X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=6c2c51ef5110a13b1849a0d250769e8d69332b75;hb=7157dfd20efd2e1db47db1ac12e879eb51c67b92;hp=e4dc83e9d35912535e26518c3aeba827f38e93e3;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index e4dc83e..6c2c51e 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
@@ -24,18 +24,21 @@ import java.awt.*;
 
 import jalview.datamodel.*;
 import jalview.gui.*;
-import jalview.schemes.*;
 
 public class HTMLOutput
 {
   AlignViewport av;
   SequenceRenderer sr;
+  FeatureRenderer fr;
   Color color;
 
-  public HTMLOutput(AlignViewport av)
+  public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr1)
   {
     this.av = av;
-    sr = new SequenceRenderer(av);
+    this.sr = sr;
+
+    fr = new FeatureRenderer(av);
+    fr.transferSettings(fr1);
 
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty(
@@ -110,13 +113,8 @@ public class HTMLOutput
         "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 
     //////////////
-    SequenceGroup[] groups;
     SequenceI seq;
-    ColourSchemeI cs = null;
     AlignmentI alignment = av.getAlignment();
-    String r;
-    String g;
-    String b;
 
     // draws the top row, the measure rule
     out.println("<tr><td colspan=\"6\"></td>");
@@ -135,38 +133,24 @@ public class HTMLOutput
     for (i = 0; i < alignment.getHeight(); i++)
     {
       seq = alignment.getSequenceAt(i);
-      groups = alignment.findAllGroups(seq);
 
-      if (av.getShowFullId())
-      {
-        out.println("<tr><td nowrap>" + seq.getDisplayId() +
-                    "&nbsp;&nbsp;</td>");
-      }
-      else
-      {
-        out.println("<tr><td nowrap>" + seq.getName() +
-                    "&nbsp;&nbsp;</td>");
-      }
+      String id = seq.getDisplayId(av.getShowJVSuffix());
+
+      out.println("<tr><td nowrap>" + id +
+                  "&nbsp;&nbsp;</td>");
 
       for (int res = 0; res < seq.getLength(); res++)
       {
-        cs = av.getGlobalColourScheme();
-
-        if (groups != null)
+        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
         {
-          for (int k = 0; k < groups.length; k++)
-          {
-            if ( (groups[k].getStartRes() <= res) &&
-                (groups[k].getEndRes() >= res))
-            {
-              cs = groups[k].cs;
+          color = sr.getResidueBoxColour(seq, res);
 
-              break;
-            }
-          }
+          color = fr.findFeatureColour(color, seq, res);
+        }
+        else
+        {
+          color = Color.white;
         }
-
-        color = sr.getResidueBoxColour(cs, seq, res);
 
         if (color.getRGB() < -1)
         {
@@ -193,9 +177,7 @@ public class HTMLOutput
     ////////////////////////////////////
     /// How many sequences and residues can we fit on a printable page?
     AlignmentI al = av.getAlignment();
-    SequenceGroup[] groups;
     SequenceI seq;
-    ColourSchemeI cs = null;
     String r;
     String g;
     String b;
@@ -205,94 +187,101 @@ public class HTMLOutput
         "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 
     for (int startRes = 0; startRes < al.getWidth();
-         startRes += av.getChunkWidth())
+         startRes += av.getWrappedWidth())
     {
-      int endRes = startRes + av.getChunkWidth();
+      int endRes = startRes + av.getWrappedWidth();
 
       if (endRes > al.getWidth())
       {
         endRes = al.getWidth();
       }
 
-      out.println("<tr>");
-      out.println("<td colspan=\"6\">&nbsp;</td>");
-
-      for (int i = startRes + 10; i < endRes; 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 (int s = 0; s < al.getHeight(); s++)
+      if (av.getScaleAboveWrapped())
       {
         out.println("<tr>");
-        seq = al.getSequenceAt(s);
-        groups = al.findAllGroups(seq);
 
-        if (av.getShowFullId())
+        if (av.getScaleLeftWrapped())
         {
-          out.println("<td nowrap>" + seq.getDisplayId() +
-                      "&nbsp;&nbsp;</td>");
+          out.println("<td colspan=\"7\">&nbsp;</td>");
         }
         else
         {
-          out.println("<td nowrap>" + seq.getName() +
-                      "&nbsp;&nbsp;</td>");
+          out.println("<td colspan=\"6\">&nbsp;</td>");
         }
 
-        for (int res = startRes; res < endRes; res++)
+        for (int i = startRes + 10; i < endRes; i += 10)
         {
-          cs = av.getGlobalColourScheme();
+          out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+        }
 
-          if (groups != null)
-          {
-            for (int k = 0; k < groups.length; k++)
-            {
-              if ( (groups[k].getStartRes() <= res) &&
-                  (groups[k].getEndRes() >= res))
-              {
-                cs = groups[k].cs;
-
-                break;
-              }
-            }
-          }
+        out.println("</tr>");
+      }
 
-          color = sr.getResidueBoxColour(cs, seq, res);
+      int startPos, endPos;
+      for (int s = 0; s < al.getHeight(); s++)
+      {
+        out.println("<tr>");
+        seq = al.getSequenceAt(s);
 
-          if (color.getRGB() < -1)
-          {
-            r = Integer.toHexString(color.getRed());
+        startPos = seq.findPosition(startRes);
+        endPos = seq.findPosition(endRes) - 1;
 
-            if (r.length() < 2)
-            {
-              r = "0" + r;
-            }
+        String id = seq.getDisplayId(av.getShowJVSuffix());
 
-            g = Integer.toHexString(color.getGreen());
+        out.println("<td nowrap>" + id +
+                    "&nbsp;&nbsp;</td>");
 
-            if (g.length() < 2)
-            {
-              g = "0" + g;
-            }
+        if (av.getScaleLeftWrapped())
+        {
+          if (startPos > seq.getEnd() || endPos == 0)
+          {
+            out.println("<td nowrap>&nbsp;</td>");
+          }
+          else
+          {
+            out.println("<td nowrap>" + startPos +
+                        "&nbsp;&nbsp;</td>");
+          }
+        }
 
-            b = Integer.toHexString(color.getBlue());
+        for (int res = startRes; res < endRes; res++)
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+          {
+            color = sr.getResidueBoxColour(seq, res);
 
-            if (b.length() < 2)
-            {
-              b = "0" + b;
-            }
+            color = fr.findFeatureColour(color, seq, res);
+          }
+          else
+          {
+            color = Color.white;
+          }
 
-            out.println("<td bgcolor=\"#" + r + g + b + "\">" +
+          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>");
           }
+
+        }
+
+        if (av.getScaleRightWrapped() &&
+            endRes < startRes + av.getWrappedWidth())
+        {
+          out.println("<td colspan=\"" +
+                      (startRes + av.getWrappedWidth() - endRes) + "\">"
+                      + "&nbsp;&nbsp;</td>");
+        }
+
+        if (av.getScaleRightWrapped() && startPos < endPos)
+        {
+          out.println("<td nowrap>&nbsp;" + endPos +
+                      "&nbsp;&nbsp;</td>");
         }
 
         out.println("</tr>");
@@ -311,88 +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");
 
   }
 }