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 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -30,12 +30,14 @@ public class HTMLOutput
 {\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 fr)\r
   {\r
     this.av = av;\r
-    sr = new SequenceRenderer(av);\r
+    this.sr = sr;\r
+    this.fr = fr;\r
 \r
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
         getProperty(\r
@@ -110,9 +112,7 @@ 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
@@ -132,7 +132,6 @@ public class HTMLOutput
     for (i = 0; i < alignment.getHeight(); i++)\r
     {\r
       seq = alignment.getSequenceAt(i);\r
-      groups = alignment.findAllGroups(seq);\r
 \r
       String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
@@ -142,25 +141,12 @@ public class HTMLOutput
 \r
       for (int res = 0; res < seq.getLength(); res++)\r
       {\r
-        cs = av.getGlobalColourScheme();\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
+        color = sr.findSequenceColour(Color.white, seq, res);\r
 \r
-        color = sr.getResidueBoxColour(cs, seq, res);\r
+        color = fr.findFeatureColour(color, seq, res);\r
 \r
-        if (color.getRGB() < -1)\r
+       if (color.getRGB() < -1)\r
         {\r
           out.println("<td bgcolor=\"#" +\r
                       jalview.util.Format.getHexString(color) + "\">" +\r
@@ -185,9 +171,7 @@ 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
@@ -206,49 +190,54 @@ 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
+      if(av.getScaleAboveWrapped())\r
       {\r
-        out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-      }\r
+        out.println("<tr>");\r
 \r
-      // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
-      //             "<br>|</td>");\r
-      out.println("</tr>");\r
+        if (av.getScaleLeftWrapped())\r
+          out.println("<td colspan=\"7\">&nbsp;</td>");\r
+        else\r
+          out.println("<td colspan=\"6\">&nbsp;</td>");\r
+\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("</tr>");\r
+      }\r
+\r
+      int startPos, endPos;\r
       for (int s = 0; s < al.getHeight(); s++)\r
       {\r
         out.println("<tr>");\r
         seq = al.getSequenceAt(s);\r
-        groups = al.findAllGroups(seq);\r
+\r
+        startPos = seq.findPosition( startRes );\r
+        endPos =   seq.findPosition( endRes )-1;\r
 \r
         String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
 \r
-          out.println("<td nowrap>" + id +\r
+        out.println("<td nowrap>" + id +\r
                       "&nbsp;&nbsp;</td>");\r
 \r
 \r
-        for (int res = startRes; res < endRes; res++)\r
+        if(av.getScaleLeftWrapped())\r
         {\r
-          cs = av.getGlobalColourScheme();\r
+          if(startPos > seq.getEnd() || endPos==0)\r
+            out.println("<td nowrap>&nbsp;</td>");\r
+          else\r
+            out.println("<td nowrap>" + startPos +\r
+                      "&nbsp;&nbsp;</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
+        for (int res = startRes; res < endRes; res++)\r
+        {\r
+          color = sr.findSequenceColour(Color.white, seq, res);\r
 \r
-          color = sr.getResidueBoxColour(cs, seq, res);\r
+          color = fr.findFeatureColour(color, seq, res);\r
 \r
           if (color.getRGB() < -1)\r
           {\r
@@ -280,8 +269,25 @@ public class HTMLOutput
           {\r
             out.println("<td>" + seq.getCharAt(res) + "</td>");\r
           }\r
+\r
+\r
+        }\r
+\r
+        if(av.getScaleRightWrapped() &&\r
+           endRes < startRes + av.getWrappedWidth())\r
+        {\r
+         out.println("<td colspan=\""+ (startRes+av.getWrappedWidth()-endRes) +"\">"\r
+                     +"&nbsp;&nbsp;</td>");\r
+       }\r
+\r
+\r
+        if(av.getScaleRightWrapped() && startPos<endPos)\r
+        {\r
+          out.println("<td nowrap>&nbsp;" + endPos +\r
+                      "&nbsp;&nbsp;</td>");\r
         }\r
 \r
+\r
         out.println("</tr>");\r
       }\r
 \r