X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=80d39e80ef783c2fa43dad6952136461b257a184;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=ab3b3793d1cb57ff2416194a7f21f42b5c3f0d69;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index ab3b379..80d39e8 100755
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,31 +1,33 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, 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 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.
-*
-* 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 - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
+ *
+ * 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
+ */
 package jalview.appletgui;
 
-import java.awt.event.*;
+import java.util.*;
+
 import java.awt.*;
+import java.awt.event.*;
 
+import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.util.*;
-import jalview.datamodel.SequenceGroup;
 
-public class AnnotationColourChooser extends Panel implements ActionListener,
+public class AnnotationColourChooser
+    extends Panel implements ActionListener,
     AdjustmentListener, ItemListener
 {
   Frame frame;
@@ -63,7 +65,9 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     slider.addAdjustmentListener(this);
 
     if (av.alignment.getAlignmentAnnotation() == null)
+    {
       return;
+    }
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -81,7 +85,9 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
+      {
         annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
+      }
     }
 
     threshold.addItem("No Threshold");
@@ -178,10 +184,9 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
   Checkbox currentColours = new Checkbox();
   BorderLayout borderLayout1 = new BorderLayout();
 
-
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource() == thresholdValue)
+    if (evt.getSource() == thresholdValue)
     {
       try
       {
@@ -193,9 +198,13 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       {}
     }
     else if (evt.getSource() == minColour)
+    {
       minColour_actionPerformed(null);
+    }
     else if (evt.getSource() == maxColour)
+    {
       maxColour_actionPerformed(null);
+    }
 
     else if (evt.getSource() == ok)
     {
@@ -210,10 +219,11 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     }
 
     else
+    {
       changeColour();
+    }
   }
 
-
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == currentColours)
@@ -256,8 +266,10 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       changeColour();
     }
     else
+    {
       new UserDefinedColours(this, "Min Colour",
-                              minColour.getBackground());
+                             minColour.getBackground());
+    }
 
   }
 
@@ -270,16 +282,19 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       changeColour();
     }
     else
+    {
       new UserDefinedColours(this, "Max Colour",
-                              maxColour.getBackground());
+                             maxColour.getBackground());
+    }
   }
 
-
   void changeColour()
   {
     // Check if combobox is still adjusting
     if (adjusting)
+    {
       return;
+    }
 
     // We removed the non-graph annotations when filling the combobox
     // so allow for them again here
@@ -287,21 +302,31 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
+      {
         nograph++;
+      }
       else
+      {
         graph++;
+      }
 
       if (graph == annotations.getSelectedIndex())
+      {
         break;
+      }
     }
 
     currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
 
     int aboveThreshold = -1;
     if (threshold.getSelectedItem().equals("Above Threshold"))
+    {
       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    }
     else if (threshold.getSelectedItem().equals("Below Threshold"))
+    {
       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+    }
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
@@ -322,7 +347,7 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
                                       Color.black));
     }
 
-    if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
 
@@ -337,16 +362,20 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
 
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
+    {
       acg = new AnnotationColourGradient(
           currentAnnotation,
           av.getGlobalColourScheme(), aboveThreshold);
+    }
     else
+    {
       acg =
           new AnnotationColourGradient(
               currentAnnotation,
               minColour.getBackground(),
               maxColour.getBackground(),
               aboveThreshold);
+    }
 
     av.setGlobalColourScheme(acg);
 
@@ -364,15 +393,19 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
         }
 
         if (currentColours.getState())
+        {
           sg.cs = new AnnotationColourGradient(
               currentAnnotation,
               sg.cs, aboveThreshold);
+        }
         else
+        {
           sg.cs = new AnnotationColourGradient(
               currentAnnotation,
               minColour.getBackground(),
               maxColour.getBackground(),
               aboveThreshold);
+        }
 
       }
     }
@@ -380,7 +413,6 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     ap.repaint();
   }
 
-
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
@@ -391,13 +423,11 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       for (int g = 0; g < allGroups.size(); g++)
       {
         sg = (SequenceGroup) allGroups.elementAt(g);
-        sg.cs = (ColourSchemeI)oldgroupColours.get(sg);
+        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }
     ap.repaint();
 
   }
 
-
-
 }