X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureColourChooser.java;h=d1d1b6d6c0516edab5718cfb8f1835af50cfed66;hb=7b39c1ea0410b4cc8410b69b2d008ed0af3b6cb5;hp=6b28937336ff480f467f2cd61c088e9a0ecef2dc;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index 6b28937..d1d1b6d 100644
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.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;
@@ -107,10 +109,10 @@ public class FeatureColourChooser extends JalviewDialog
       }
     });
 
-    float mm[] = ((float[][]) fr.minmax.get(type))[0];
+    float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
     min = mm[0];
     max = mm[1];
-    oldcs = fr.featureColours.get(type);
+    oldcs = fr.getFeatureColours().get(type);
     if (oldcs instanceof GraduatedColor)
     {
       if (((GraduatedColor) oldcs).isAutoScale())
@@ -225,10 +227,14 @@ public class FeatureColourChooser extends JalviewDialog
         threshold_actionPerformed(e);
       }
     });
-    threshold.setToolTipText(MessageManager.getString("label.threshold_feature_display_by_score"));
-    threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); // index 0
-    threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); // index 1
-    threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); // index 2
+    threshold.setToolTipText(MessageManager
+            .getString("label.threshold_feature_display_by_score"));
+    threshold.addItem(MessageManager
+            .getString("label.threshold_feature_no_thereshold")); // index 0
+    threshold.addItem(MessageManager
+            .getString("label.threshold_feature_above_thereshold")); // index 1
+    threshold.addItem(MessageManager
+            .getString("label.threshold_feature_below_thereshold")); // index 2
     jPanel3.setLayout(flowLayout2);
     thresholdValue.addActionListener(new ActionListener()
     {
@@ -243,14 +249,16 @@ public class FeatureColourChooser extends JalviewDialog
     slider.setEnabled(false);
     slider.setOpaque(false);
     slider.setPreferredSize(new Dimension(100, 32));
-    slider.setToolTipText(MessageManager.getString("label.adjust_thereshold"));
+    slider.setToolTipText(MessageManager
+            .getString("label.adjust_thereshold"));
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(7);
     jPanel3.setBackground(Color.white);
     thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
-    thresholdIsMin
-            .setToolTipText(MessageManager.getString("label.toggle_absolute_relative_display_threshold"));
+    thresholdIsMin.setText(MessageManager
+            .getString("label.threshold_minmax"));
+    thresholdIsMin.setToolTipText(MessageManager
+            .getString("label.toggle_absolute_relative_display_threshold"));
     thresholdIsMin.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -259,9 +267,11 @@ public class FeatureColourChooser extends JalviewDialog
       }
     });
     colourByLabel.setBackground(Color.white);
-    colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
     colourByLabel
-            .setToolTipText(MessageManager.getString("label.display_features_same_type_different_label_using_different_colour"));
+            .setText(MessageManager.getString("label.colour_by_label"));
+    colourByLabel
+            .setToolTipText(MessageManager
+                    .getString("label.display_features_same_type_different_label_using_different_colour"));
     colourByLabel.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -331,7 +341,8 @@ public class FeatureColourChooser extends JalviewDialog
   public void minColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
     if (col != null)
     {
       minColour.setBackground(col);
@@ -344,7 +355,8 @@ public class FeatureColourChooser extends JalviewDialog
   public void maxColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
     if (col != null)
     {
       maxColour.setBackground(col);
@@ -363,11 +375,11 @@ public class FeatureColourChooser extends JalviewDialog
     }
 
     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
-    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;
     }
@@ -458,7 +470,7 @@ public class FeatureColourChooser extends JalviewDialog
       maxColour.setForeground(oldmaxColour);
       minColour.setForeground(oldminColour);
     }
-    fr.featureColours.put(type, acg);
+    fr.setColour(type, acg);
     cs = acg;
     ap.paintAlignment(false);
   }
@@ -483,7 +495,7 @@ public class FeatureColourChooser extends JalviewDialog
 
   void reset()
   {
-    fr.featureColours.put(type, oldcs);
+    fr.setColour(type, oldcs);
     ap.paintAlignment(false);
     cs = null;
   }