JAL-1620 version bump and release notes

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

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 3e7a3fd..c1363d7 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * 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;
@@ -86,8 +88,9 @@ public class AnnotationColourChooser extends Panel implements
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null);
-      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+      currentColours.setState(acg.isPredefinedColours()
+              || acg.getBaseColour() != null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
@@ -95,7 +98,6 @@ public class AnnotationColourChooser extends Panel implements
       // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-
     Vector list = new Vector();
     int index = 1;
     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
@@ -112,9 +114,12 @@ public class AnnotationColourChooser extends Panel implements
       annotations.addItem(list.elementAt(i).toString());
     }
 
-    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"));
+    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)
     {
@@ -132,8 +137,7 @@ public class AnnotationColourChooser extends Panel implements
         threshold.select(1);
         break;
       default:
-        throw new Error(
-                "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+        throw new Error(MessageManager.getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
       }
       thresholdIsMin.setState(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -145,7 +149,8 @@ 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();
   }
@@ -200,11 +205,13 @@ 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);
 
@@ -402,11 +409,11 @@ public class AnnotationColourChooser extends Panel implements
             .getSelectedIndex()];
 
     int aboveThreshold = -1;
-    if (threshold.getSelectedIndex()==1)
+    if (threshold.getSelectedIndex() == 1)
     {
       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
     }
-    else if (threshold.getSelectedIndex()==2)
+    else if (threshold.getSelectedIndex() == 2)
     {
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
     }