X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=a907187593e54cabc31ae1e8e8ed352812daaf83;hb=1cc813e8e4285a86d3167c657e3a367c2e759c16;hp=37824fe1688913d7726caaf9837d1544e2ae07b9;hpb=9f9ebe83d2906c9bcb553f86dad16a6cf1be4da8;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 37824fe..a907187 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.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.
  * 
@@ -20,16 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.datamodel.SequenceGroup;
-import jalview.io.JalviewFileChooser;
-import jalview.jbgui.GUserDefinedColours;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
@@ -50,6 +40,16 @@ import javax.swing.JOptionPane;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
 /**
  * This panel allows the user to assign colours to Amino Acid residue codes, and
  * save the colour scheme.
@@ -454,26 +454,40 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   protected void okButton_actionPerformed(ActionEvent e)
   {
-		//Check if the user have done any selection
-		boolean showWarning = (upperCaseButtons==null) ||
-					((upperCaseButtons!=null) && (upperCaseButtons.size()==0)) ||
-					(lowerCaseButtons==null) ||
-					((lowerCaseButtons!=null) && (lowerCaseButtons.size()==0));
-		if (showWarning){
-	        JOptionPane.showMessageDialog(Desktop.desktop,
-	                MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
-	                JOptionPane.WARNING_MESSAGE);
-			
-		}else{
-		    applyButton_actionPerformed(null);
-		
-		    try
-		    {
-		      frame.setClosed(true);
-		    } catch (Exception ex)
-		    {
-		    }
-		}
+    if (isNoSelectionMade())
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .getString("label.no_colour_selection_in_scheme"),
+              MessageManager.getString("label.no_colour_selection_warn"),
+              JOptionPane.WARNING_MESSAGE);
+    }
+    else
+    {
+      applyButton_actionPerformed(null);
+
+      try
+      {
+        frame.setClosed(true);
+      } catch (Exception ex)
+      {
+      }
+    }
+  }
+
+  /**
+   * Returns true if the user has not made any colour selection (including if
+   * 'case-sensitive' selected and no lower-case colour chosen).
+   * 
+   * @return
+   */
+  protected boolean isNoSelectionMade()
+  {
+    final boolean noUpperCaseSelected = upperCaseButtons == null
+            || upperCaseButtons.isEmpty();
+    final boolean noLowerCaseSelected = caseSensitive.isSelected()
+            && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
+    final boolean noSelectionMade = noUpperCaseSelected || noLowerCaseSelected;
+    return noSelectionMade;
   }
 
   /**
@@ -485,12 +499,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   protected void applyButton_actionPerformed(ActionEvent e)
   {
-	//Check if the user have done any selection
-	boolean showWarning = (upperCaseButtons==null) ||
-				((upperCaseButtons!=null) && (upperCaseButtons.size()==0)) ||
-				(lowerCaseButtons==null) ||
-				((lowerCaseButtons!=null) && (lowerCaseButtons.size()==0));
-	if (showWarning){
+    if (isNoSelectionMade())
+    {
         JOptionPane.showMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
                 JOptionPane.WARNING_MESSAGE);
@@ -528,7 +538,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     	}
     }else{
     	for (int i = 0; i < 24; i++){
-    		JButton button = (JButton) upperCaseButtons.get(i);
+    		JButton button = upperCaseButtons.get(i);
     		newColours[i] = button.getBackground();
     	}
     }
@@ -547,7 +557,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     	  }
       }else{
     	  for (int i = 0; i < 23; i++){
-    		  JButton button = (JButton) lowerCaseButtons.get(i);
+    		  JButton button = lowerCaseButtons.get(i);
     		  newColours[i] = button.getBackground();
     	  }
       }
@@ -556,7 +566,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (ap != null)
     {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     return ucs;
@@ -700,7 +710,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
         name = jucs.getColour(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
-          index = ((Integer) ResidueProperties.aa3Hash.get(name))
+          index = ResidueProperties.aa3Hash.get(name)
                   .intValue();
         }
         else