X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=5376fa4846bb73f0ac8f5acfe0abdee739b5a546;hb=63e93122d1722a69e997a9ac64502ef74c4a7a17;hp=50b07e4b4c459b594852383f49a563b723fcb8c5;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 50b07e4..5376fa4 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,21 +20,29 @@
  */
 package jalview.io;
 
-import java.io.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.util.BrowserLauncher;
+import jalview.util.Comparison;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.io.PrintWriter;
+
 public class HTMLOutput
 {
   AlignViewport av;
 
   SequenceRenderer sr;
 
-  FeatureRenderer fr;
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   Color color;
 
@@ -48,7 +56,7 @@ public class HTMLOutput
     fr.transferSettings(fr1);
 
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "html" }, new String[]
             { "HTML files" }, "HTML files");
 
@@ -61,7 +69,7 @@ public class HTMLOutput
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       try
@@ -102,7 +110,7 @@ public class HTMLOutput
 
         out.println("\n</body>\n</html>");
         out.close();
-        jalview.util.BrowserLauncher.openURL("file:///" + choice);
+        BrowserLauncher.openURL("file:///" + choice);
       } catch (Exception ex)
       {
         ex.printStackTrace();
@@ -143,7 +151,7 @@ public class HTMLOutput
 
       for (int res = 0; res < seq.getLength(); res++)
       {
-        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+        if (!Comparison.isGap(seq.getCharAt(res)))
         {
           color = sr.getResidueBoxColour(seq, res);
 
@@ -156,9 +164,8 @@ public class HTMLOutput
 
         if (color.getRGB() < -1)
         {
-          out.println("<td bgcolor=\"#"
-                  + jalview.util.Format.getHexString(color) + "\">"
-                  + seq.getCharAt(res) + "</td>");
+          out.println("<td bgcolor=\"#" + Format.getHexString(color)
+                  + "\">" + seq.getCharAt(res) + "</td>");
         }
         else
         {
@@ -245,7 +252,7 @@ public class HTMLOutput
 
         for (int res = startRes; res < endRes; res++)
         {
-          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+          if (!Comparison.isGap(seq.getCharAt(res)))
           {
             color = sr.getResidueBoxColour(seq, res);
 
@@ -258,9 +265,8 @@ public class HTMLOutput
 
           if (color.getRGB() < -1)
           {
-            out.println("<td bgcolor=\"#"
-                    + jalview.util.Format.getHexString(color) + "\">"
-                    + seq.getCharAt(res) + "</td>");
+            out.println("<td bgcolor=\"#" + Format.getHexString(color)
+                    + "\">" + seq.getCharAt(res) + "</td>");
           }
           else
           {