JAL-1517 source formatting

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

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index f9594eb..f85a073 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,19 +1,22 @@
 /*
- * 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.
  * 
  * 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.appletgui;
 
@@ -81,19 +84,20 @@ public class AnnotationColourChooser extends Panel implements
 
     setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setState(acg.isPredefinedColours());
-      if (!acg.isPredefinedColours())
+      currentColours.setState(acg.isPredefinedColours()
+              || acg.getBaseColour() != null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
+      // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    adjusting = true;
-
     Vector list = new Vector();
     int index = 1;
     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
@@ -110,9 +114,12 @@ public class AnnotationColourChooser extends Panel implements
       annotations.addItem(list.elementAt(i).toString());
     }
 
-    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)
     {
@@ -121,13 +128,13 @@ public class AnnotationColourChooser extends Panel implements
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
-        threshold.select("No Threshold");
+        threshold.select(0);
         break;
       case AnnotationColourGradient.ABOVE_THRESHOLD:
-        threshold.select("Above Threshold");
+        threshold.select(1);
         break;
       case AnnotationColourGradient.BELOW_THRESHOLD:
-        threshold.select("Below Threshold");
+        threshold.select(1);
         break;
       default:
         throw new Error(
@@ -143,7 +150,8 @@ public class AnnotationColourChooser extends Panel implements
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560,
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.colour_by_annotation"), 560,
             175);
     validate();
   }
@@ -198,11 +206,13 @@ public class AnnotationColourChooser extends Panel implements
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(5);
     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    currentColours.setLabel(MessageManager.getString("label.use_original_colours"));
+    currentColours.setLabel(MessageManager
+            .getString("label.use_original_colours"));
     currentColours.addItemListener(this);
 
     thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
+    thresholdIsMin.setLabel(MessageManager
+            .getString("label.threshold_minmax"));
 
     this.setLayout(borderLayout1);
 
@@ -400,11 +410,11 @@ public class AnnotationColourChooser extends Panel implements
             .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;
     }
@@ -492,6 +502,7 @@ public class AnnotationColourChooser extends Panel implements
     }
 
     // update colours in linked windows
+    ap.alignmentChanged();
     ap.paintAlignment(true);
   }