X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FUserDefinedColours.java;h=bfce8806f24c92d8df11ecfa1a8a3f0e404ee6ee;hb=2ab7b9b152018bb808693218ad88dc3778166492;hp=a81e8317616324615285b57a85b3a3d7e4045683;hpb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;p=jalview.git

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index a81e831..bfce880 100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,25 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
 
+import jalview.analysis.AAFrequency;
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
@@ -41,11 +49,13 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
 import java.awt.event.MouseEvent;
 import java.util.Vector;
 
-public class UserDefinedColours extends Panel implements ActionListener,
-        AdjustmentListener
+public class UserDefinedColours extends Panel
+        implements ActionListener, AdjustmentListener, FocusListener
 {
 
   AlignmentPanel ap;
@@ -54,7 +64,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
   Button selectedButton;
 
-  Vector oldColours = new Vector();
+  Vector<Color> oldColours = new Vector<>();
 
   ColourSchemeI oldColourScheme;
 
@@ -70,7 +80,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
   String originalLabel;
 
-  Object originalColour;
+  FeatureColourI originalColour;
 
   int R = 0, G = 0, B = 0;
 
@@ -87,7 +97,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -112,7 +122,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
   public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
   {
     caller = fr;
-    originalColour = fr.colourPanel.getBackground();
+    originalColour = new FeatureColour(fr.colourPanel.getBackground());
     originalLabel = "Feature Colour";
     setForDialog("Select Feature Colour", alignframe);
     setTargetColour(fr.colourPanel.getBackground());
@@ -129,21 +139,21 @@ public class UserDefinedColours extends Panel implements ActionListener,
    * 
    * @param caller
    *          - handles events
-   * @param col1
+   * @param col
    *          - original colour
    * @param alignframe
    *          - the parent Frame for the dialog
    * @param title
    *          - window title
    */
-  public UserDefinedColours(Component caller, Color col1, Frame alignframe,
+  public UserDefinedColours(Component caller, Color col, Frame alignframe,
           String title)
   {
     this.caller = caller;
-    originalColour = col1;
+    originalColour = new FeatureColour(col);
     originalLabel = title;
     setForDialog(title, alignframe);
-    setTargetColour(col1);
+    setTargetColour(col);
     dialog.setVisible(true);
   }
 
@@ -156,7 +166,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
    */
   public UserDefinedColours(Object caller, String label, Color colour)
   {
-    this(caller, label, colour, colour);
+    this(caller, label, new FeatureColour(colour), colour);
   }
 
   /**
@@ -167,13 +177,13 @@ public class UserDefinedColours extends Panel implements ActionListener,
    * @param graduatedColor
    */
   public UserDefinedColours(FeatureSettings me, String type,
-          GraduatedColor graduatedColor)
+          FeatureColourI graduatedColor)
   {
-    this(me, type, graduatedColor, graduatedColor.getMaxColor());
+    this(me, type, graduatedColor, graduatedColor.getMaxColour());
   }
 
-  private UserDefinedColours(Object caller, String label, Object ocolour,
-          Color colour)
+  private UserDefinedColours(Object caller, String label,
+          FeatureColourI ocolour, Color colour)
   {
     this.caller = caller;
     originalColour = ocolour;
@@ -184,7 +194,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
     setTargetColour(colour);
 
     okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
-    frame.setTitle("User Defined Colours - " + label);
+    frame.setTitle(MessageManager.getString("label.user_defined_colours")
+            + " - " + label);
     frame.setSize(420, 200);
   }
 
@@ -203,7 +214,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
       // // not 1.1 compatible!
       // dialog = new Dialog(((JVDialog)alignframe), title, true);
       // } else {
-      throw new Error("Unsupported owner for User Colour scheme dialog.");
+      throw new Error(MessageManager.getString(
+              "label.error_unsupported_owwner_user_colour_scheme"));
     }
 
     dialog.add(this);
@@ -212,42 +224,46 @@ public class UserDefinedColours extends Panel implements ActionListener,
     int height = 160 + alignframe.getInsets().top + getInsets().bottom;
     int width = 400;
 
-    dialog.setBounds(alignframe.getBounds().x
-            + (alignframe.getSize().width - width) / 2,
+    dialog.setBounds(
+            alignframe.getBounds().x
+                    + (alignframe.getSize().width - width) / 2,
             alignframe.getBounds().y
-                    + (alignframe.getSize().height - height) / 2, width,
-            height);
+                    + (alignframe.getSize().height - height) / 2,
+            width, height);
 
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
-    if (evt.getSource() == okButton)
+    final Object source = evt.getSource();
+    if (source == okButton)
     {
       okButton_actionPerformed();
     }
-    else if (evt.getSource() == applyButton)
+    else if (source == applyButton)
     {
       applyButton_actionPerformed();
     }
-    else if (evt.getSource() == cancelButton)
+    else if (source == cancelButton)
     {
       cancelButton_actionPerformed();
     }
-    else if (evt.getSource() == rText)
+    else if (source == rText)
     {
       rText_actionPerformed();
     }
-    else if (evt.getSource() == gText)
+    else if (source == gText)
     {
       gText_actionPerformed();
     }
-    else if (evt.getSource() == bText)
+    else if (source == bText)
     {
       bText_actionPerformed();
     }
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (evt.getSource() == rScroller)
@@ -275,7 +291,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
     }
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420,
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.user_defined_colours"), 420,
             345);
 
     if (seqGroup != null)
@@ -394,14 +411,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
   {
     final Button button = new Button();
     Color col = Color.white;
-    if (oldColourScheme != null)
+    if (oldColourScheme != null && oldColourScheme.isSimple())
     {
-      try
-      {
-        col = oldColourScheme.findColour(aa.charAt(0), -1, null);
-      } catch (Exception ex)
-      {
-      }
+      col = oldColourScheme.findColour(aa.charAt(0), 0, null, null, 0f);
     }
     button.setBackground(col);
     oldColours.addElement(col);
@@ -410,6 +422,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     button.setFont(new java.awt.Font("Verdana", 1, 10));
     button.addMouseListener(new java.awt.event.MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         colourButtonPressed(e);
@@ -423,7 +436,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
   {
     applyButton_actionPerformed();
     if (dialog != null)
+    {
       dialog.setVisible(false);
+    }
 
     frame.setVisible(false);
   }
@@ -439,7 +454,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (caller instanceof FeatureSettings)
       {
-        ((FeatureSettings) caller).setUserColour(originalLabel, getColor());
+        ((FeatureSettings) caller).setUserColour(originalLabel,
+                new FeatureColour(getColor()));
       }
       else if (caller instanceof AnnotationColourChooser)
       {
@@ -456,7 +472,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
       }
       else if (caller instanceof FeatureRenderer)
       {
-        ((FeatureRenderer) caller).colourPanel.updateColor(getColor());
+        ((FeatureRenderer) caller).colourPanel
+                .updateColor(new FeatureColour(getColor()));
       }
       else if (caller instanceof FeatureColourChooser)
       {
@@ -483,27 +500,31 @@ public class UserDefinedColours extends Panel implements ActionListener,
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     if (ap != null)
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = ucs;
+        seqGroup.cs = new ResidueShader(ucs);
+        seqGroup.getGroupColourScheme().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       else
       {
         ap.av.setGlobalColourScheme(ucs);
+        ap.av.getResidueShading().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       ap.seqPanel.seqCanvas.img = null;
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
     else if (jmol != null)
     {
-      jmol.setJalviewColourScheme(ucs);
+      jmol.colourByJalviewColourScheme(ucs);
     }
     else if (pdbcanvas != null)
     {
@@ -525,12 +546,12 @@ public class UserDefinedColours extends Panel implements ActionListener,
         if (originalLabel.equals("Min Colour"))
         {
           ((AnnotationColourChooser) caller)
-                  .minColour_actionPerformed((Color) originalColour);
+                  .minColour_actionPerformed(originalColour.getColour());
         }
         else
         {
           ((AnnotationColourChooser) caller)
-                  .maxColour_actionPerformed((Color) originalColour);
+                  .maxColour_actionPerformed(originalColour.getColour());
         }
       }
       else if (caller instanceof FeatureRenderer)
@@ -544,49 +565,41 @@ public class UserDefinedColours extends Panel implements ActionListener,
         if (originalLabel.indexOf("inimum") > -1)
         {
           ((FeatureColourChooser) caller)
-                  .minColour_actionPerformed((Color) originalColour);
+                  .minColour_actionPerformed(originalColour.getColour());
         }
         else
         {
           ((FeatureColourChooser) caller)
-                  .maxColour_actionPerformed((Color) originalColour);
+                  .maxColour_actionPerformed(originalColour.getColour());
         }
       }
       if (dialog != null)
+      {
         dialog.setVisible(false);
+      }
 
       frame.setVisible(false);
       return;
     }
 
-    Color[] newColours = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      newColours[i] = (Color) oldColours.elementAt(i);
-      buttonPanel.getComponent(i).setBackground(newColours[i]);
-    }
-
-    UserColourScheme ucs = new UserColourScheme(newColours);
-
     if (ap != null)
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = ucs;
+        seqGroup.cs = new ResidueShader(oldColourScheme);
+        if (oldColourScheme instanceof PIDColourScheme
+                || oldColourScheme instanceof Blosum62ColourScheme)
+        {
+          seqGroup.cs.setConsensus(AAFrequency.calculate(
+                  seqGroup.getSequences(ap.av.getHiddenRepSequences()), 0,
+                  ap.av.getAlignment().getWidth()));
+        }
       }
       else
       {
-        ap.av.setGlobalColourScheme(ucs);
+        ap.av.setGlobalColourScheme(oldColourScheme);
       }
-      ap.paintAlignment(true);
-    }
-    else if (jmol != null)
-    {
-      jmol.setJalviewColourScheme(ucs);
-    }
-    else if (pdbcanvas != null)
-    {
-      pdbcanvas.pdb.setColours(ucs);
+      ap.paintAlignment(true, true);
     }
 
     frame.setVisible(false);
@@ -656,6 +669,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     rText.setText("0        ");
     rText.setBounds(new Rectangle(156, 27, 53, 19));
     rText.addActionListener(this);
+    rText.addFocusListener(this);
     label4.setAlignment(Label.RIGHT);
     label4.setText("G");
     label4.setBounds(new Rectangle(15, 56, 20, 15));
@@ -670,6 +684,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     gText.setText("0        ");
     gText.setBounds(new Rectangle(156, 52, 53, 20));
     gText.addActionListener(this);
+    gText.addFocusListener(this);
     label5.setAlignment(Label.RIGHT);
     label5.setText("B");
     label5.setBounds(new Rectangle(14, 82, 20, 15));
@@ -684,12 +699,16 @@ public class UserDefinedColours extends Panel implements ActionListener,
     bText.setText("0        ");
     bText.setBounds(new Rectangle(157, 78, 52, 20));
     bText.addActionListener(this);
+    bText.addFocusListener(this);
     target.setBackground(Color.black);
     target.setBounds(new Rectangle(229, 26, 134, 79));
     this.add(okcancelPanel, null);
     okcancelPanel.add(okButton, null);
     okcancelPanel.add(applyButton, null);
     okcancelPanel.add(cancelButton, null);
+    this.add(rText);
+    this.add(gText);
+    this.add(bText);
     this.add(buttonPanel, null);
     this.add(target, null);
     this.add(gScroller);
@@ -698,9 +717,40 @@ public class UserDefinedColours extends Panel implements ActionListener,
     this.add(label5);
     this.add(label4);
     this.add(label1);
-    this.add(gText);
-    this.add(rText);
-    this.add(bText);
+  }
+
+  @Override
+  public void focusGained(FocusEvent e)
+  {
+    // noop
+  }
+
+  /**
+   * This method applies any change to an RGB value if the user tabs out of the
+   * field instead of pressing Enter
+   */
+  @Override
+  public void focusLost(FocusEvent e)
+  {
+    Component c = e.getComponent();
+    if (c == rText)
+    {
+      rText_actionPerformed();
+    }
+    else
+    {
+      if (c == gText)
+      {
+        gText_actionPerformed();
+      }
+      else
+      {
+        if (c == bText)
+        {
+          bText_actionPerformed();
+        }
+      }
+    }
   }
 
 }