X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=8406f3d27c381891d0d312f5798c06bfb872900b;hb=31d4457b311d9954a2106623d318860c0c9dc151;hp=f7a0f3fa06e295e2d7ec414ae8aa7a3bdc50bae1;hpb=3caa3405a5822c7248bab517b8d1a7776e0dc210;p=jalview.git

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index f7a0f3f..8406f3d 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -32,12 +32,12 @@ public class HTMLOutput
   FeatureRenderer fr;
   Color color;
 
-  public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr1)
+  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)
   {
-    this.av = av;
+    this.av = ap.av;
     this.sr = sr;
 
-    fr = new FeatureRenderer(av);
+    fr = new FeatureRenderer(ap);
     fr.transferSettings(fr1);
 
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
@@ -137,8 +137,7 @@ public class HTMLOutput
       String id = seq.getDisplayId(av.getShowJVSuffix());
 
       out.println("<tr><td nowrap>" + id +
-                    "&nbsp;&nbsp;</td>");
-
+                  "&nbsp;&nbsp;</td>");
 
       for (int res = 0; res < seq.getLength(); res++)
       {
@@ -149,10 +148,11 @@ public class HTMLOutput
           color = fr.findFeatureColour(color, seq, res);
         }
         else
-            color = Color.white;
-
+        {
+          color = Color.white;
+        }
 
-       if (color.getRGB() < -1)
+        if (color.getRGB() < -1)
         {
           out.println("<td bgcolor=\"#" +
                       jalview.util.Format.getHexString(color) + "\">" +
@@ -196,15 +196,18 @@ public class HTMLOutput
         endRes = al.getWidth();
       }
 
-      if(av.getScaleAboveWrapped())
+      if (av.getScaleAboveWrapped())
       {
         out.println("<tr>");
 
         if (av.getScaleLeftWrapped())
+        {
           out.println("<td colspan=\"7\">&nbsp;</td>");
+        }
         else
+        {
           out.println("<td colspan=\"6\">&nbsp;</td>");
-
+        }
 
         for (int i = startRes + 10; i < endRes; i += 10)
         {
@@ -220,25 +223,27 @@ public class HTMLOutput
         out.println("<tr>");
         seq = al.getSequenceAt(s);
 
-        startPos = seq.findPosition( startRes );
-        endPos =   seq.findPosition( endRes )-1;
+        startPos = seq.findPosition(startRes);
+        endPos = seq.findPosition(endRes) - 1;
 
         String id = seq.getDisplayId(av.getShowJVSuffix());
 
         out.println("<td nowrap>" + id +
-                      "&nbsp;&nbsp;</td>");
-
+                    "&nbsp;&nbsp;</td>");
 
-        if(av.getScaleLeftWrapped())
+        if (av.getScaleLeftWrapped())
         {
-          if(startPos > seq.getEnd() || endPos==0)
+          if (startPos > seq.getEnd() || endPos == 0)
+          {
             out.println("<td nowrap>&nbsp;</td>");
+          }
           else
+          {
             out.println("<td nowrap>" + startPos +
-                      "&nbsp;&nbsp;</td>");
+                        "&nbsp;&nbsp;</td>");
+          }
         }
 
-
         for (int res = startRes; res < endRes; res++)
         {
           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
@@ -248,32 +253,14 @@ public class HTMLOutput
             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 + "\">" +
+            out.println("<td bgcolor=\"#" +
+                        jalview.util.Format.getHexString(color) + "\">" +
                         seq.getCharAt(res) + "</td>");
           }
           else
@@ -281,24 +268,22 @@ public class HTMLOutput
             out.println("<td>" + seq.getCharAt(res) + "</td>");
           }
 
-
         }
 
-        if(av.getScaleRightWrapped() &&
-           endRes < startRes + av.getWrappedWidth())
+        if (av.getScaleRightWrapped() &&
+            endRes < startRes + av.getWrappedWidth())
         {
-         out.println("<td colspan=\""+ (startRes+av.getWrappedWidth()-endRes) +"\">"
-                     +"&nbsp;&nbsp;</td>");
-       }
-
+          out.println("<td colspan=\"" +
+                      (startRes + av.getWrappedWidth() - endRes) + "\">"
+                      + "&nbsp;&nbsp;</td>");
+        }
 
-        if(av.getScaleRightWrapped() && startPos<endPos)
+        if (av.getScaleRightWrapped() && startPos < endPos)
         {
           out.println("<td nowrap>&nbsp;" + endPos +
                       "&nbsp;&nbsp;</td>");
         }
 
-
         out.println("</tr>");
       }
 
@@ -315,88 +300,90 @@ public class HTMLOutput
   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\">&nbsp;' + msg +\n"
-      +"    '&nbsp;</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");
+        "<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\">&nbsp;' + msg +\n"
+        + "    '&nbsp;</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");
 
   }
 }