/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
\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(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)\r
{\r
- this.av = av;\r
- sr = new SequenceRenderer(av);\r
+ this.av = ap.av;\r
+ this.sr = sr;\r
+\r
+ fr = new FeatureRenderer(ap);\r
+ fr.transferSettings(fr1);\r
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
getProperty(\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
for (i = 0; i < alignment.getHeight(); i++)\r
{\r
seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups(seq);\r
\r
- if (av.getShowFullId())\r
- {\r
- out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
- " </td>");\r
- }\r
- else\r
- {\r
- out.println("<tr><td nowrap>" + seq.getName() +\r
- " </td>");\r
- }\r
+ String id = seq.getDisplayId(av.getShowJVSuffix());\r
+\r
+ out.println("<tr><td nowrap>" + id +\r
+ " </td>");\r
\r
for (int res = 0; res < seq.getLength(); res++)\r
{\r
- cs = av.getGlobalColourScheme();\r
-\r
- if (groups != null)\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))\r
{\r
- for (int k = 0; k < groups.length; k++)\r
- {\r
- if ( (groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res))\r
- {\r
- cs = groups[k].cs;\r
+ color = sr.getResidueBoxColour(seq, res);\r
\r
- break;\r
- }\r
- }\r
+ color = fr.findFeatureColour(color, seq, res);\r
+ }\r
+ else\r
+ {\r
+ color = Color.white;\r
}\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
\r
if (color.getRGB() < -1)\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;\r
String g;\r
String b;\r
"<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
\r
for (int startRes = 0; startRes < al.getWidth();\r
- startRes += av.getChunkWidth())\r
+ startRes += av.getWrappedWidth())\r
{\r
- int endRes = startRes + av.getChunkWidth();\r
+ int endRes = startRes + av.getWrappedWidth();\r
\r
if (endRes > al.getWidth())\r
{\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
- {\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 (int s = 0; s < al.getHeight(); s++)\r
+ if (av.getScaleAboveWrapped())\r
{\r
out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups(seq);\r
\r
- if (av.getShowFullId())\r
+ if (av.getScaleLeftWrapped())\r
{\r
- out.println("<td nowrap>" + seq.getDisplayId() +\r
- " </td>");\r
+ out.println("<td colspan=\"7\"> </td>");\r
}\r
else\r
{\r
- out.println("<td nowrap>" + seq.getName() +\r
- " </td>");\r
+ out.println("<td colspan=\"6\"> </td>");\r
}\r
\r
- for (int res = startRes; res < endRes; res++)\r
+ for (int i = startRes + 10; i < endRes; i += 10)\r
{\r
- cs = av.getGlobalColourScheme();\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+ }\r
\r
- if (groups != null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- {\r
- if ( (groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res))\r
- {\r
- cs = groups[k].cs;\r
-\r
- break;\r
- }\r
- }\r
- }\r
+ out.println("</tr>");\r
+ }\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);\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
- if (color.getRGB() < -1)\r
- {\r
- r = Integer.toHexString(color.getRed());\r
+ startPos = seq.findPosition(startRes);\r
+ endPos = seq.findPosition(endRes) - 1;\r
\r
- if (r.length() < 2)\r
- {\r
- r = "0" + r;\r
- }\r
+ String id = seq.getDisplayId(av.getShowJVSuffix());\r
\r
- g = Integer.toHexString(color.getGreen());\r
+ out.println("<td nowrap>" + id +\r
+ " </td>");\r
\r
- if (g.length() < 2)\r
- {\r
- g = "0" + g;\r
- }\r
+ if (av.getScaleLeftWrapped())\r
+ {\r
+ if (startPos > seq.getEnd() || endPos == 0)\r
+ {\r
+ out.println("<td nowrap> </td>");\r
+ }\r
+ else\r
+ {\r
+ out.println("<td nowrap>" + startPos +\r
+ " </td>");\r
+ }\r
+ }\r
\r
- b = Integer.toHexString(color.getBlue());\r
+ for (int res = startRes; res < endRes; res++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))\r
+ {\r
+ color = sr.getResidueBoxColour(seq, res);\r
\r
- if (b.length() < 2)\r
- {\r
- b = "0" + b;\r
- }\r
+ color = fr.findFeatureColour(color, seq, res);\r
+ }\r
+ else\r
+ {\r
+ color = Color.white;\r
+ }\r
\r
- out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
+ if (color.getRGB() < -1)\r
+ {\r
+ out.println("<td bgcolor=\"#" +\r
+ jalview.util.Format.getHexString(color) + "\">" +\r
seq.getCharAt(res) + "</td>");\r
}\r
else\r
{\r
out.println("<td>" + seq.getCharAt(res) + "</td>");\r
}\r
+\r
+ }\r
+\r
+ if (av.getScaleRightWrapped() &&\r
+ endRes < startRes + av.getWrappedWidth())\r
+ {\r
+ out.println("<td colspan=\"" +\r
+ (startRes + av.getWrappedWidth() - endRes) + "\">"\r
+ + " </td>");\r
+ }\r
+\r
+ if (av.getScaleRightWrapped() && startPos < endPos)\r
+ {\r
+ out.println("<td nowrap> " + endPos +\r
+ " </td>");\r
}\r
\r
out.println("</tr>");\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
+ "<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
+ +\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
+ +\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