From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 17 Nov 2005 15:17:08 +0000 (+0000)
Subject: Now outputs features and groups, and wrapped alignment limits
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=ff5993cdddf0e67bd8605060cab189b6902036cd

Now outputs features and groups, and wrapped alignment limits
---

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 257e9fa..7290828 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -30,12 +30,14 @@ public class HTMLOutput
 {
   AlignViewport av;
   SequenceRenderer sr;
+  FeatureRenderer fr;
   Color color;
 
-  public HTMLOutput(AlignViewport av)
+  public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr)
   {
     this.av = av;
-    sr = new SequenceRenderer(av);
+    this.sr = sr;
+    this.fr = fr;
 
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty(
@@ -110,9 +112,7 @@ public class HTMLOutput
         "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 
     //////////////
-    SequenceGroup[] groups;
     SequenceI seq;
-    ColourSchemeI cs = null;
     AlignmentI alignment = av.getAlignment();
 
     // draws the top row, the measure rule
@@ -132,7 +132,6 @@ public class HTMLOutput
     for (i = 0; i < alignment.getHeight(); i++)
     {
       seq = alignment.getSequenceAt(i);
-      groups = alignment.findAllGroups(seq);
 
       String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
 
@@ -142,25 +141,12 @@ public class HTMLOutput
 
       for (int res = 0; res < seq.getLength(); res++)
       {
-        cs = av.getGlobalColourScheme();
 
-        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;
-            }
-          }
-        }
+        color = sr.findSequenceColour(Color.white, seq, res);
 
-        color = sr.getResidueBoxColour(cs, seq, res);
+        color = fr.findFeatureColour(color, seq, res);
 
-        if (color.getRGB() < -1)
+       if (color.getRGB() < -1)
         {
           out.println("<td bgcolor=\"#" +
                       jalview.util.Format.getHexString(color) + "\">" +
@@ -185,9 +171,7 @@ 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;
@@ -206,49 +190,54 @@ public class HTMLOutput
         endRes = al.getWidth();
       }
 
-      out.println("<tr>");
-      out.println("<td colspan=\"6\">&nbsp;</td>");
-
-      for (int i = startRes + 10; i < endRes; i += 10)
+      if(av.getScaleAboveWrapped())
       {
-        out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
-      }
+        out.println("<tr>");
 
-      // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
-      //             "<br>|</td>");
-      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)
+        {
+          out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+        }
 
+        out.println("</tr>");
+      }
+
+      int startPos, endPos;
       for (int s = 0; s < al.getHeight(); s++)
       {
         out.println("<tr>");
         seq = al.getSequenceAt(s);
-        groups = al.findAllGroups(seq);
+
+        startPos = seq.findPosition( startRes );
+        endPos =   seq.findPosition( endRes )-1;
 
         String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
 
-          out.println("<td nowrap>" + id +
+        out.println("<td nowrap>" + id +
                       "&nbsp;&nbsp;</td>");
 
 
-        for (int res = startRes; res < endRes; res++)
+        if(av.getScaleLeftWrapped())
         {
-          cs = av.getGlobalColourScheme();
+          if(startPos > seq.getEnd() || endPos==0)
+            out.println("<td nowrap>&nbsp;</td>");
+          else
+            out.println("<td nowrap>" + startPos +
+                      "&nbsp;&nbsp;</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;
-              }
-            }
-          }
+        for (int res = startRes; res < endRes; res++)
+        {
+          color = sr.findSequenceColour(Color.white, seq, res);
 
-          color = sr.getResidueBoxColour(cs, seq, res);
+          color = fr.findFeatureColour(color, seq, res);
 
           if (color.getRGB() < -1)
           {
@@ -280,8 +269,25 @@ public class HTMLOutput
           {
             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>");
       }