JAL-2401 code and help tidy for review comments

diff --git a/help/html/colourSchemes/user.html b/help/html/colourSchemes/user.html
index fb6c356..c2fde1c 100755 (executable)
--- a/help/html/colourSchemes/user.html
+++ b/help/html/colourSchemes/user.html
@@ -27,7 +27,7 @@
     <strong>User Defined Colours</strong>
   </p>
   <p>
-    <img src="userDefined_java6.gif" width="815" height="402">
+    <img src="userDefined_java7.gif" width="815" height="402">
   </p>
   <p>
     You may define any number of new colour schemes, each with a unique
@@ -41,7 +41,7 @@
     The <strong>Case Sensitive</strong> option allows you to choose
     distinct colours for upper and lower case residue codes.
   <p>
-    The <strong>Lower Case Colour</strong> option allows you to apply a selected colour
+    The <strong>Colour All Lower Case  </strong> option allows you to apply a selected colour
     to all lower case residues.
   <p>
     Click <strong>Apply</strong> or <strong>OK</strong> to set your new
@@ -56,11 +56,5 @@
   <br> Any saved colour schemes will be automatically loaded the
   next time you use Jalview.
   <br>
-  <br>
-  <em>Note: the screenshot shows the appearance when running Java
-    version 6. For Java 7 (from Jalview 2.8.2) only the Swatches colour
-    chooser is currently supported (for reasons of available screen
-    space).</em>
-  <p />
 </body>
 </html>

diff --git a/help/html/colourSchemes/userDefined_java6.gif b/help/html/colourSchemes/userDefined_java6.gif
deleted file mode 100644 (file)
index d737e80..0000000
Binary files a/help/html/colourSchemes/userDefined_java6.gif and /dev/null differ

diff --git a/help/html/colourSchemes/userDefined_java7.gif b/help/html/colourSchemes/userDefined_java7.gif
index f0ced11..de80b84 100644 (file)
Binary files a/help/html/colourSchemes/userDefined_java7.gif and b/help/html/colourSchemes/userDefined_java7.gif differ

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 6e9a121..9ab4327 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -591,11 +591,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    // if (ap != null)
-    // {
-    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    // }
-
     return ucs;
   }