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[jalview.git] / src / jalview / io / HTMLOutput.java
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 201ff0c..6c2c51e 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,6 +1,6 @@
 /*\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
@@ -24,18 +24,21 @@ import java.awt.*;
 \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 fr1)\r
   {\r
     this.av = av;\r
-    sr = new SequenceRenderer(av);\r
+    this.sr = sr;\r
+\r
+    fr = new FeatureRenderer(av);\r
+    fr.transferSettings(fr1);\r
 \r
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
         getProperty(\r
@@ -110,9 +113,7 @@ public class HTMLOutput
         "<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
 \r
     // draws the top row, the measure rule\r
@@ -132,38 +133,24 @@ public class HTMLOutput
     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
-                    "&nbsp;&nbsp;</td>");\r
-      }\r
-      else\r
-      {\r
-        out.println("<tr><td nowrap>" + seq.getName() +\r
-                    "&nbsp;&nbsp;</td>");\r
-      }\r
+      String id = seq.getDisplayId(av.getShowJVSuffix());\r
+\r
+      out.println("<tr><td nowrap>" + id +\r
+                  "&nbsp;&nbsp;</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
@@ -190,9 +177,7 @@ public class HTMLOutput
     ////////////////////////////////////\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
@@ -211,85 +196,92 @@ public class HTMLOutput
         endRes = al.getWidth();\r
       }\r
 \r
-      out.println("<tr>");\r
-      out.println("<td colspan=\"6\">&nbsp;</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
-                      "&nbsp;&nbsp;</td>");\r
+          out.println("<td colspan=\"7\">&nbsp;</td>");\r
         }\r
         else\r
         {\r
-          out.println("<td nowrap>" + seq.getName() +\r
-                      "&nbsp;&nbsp;</td>");\r
+          out.println("<td colspan=\"6\">&nbsp;</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
+                    "&nbsp;&nbsp;</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>&nbsp;</td>");\r
+          }\r
+          else\r
+          {\r
+            out.println("<td nowrap>" + startPos +\r
+                        "&nbsp;&nbsp;</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
+                      + "&nbsp;&nbsp;</td>");\r
+        }\r
+\r
+        if (av.getScaleRightWrapped() && startPos < endPos)\r
+        {\r
+          out.println("<td nowrap>&nbsp;" + endPos +\r
+                      "&nbsp;&nbsp;</td>");\r
         }\r
 \r
         out.println("</tr>");\r
@@ -308,88 +300,90 @@ public class HTMLOutput
   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\">&nbsp;' + msg +\n"\r
-      +"    '&nbsp;</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\">&nbsp;' + msg +\n"\r
+        + "    '&nbsp;</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