\r
+ color = fr.findFeatureColour(color, seq, res);\r
+\r
+ if (color.getRGB() < -1)\r
+ {\r
+ r = Integer.toHexString(color.getRed());\r
+\r
+ if (r.length() < 2)\r
+ {\r
+ r = "0" + r;\r
+ }\r
\r
+ g = Integer.toHexString(color.getGreen());\r
\r
+ if (g.length() < 2)\r
+ {\r
+ g = "0" + g;\r
+ }\r
\r
+ b = Integer.toHexString(color.getBlue());\r
+\r
+ if (b.length() < 2)\r
+ {\r
+ b = "0" + b;\r
+ }\r
+\r
+ out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
+ seq.getCharAt(res) + "</td>");\r
+ }\r
+ else\r
+ {\r
+ out.println("<td>" + seq.getCharAt(res) + "</td>");\r
+ }\r
+\r
+\r
+ }\r
+\r
+ if(av.getScaleRightWrapped() &&\r
+ endRes < startRes + av.getWrappedWidth())\r
+ {\r
+ out.println("<td colspan=\""+ (startRes+av.getWrappedWidth()-endRes) +"\">"\r
+ +" </td>");\r
+ }\r
+\r
+\r
+ if(av.getScaleRightWrapped() && startPos<endPos)\r
+ {\r
+ out.println("<td nowrap> " + endPos +\r
+ " </td>");\r
+ }\r
+\r
+\r
+ out.println("</tr>");\r
+ }\r
+\r
+ if (endRes < al.getWidth())\r
+ {\r
+ out.println("<tr><td height=\"5\"></td></tr>");\r
+ }\r
+ }\r
+\r
+ out.println("</table>");\r
+ out.println("</table>");\r
}\r
\r
+ public static String getImageMapHTML()\r
+ {\r
+ return new String(\r
+ "<html>\n"\r
+ +"<head>\n"\r
+ +"<script language=\"JavaScript\">\n"\r
+ +"var ns4 = document.layers;\n"\r
+ +"var ns6 = document.getElementById && !document.all;\n"\r
+ +"var ie4 = document.all;\n"\r
+ +"offsetX = 0;\n"\r
+ +"offsetY = 20;\n"\r
+ +"var toolTipSTYLE=\"\";\n"\r
+ +"function initToolTips()\n"\r
+ +"{\n"\r
+ +" if(ns4||ns6||ie4)\n"\r
+ +" {\n"\r
+ +" if(ns4) toolTipSTYLE = document.toolTipLayer;\n"\r
+ +" else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"\r
+ +" else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"\r
+ +" if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"\r
+ +" else\n"\r
+ +" {\n"\r
+ +" toolTipSTYLE.visibility = \"visible\";\n"\r
+ +" toolTipSTYLE.display = \"none\";\n"\r
+ +" }\n"\r
+ +" document.onmousemove = moveToMouseLoc;\n"\r
+ +" }\n"\r
+ +"}\n"\r
+ +"function toolTip(msg, fg, bg)\n"\r
+ +"{\n"\r
+ +" if(toolTip.arguments.length < 1) // hide\n"\r
+ +" {\n"\r
+ +" if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"\r
+ +" else toolTipSTYLE.display = \"none\";\n"\r
+ +" }\n"\r
+ +" else // show\n"\r
+ +" {\n"\r
+ +" if(!fg) fg = \"#555555\";\n"\r
+ +" if(!bg) bg = \"#FFFFFF\";\n"\r
+ +" var content =\n"\r
+ +" '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"\r
+ +" '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"\r
+ +" '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"\r
+ +" '\" size=\"-2\"> ' + msg +\n"\r
+ +" ' </font></td></table></td></table>';\n"\r
+ +" if(ns4)\n"\r
+ +" {\n"\r
+ +" toolTipSTYLE.document.write(content);\n"\r
+ +" toolTipSTYLE.document.close();\n"\r
+ +" toolTipSTYLE.visibility = \"visible\";\n"\r
+ +" }\n"\r
+ +" if(ns6)\n"\r
+ +" {\n"\r
+ +" document.getElementById(\"toolTipLayer\").innerHTML = content;\n"\r
+ +" toolTipSTYLE.display='block'\n"\r
+ +" }\n"\r
+ +" if(ie4)\n"\r
+ +" {\n"\r
+ +" document.all(\"toolTipLayer\").innerHTML=content;\n"\r
+ +" toolTipSTYLE.display='block'\n"\r
+ +" }\n"\r
+ +" }\n"\r
+ +"}\n"\r
+ +"function moveToMouseLoc(e)\n"\r
+ +"{\n"\r
+ +" if(ns4||ns6)\n"\r
+ +" {\n"\r
+ +" x = e.pageX;\n"\r
+ +" y = e.pageY;\n"\r
+ +" }\n"\r
+ +" else\n"\r
+ +" {\n"\r
+ +" x = event.x + document.body.scrollLeft;\n"\r
+ +" y = event.y + document.body.scrollTop;\n"\r
+ +" }\n"\r
+ +" toolTipSTYLE.left = x + offsetX;\n"\r
+ +" toolTipSTYLE.top = y + offsetY;\n"\r
+ +" return true;\n"\r
+ +"}\n"\r
+ +"</script>\n"\r
+ +"</head>\n"\r
+ +"<body>\n"\r
+ +"<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"\r
+ +"<script language=\"JavaScript\"><!--\n"\r
+ +"initToolTips(); //--></script>\n");\r
\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff