default parameter for colours in annotation shading (JAL-234), ensure

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

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 4c7bc0c..639140e 100755 (executable)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.gui;
 
@@ -25,6 +24,7 @@ import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 
+import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import java.awt.Dimension;
@@ -93,16 +93,21 @@ public class AnnotationColourChooser extends JPanel
       return;
     }
 
+    // Always get default shading from preferences.
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      minColour.setBackground(acg.getMinColour());
-      maxColour.setBackground(acg.getMaxColour());
-    }
-    else
-    {
-      minColour.setBackground(Color.orange);
-      maxColour.setBackground(Color.red);
+      currentColours.setSelected(acg.predefinedColours);
+      if (acg.predefinedColours)
+      {
+        
+      } else {
+        minColour.setBackground(acg.getMinColour());
+        maxColour.setBackground(acg.getMaxColour());
+      }
     }
 
     adjusting = true;
@@ -123,6 +128,27 @@ public class AnnotationColourChooser extends JPanel
     threshold.addItem("Above Threshold");
     threshold.addItem("Below Threshold");
 
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.setSelectedItem(acg.getAnnotation());
+      switch (acg.getAboveThreshold()) {
+      case AnnotationColourGradient.NO_THRESHOLD:
+          threshold.setSelectedItem("No Threshold");
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+          threshold.setSelectedItem("Above Threshold");
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        threshold.setSelectedItem("Below Threshold");
+        break;
+        default:
+          throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+      }
+      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdValue.setText(""+acg.getAnnotationThreshold());
+    }
+
     try
     {
       jbInit();
@@ -133,6 +159,7 @@ public class AnnotationColourChooser extends JPanel
     adjusting = false;
 
     changeColour();
+    validate();
 
   }
 
@@ -378,13 +405,14 @@ public class AnnotationColourChooser extends JPanel
     AnnotationColourGradient acg = null;
     if (currentColours.isSelected())
     {
-      acg = new AnnotationColourGradient(currentAnnotation, av
-              .getGlobalColourScheme(), aboveThreshold);
+      acg = new AnnotationColourGradient(currentAnnotation,
+              av.getGlobalColourScheme(), aboveThreshold);
     }
     else
     {
-      acg = new AnnotationColourGradient(currentAnnotation, minColour
-              .getBackground(), maxColour.getBackground(), aboveThreshold);
+      acg = new AnnotationColourGradient(currentAnnotation,
+              minColour.getBackground(), maxColour.getBackground(),
+              aboveThreshold);
     }
 
     if (currentAnnotation.graphMin == 0f
@@ -417,15 +445,15 @@ public class AnnotationColourChooser extends JPanel
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, minColour
-                  .getBackground(), maxColour.getBackground(),
+          sg.cs = new AnnotationColourGradient(currentAnnotation,
+                  minColour.getBackground(), maxColour.getBackground(),
                   aboveThreshold);
         }
 
       }
     }
-
-    ap.paintAlignment(false);
+    // ensure all associated views (overviews, structures, etc) are notified of updated colours.
+    ap.paintAlignment(true);
   }
 
   public void ok_actionPerformed(ActionEvent e)