JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index ed3fc52..02a8ed7 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,31 +1,39 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
 
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Iterator;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 /**
  * DOCUMENT ME!
@@ -68,13 +76,15 @@ public class SliderPanel extends GSliderPanel
 
     if (forConservation)
     {
-      label.setText("Enter value to increase conservation visibility");
+      label.setText(MessageManager
+              .getString("label.enter_value_increase_conservation_visibility"));
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
     else
     {
-      label.setText("Enter % identity above which to colour residues");
+      label.setText(MessageManager
+              .getString("label.enter_percentage_identity_above_which_colour_residues"));
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
@@ -130,10 +140,12 @@ public class SliderPanel extends GSliderPanel
       sp.cs = cs;
     }
 
-    conservationSlider.setTitle("Conservation Colour Increment  (" + source
-            + ")");
+    conservationSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.conservation_colour_increment",
+                    new String[] { source }));
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       sp.setAllGroupsCheckEnabled(true);
     }
@@ -207,9 +219,11 @@ public class SliderPanel extends GSliderPanel
       pid.cs = cs;
     }
 
-    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+    PIDSlider.setTitle(MessageManager
+            .formatMessage("label.percentage_identity_thereshold",
+                    new String[] { source }));
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       pid.setAllGroupsCheckEnabled(true);
     }
@@ -265,50 +279,39 @@ public class SliderPanel extends GSliderPanel
       return;
     }
 
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
+    ColourSchemeI toChange = cs;
+    Iterator<SequenceGroup> allGroups = null;
 
     if (allGroupsCheck.isSelected())
     {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
-    }
-    else
-    {
-      toChange = cs;
+      allGroups = ap.av.getAlignment().getGroups().listIterator();
     }
 
-    while (groupIndex > -1)
+    while (toChange != null)
     {
-      if (allGroups != null)
+      if (forConservation)
       {
-        toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
-
-        if (toChange == null)
-        {
-          groupIndex--;
-
-          continue;
-        }
+        toChange.setConservationInc(i);
       }
-
-      if (forConservation)
+      else
       {
-        if (toChange.conservationApplied())
+        toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
+      }
+      if (allGroups != null && allGroups.hasNext())
+      {
+        while ((toChange = allGroups.next().cs) == null
+                && allGroups.hasNext())
         {
-          toChange.setConservationInc(i);
+          ;
         }
       }
       else
       {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+        toChange = null;
       }
-
-      groupIndex--;
     }
 
-    ap.seqPanel.seqCanvas.repaint();
+    ap.getSeqPanel().seqCanvas.repaint();
   }
 
   /**