X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=c38004900fc145d196ab1c1e458a618b1e431754;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=7bf2e6c4429d0296731f42a8fa68b5dbe2781bf6;hpb=be5302e00fffeacc62877c2aca981eb9ede3525e;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 7bf2e6c..c380049 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.
  * 
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
 import jalview.datamodel.SequenceGroup;
 import jalview.io.JalviewFileChooser;
 import jalview.jbgui.GUserDefinedColours;
@@ -454,17 +455,44 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   protected void okButton_actionPerformed(ActionEvent e)
   {
-    applyButton_actionPerformed(null);
-
-    try
+    if (isNoSelectionMade())
     {
-      frame.setClosed(true);
-    } catch (Exception ex)
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .getString("label.no_colour_selection_in_scheme"),
+              MessageManager.getString("label.no_colour_selection_warn"),
+              JvOptionPane.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;
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param e
@@ -473,6 +501,14 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   protected void applyButton_actionPerformed(ActionEvent e)
   {
+    if (isNoSelectionMade())
+    {
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .getString("label.no_colour_selection_in_scheme"),
+              MessageManager.getString("label.no_colour_selection_warn"),
+              JvOptionPane.WARNING_MESSAGE);
+
+    }
     UserColourScheme ucs = getSchemeFromButtons();
     ucs.setName(schemeName.getText());
 
@@ -496,10 +532,23 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     Color[] newColours = new Color[24];
 
-    for (int i = 0; i < 24; i++)
+    int length = upperCaseButtons.size();
+    if (length < 24)
     {
-      JButton button = upperCaseButtons.get(i);
-      newColours[i] = button.getBackground();
+      int i = 0;
+      for (JButton btn : upperCaseButtons)
+      {
+        newColours[i] = btn.getBackground();
+        i++;
+      }
+    }
+    else
+    {
+      for (int i = 0; i < 24; i++)
+      {
+        JButton button = upperCaseButtons.get(i);
+        newColours[i] = button.getBackground();
+      }
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
@@ -507,17 +556,30 @@ public class UserDefinedColours extends GUserDefinedColours implements
     if (caseSensitive.isSelected())
     {
       newColours = new Color[23];
-      for (int i = 0; i < 23; i++)
+      length = lowerCaseButtons.size();
+      if (length < 23)
       {
-        JButton button = lowerCaseButtons.get(i);
-        newColours[i] = button.getBackground();
+        int i = 0;
+        for (JButton btn : lowerCaseButtons)
+        {
+          newColours[i] = btn.getBackground();
+          i++;
+        }
+      }
+      else
+      {
+        for (int i = 0; i < 23; i++)
+        {
+          JButton button = lowerCaseButtons.get(i);
+          newColours[i] = button.getBackground();
+        }
       }
       ucs.setLowerCaseColours(newColours);
     }
 
     if (ap != null)
     {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     return ucs;
@@ -536,9 +598,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     lowerCaseButtons = new ArrayList<JButton>();
 
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jc" }, new String[]
-            { "Jalview User Colours" }, "Jalview User Colours");
+            Cache.getProperty("LAST_DIRECTORY"), "jc",
+            "Jalview User Colours", "Jalview User Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_colour_scheme"));
@@ -661,8 +722,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
         name = jucs.getColour(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
-          index = ((Integer) ResidueProperties.aa3Hash.get(name))
-                  .intValue();
+          index = ResidueProperties.aa3Hash.get(name).intValue();
         }
         else
         {
@@ -749,23 +809,23 @@ public class UserDefinedColours extends GUserDefinedColours implements
   {
     if (schemeName.getText().trim().length() < 1)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("label.user_colour_scheme_must_have_name"),
               MessageManager.getString("label.no_name_colour_scheme"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       return;
     }
 
     if (userColourSchemes != null
             && userColourSchemes.containsKey(schemeName.getText()))
     {
-      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+      int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
               MessageManager.formatMessage(
-                      "label.colour_scheme_exists_overwrite", new Object[]
-                      { schemeName.getText(), schemeName.getText() }),
+                      "label.colour_scheme_exists_overwrite", new Object[] {
+                          schemeName.getText(), schemeName.getText() }),
               MessageManager.getString("label.duplicate_scheme_name"),
-              JOptionPane.YES_NO_OPTION);
-      if (reply != JOptionPane.YES_OPTION)
+              JvOptionPane.YES_NO_OPTION);
+      if (reply != JvOptionPane.YES_OPTION)
       {
         return;
       }
@@ -773,12 +833,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
       userColourSchemes.remove(schemeName.getText());
     }
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jc" }, new String[]
-            { "Jalview User Colours" }, "Jalview User Colours");
+            Cache.getProperty("LAST_DIRECTORY"), "jc",
+            "Jalview User Colours", "Jalview User Colours");
 
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_colour_scheme"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);