JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
old mode 100755 (executable)
new mode 100644 (file)
index 96bf602..9afe54f
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -30,6 +31,8 @@ import net.miginfocom.swing.MigLayout;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.util.MessageManager;
+
 import java.awt.Dimension;
 
 public class AnnotationColourChooser extends JPanel
@@ -71,7 +74,7 @@ public class AnnotationColourChooser extends JPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
 
     slider.addChangeListener(new ChangeListener()
     {
@@ -118,24 +121,25 @@ public class AnnotationColourChooser extends JPanel
     // Always get default shading from preferences.
     setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.predefinedColours);
-      if (!acg.predefinedColours)
+      currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
       seqAssociated.setSelected(acg.isSeqAssociated());
+      
     }
-    adjusting = true;
     annotations = new JComboBox(
             getAnnotationItems(seqAssociated.isSelected()));
 
-    threshold.addItem("No Threshold");
-    threshold.addItem("Above Threshold");
-    threshold.addItem("Below Threshold");
+    threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
+    threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
+    threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -144,13 +148,13 @@ public class AnnotationColourChooser extends JPanel
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
-        threshold.setSelectedItem("No Threshold");
+        threshold.setSelectedIndex(0);
         break;
       case AnnotationColourGradient.ABOVE_THRESHOLD:
-        threshold.setSelectedItem("Above Threshold");
+        threshold.setSelectedIndex(1);
         break;
       case AnnotationColourGradient.BELOW_THRESHOLD:
-        threshold.setSelectedItem("Below Threshold");
+        threshold.setSelectedIndex(2);
         break;
       default:
         throw new Error(
@@ -239,7 +243,7 @@ public class AnnotationColourChooser extends JPanel
     minColour.setFont(JvSwingUtils.getLabelFont());
     minColour.setBorder(BorderFactory.createEtchedBorder());
     minColour.setPreferredSize(new Dimension(40, 20));
-    minColour.setToolTipText("Minimum Colour");
+    minColour.setToolTipText(MessageManager.getString("label.min_colour"));
     minColour.addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent e)
@@ -253,7 +257,7 @@ public class AnnotationColourChooser extends JPanel
     maxColour.setFont(JvSwingUtils.getLabelFont());
     maxColour.setBorder(BorderFactory.createEtchedBorder());
     maxColour.setPreferredSize(new Dimension(40, 20));
-    maxColour.setToolTipText("Maximum Colour");
+    maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
     maxColour.addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent e)
@@ -265,7 +269,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     ok.setOpaque(false);
-    ok.setText("OK");
+    ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -274,7 +278,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     cancel.setOpaque(false);
-    cancel.setText("Cancel");
+    cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -283,9 +287,9 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     defColours.setOpaque(false);
-    defColours.setText("Defaults");
+    defColours.setText(MessageManager.getString("action.set_defaults"));
     defColours
-            .setToolTipText("Reset min and max colours to defaults from user preferences.");
+            .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
     defColours.addActionListener(new ActionListener()
     {
 
@@ -327,7 +331,7 @@ public class AnnotationColourChooser extends JPanel
     thresholdValue.setColumns(7);
     currentColours.setFont(JvSwingUtils.getLabelFont());
     currentColours.setOpaque(false);
-    currentColours.setText("Use Original Colours");
+    currentColours.setText(MessageManager.getString("label.use_original_colours"));
     currentColours.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -337,7 +341,7 @@ public class AnnotationColourChooser extends JPanel
     });
     thresholdIsMin.setBackground(Color.white);
     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
-    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
     thresholdIsMin.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -347,7 +351,7 @@ public class AnnotationColourChooser extends JPanel
     });
     seqAssociated.setBackground(Color.white);
     seqAssociated.setFont(JvSwingUtils.getLabelFont());
-    seqAssociated.setText("Per-sequence only");
+    seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
     seqAssociated.addActionListener(new ActionListener()
     {
 
@@ -486,11 +490,11 @@ public class AnnotationColourChooser extends JPanel
             .getSelectedIndex()]];
 
     int aboveThreshold = -1;
-    if (threshold.getSelectedItem().equals("Above Threshold"))
+    if (threshold.getSelectedIndex()==1)
     {
       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
     }
-    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    else if (threshold.getSelectedIndex()==2)
     {
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
     }
@@ -548,7 +552,7 @@ public class AnnotationColourChooser extends JPanel
     if (currentAnnotation.graphMin == 0f
             && currentAnnotation.graphMax == 0f)
     {
-      acg.predefinedColours = true;
+      acg.setPredefinedColours(true);
     }
 
     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
@@ -672,7 +676,7 @@ public class AnnotationColourChooser extends JPanel
     {
       return;
     }
-    // TODO: only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+    // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
 
     float thr = currentAnnotation.threshold.value;
     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)