JAL-2383 check for null, spelling

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

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 1bac450..7d733c9 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.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 +20,22 @@
  */
 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.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyVetoException;
+import java.util.Iterator;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 /**
  * DOCUMENT ME!
@@ -72,19 +78,22 @@ public class SliderPanel extends GSliderPanel
 
     if (forConservation)
     {
-      label.setText(MessageManager.getString("label.enter_value_increase_conservation_visibility"));
+      label.setText(MessageManager
+              .getString("label.enter_value_increase_conservation_visibility"));
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
     else
     {
-      label.setText(MessageManager.getString("label.enter_percentage_identity_above_which_colour_residues"));
+      label.setText(MessageManager
+              .getString("label.enter_percentage_identity_above_which_colour_residues"));
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
 
     slider.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         valueField.setText(slider.getValue() + "");
@@ -94,6 +103,7 @@ public class SliderPanel extends GSliderPanel
 
     slider.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mouseReleased(MouseEvent evt)
       {
         ap.paintAlignment(true);
@@ -131,11 +141,14 @@ public class SliderPanel extends GSliderPanel
     else
     {
       sp = (SliderPanel) conservationSlider.getContentPane();
+      sp.slider.setValue(cs.getConservationInc());
       sp.cs = cs;
     }
 
-    conservationSlider.setTitle("Conservation Colour Increment  (" + source
-            + ")");
+    conservationSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.conservation_colour_increment",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -150,27 +163,55 @@ public class SliderPanel extends GSliderPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Hides the PID slider panel if it is shown
    */
-  public static void showConservationSlider()
+  public static void hidePIDSlider()
   {
-    try
+    if (PIDSlider != null)
     {
-      PIDSlider.setClosed(true);
-      PIDSlider = null;
-    } catch (Exception ex)
+      try
+      {
+        PIDSlider.setClosed(true);
+        PIDSlider = null;
+      } catch (PropertyVetoException ex)
+      {
+      }
+    }
+  }
+
+  /**
+   * Hides the conservation slider panel if it is shown
+   */
+  public static void hideConservationSlider()
+  {
+    if (conservationSlider != null)
     {
+      try
+      {
+        conservationSlider.setClosed(true);
+        conservationSlider = null;
+      } catch (PropertyVetoException ex)
+      {
+      }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showConservationSlider()
+  {
+    hidePIDSlider();
 
     if (!conservationSlider.isVisible())
     {
       Desktop.addInternalFrame(conservationSlider,
               conservationSlider.getTitle(), 420, 90, false);
       conservationSlider
-              .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+              .addInternalFrameListener(new InternalFrameAdapter()
               {
-                public void internalFrameClosed(
-                        javax.swing.event.InternalFrameEvent e)
+                @Override
+                public void internalFrameClosed(InternalFrameEvent e)
                 {
                   conservationSlider = null;
                 }
@@ -208,10 +249,14 @@ public class SliderPanel extends GSliderPanel
     else
     {
       pid = (SliderPanel) PIDSlider.getContentPane();
+      pid.slider.setValue(cs.getThreshold());
       pid.cs = cs;
     }
 
-    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+    PIDSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.percentage_identity_threshold",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -230,28 +275,21 @@ public class SliderPanel extends GSliderPanel
    */
   public static void showPIDSlider()
   {
-    try
-    {
-      conservationSlider.setClosed(true);
-      conservationSlider = null;
-    } catch (Exception ex)
-    {
-    }
+    hideConservationSlider();
 
     if (!PIDSlider.isVisible())
     {
       Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
               false);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-      PIDSlider
-              .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-              {
-                public void internalFrameClosed(
-                        javax.swing.event.InternalFrameEvent e)
-                {
-                  PIDSlider = null;
-                }
-              });
+      PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
+      {
+        @Override
+        public void internalFrameClosed(InternalFrameEvent e)
+        {
+          PIDSlider = null;
+        }
+      });
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
   }
@@ -285,13 +323,15 @@ public class SliderPanel extends GSliderPanel
       }
       else
       {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+        toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
       }
       if (allGroups != null && allGroups.hasNext())
       {
         while ((toChange = allGroups.next().cs) == null
                 && allGroups.hasNext())
+        {
           ;
+        }
       }
       else
       {
@@ -299,7 +339,7 @@ public class SliderPanel extends GSliderPanel
       }
     }
 
-    ap.seqPanel.seqCanvas.repaint();
+    ap.getSeqPanel().seqCanvas.repaint();
   }
 
   /**
@@ -316,24 +356,6 @@ public class SliderPanel extends GSliderPanel
   /**
    * DOCUMENT ME!
    * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    } catch (NumberFormatException ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param value
    *          DOCUMENT ME!
    */
@@ -352,6 +374,7 @@ public class SliderPanel extends GSliderPanel
     return Integer.parseInt(valueField.getText());
   }
 
+  @Override
   public void slider_mouseReleased(MouseEvent e)
   {
     if (ap.overviewPanel != null)