Merge branch 'develop' into Release_2_9_Branch

[jalview.git] / src / jalview / gui / UserDefinedColours.java

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a907187..c9c1531 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -20,6 +20,16 @@
  */
 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;
@@ -40,16 +50,6 @@ 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.
@@ -486,7 +486,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
             || upperCaseButtons.isEmpty();
     final boolean noLowerCaseSelected = caseSensitive.isSelected()
             && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
-    final boolean noSelectionMade = noUpperCaseSelected || noLowerCaseSelected;
+    final boolean noSelectionMade = noUpperCaseSelected
+            || noLowerCaseSelected;
     return noSelectionMade;
   }
 
@@ -501,12 +502,13 @@ public class UserDefinedColours extends GUserDefinedColours implements
   {
     if (isNoSelectionMade())
     {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
-                JOptionPane.WARNING_MESSAGE);
-               
-       }
-       UserColourScheme ucs = getSchemeFromButtons();
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .getString("label.no_colour_selection_in_scheme"),
+              MessageManager.getString("label.no_colour_selection_warn"),
+              JOptionPane.WARNING_MESSAGE);
+
+    }
+    UserColourScheme ucs = getSchemeFromButtons();
     ucs.setName(schemeName.getText());
 
     if (seqGroup != null)
@@ -530,17 +532,22 @@ public class UserDefinedColours extends GUserDefinedColours implements
     Color[] newColours = new Color[24];
 
     int length = upperCaseButtons.size();
-    if (length<24){
-       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();
-       }
+    if (length < 24)
+    {
+      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);
@@ -549,17 +556,22 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       newColours = new Color[23];
       length = lowerCaseButtons.size();
-      if (length<23){
-         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();
-         }
+      if (length < 23)
+      {
+        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);
     }
@@ -585,9 +597,9 @@ 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");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "jc" }, new String[] { "Jalview User Colours" },
+            "Jalview User Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_colour_scheme"));
@@ -710,8 +722,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
         name = jucs.getColour(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
-          index = ResidueProperties.aa3Hash.get(name)
-                  .intValue();
+          index = ResidueProperties.aa3Hash.get(name).intValue();
         }
         else
         {
@@ -810,8 +821,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       int reply = JOptionPane.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)
@@ -822,12 +833,13 @@ 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");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "jc" }, new String[] { "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);