JAL-1517 source formatting

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

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 60a0759..39f3a13 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.gui;
@@ -50,8 +52,10 @@ public class AnnotationColourChooser extends JPanel
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
+
   /**
-   * enabled if the user is dragging the slider - try to keep updates to a minimun
+   * enabled if the user is dragging the slider - try to keep updates to a
+   * minimun
    */
   boolean sliderDragging = false;
 
@@ -74,7 +78,9 @@ public class AnnotationColourChooser extends JPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+    Desktop.addInternalFrame(frame,
+            MessageManager.getString("label.colour_by_annotation"), 520,
+            215);
 
     slider.addChangeListener(new ChangeListener()
     {
@@ -92,21 +98,22 @@ public class AnnotationColourChooser extends JPanel
       @Override
       public void mousePressed(MouseEvent e)
       {
-        sliderDragging=true;
+        sliderDragging = true;
         super.mousePressed(e);
       }
 
       @Override
       public void mouseDragged(MouseEvent e)
       {
-        sliderDragging=true;
+        sliderDragging = true;
         super.mouseDragged(e);
       }
+
       public void mouseReleased(MouseEvent evt)
       {
         if (sliderDragging)
         {
-          sliderDragging=false;
+          sliderDragging = false;
           valueChanged(true);
         }
         ap.paintAlignment(true);
@@ -125,21 +132,25 @@ public class AnnotationColourChooser extends JPanel
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
-      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+      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());
-      
+
     }
     annotations = new JComboBox(
             getAnnotationItems(seqAssociated.isSelected()));
 
-    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)
     {
@@ -219,6 +230,7 @@ public class AnnotationColourChooser extends JPanel
     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
     return list;
   }
+
   private void setDefaultMinMax()
   {
     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
@@ -288,8 +300,8 @@ public class AnnotationColourChooser extends JPanel
     });
     defColours.setOpaque(false);
     defColours.setText(MessageManager.getString("action.set_defaults"));
-    defColours
-            .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+    defColours.setToolTipText(MessageManager
+            .getString("label.reset_min_max_colours_to_defaults"));
     defColours.addActionListener(new ActionListener()
     {
 
@@ -331,7 +343,8 @@ public class AnnotationColourChooser extends JPanel
     thresholdValue.setColumns(7);
     currentColours.setFont(JvSwingUtils.getLabelFont());
     currentColours.setOpaque(false);
-    currentColours.setText(MessageManager.getString("label.use_original_colours"));
+    currentColours.setText(MessageManager
+            .getString("label.use_original_colours"));
     currentColours.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -341,7 +354,8 @@ public class AnnotationColourChooser extends JPanel
     });
     thresholdIsMin.setBackground(Color.white);
     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
-    thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
+    thresholdIsMin.setText(MessageManager
+            .getString("label.threshold_minmax"));
     thresholdIsMin.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -351,7 +365,8 @@ public class AnnotationColourChooser extends JPanel
     });
     seqAssociated.setBackground(Color.white);
     seqAssociated.setFont(JvSwingUtils.getLabelFont());
-    seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
+    seqAssociated.setText(MessageManager
+            .getString("label.per_sequence_only"));
     seqAssociated.addActionListener(new ActionListener()
     {
 
@@ -490,11 +505,11 @@ public class AnnotationColourChooser extends JPanel
             .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;
     }
@@ -676,7 +691,8 @@ public class AnnotationColourChooser extends JPanel
     {
       return;
     }
-    // TODO: JAL-1327 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++)