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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 e4dc83e..257e9fa 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -114,9 +114,6 @@ public class HTMLOutput
     SequenceI seq;\r
     ColourSchemeI cs = null;\r
     AlignmentI alignment = av.getAlignment();\r
-    String r;\r
-    String g;\r
-    String b;\r
 \r
     // draws the top row, the measure rule\r
     out.println("<tr><td colspan=\"6\"></td>");\r
@@ -137,16 +134,11 @@ public class HTMLOutput
       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
+      String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
+\r
+      out.println("<tr><td nowrap>" + id +\r
                     "&nbsp;&nbsp;</td>");\r
-      }\r
+\r
 \r
       for (int res = 0; res < seq.getLength(); res++)\r
       {\r
@@ -205,9 +197,9 @@ public class HTMLOutput
         "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
 \r
     for (int startRes = 0; startRes < al.getWidth();\r
-         startRes += av.getChunkWidth())\r
+         startRes += av.getWrappedWidth())\r
     {\r
-      int endRes = startRes + av.getChunkWidth();\r
+      int endRes = startRes + av.getWrappedWidth();\r
 \r
       if (endRes > al.getWidth())\r
       {\r
@@ -232,16 +224,11 @@ public class HTMLOutput
         seq = al.getSequenceAt(s);\r
         groups = al.findAllGroups(seq);\r
 \r
-        if (av.getShowFullId())\r
-        {\r
-          out.println("<td nowrap>" + seq.getDisplayId() +\r
-                      "&nbsp;&nbsp;</td>");\r
-        }\r
-        else\r
-        {\r
-          out.println("<td nowrap>" + seq.getName() +\r
+        String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());\r
+\r
+          out.println("<td nowrap>" + id +\r
                       "&nbsp;&nbsp;</td>");\r
-        }\r
+\r
 \r
         for (int res = startRes; res < endRes; res++)\r
         {\r