Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index f85a073..487b75c 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,15 +20,35 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
 public class AnnotationColourChooser extends Panel implements
         ActionListener, AdjustmentListener, ItemListener, MouseListener
 {
@@ -61,9 +81,9 @@ public class AnnotationColourChooser extends Panel implements
       oldgroupColours = new Hashtable();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.cs != null)
+        if (sg.getColourScheme() != null)
         {
-          oldgroupColours.put(sg, sg.cs);
+          oldgroupColours.put(sg, sg.getColourScheme());
         }
         else
         {
@@ -77,7 +97,8 @@ public class AnnotationColourChooser extends Panel implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.getAlignment().getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
@@ -98,15 +119,23 @@ public class AnnotationColourChooser extends Panel implements
       // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < anns.length; i++)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
       if (!list.contains(label))
+      {
         list.addElement(label);
+      }
       else
+      {
         list.addElement(label + "_" + (index++));
+      }
     }
 
     for (int i = 0; i < list.size(); i++)
@@ -115,11 +144,11 @@ public class AnnotationColourChooser extends Panel implements
     }
 
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
+            .getString("label.threshold_feature_no_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
+            .getString("label.threshold_feature_above_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+            .getString("label.threshold_feature_below_threshold"));
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -138,7 +167,8 @@ public class AnnotationColourChooser extends Panel implements
         break;
       default:
         throw new Error(
-                "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+                MessageManager
+                        .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
       }
       thresholdIsMin.setState(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -285,6 +315,7 @@ public class AnnotationColourChooser extends Panel implements
 
   Checkbox thresholdIsMin = new Checkbox();
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)
@@ -312,7 +343,6 @@ public class AnnotationColourChooser extends Panel implements
     }
     else if (evt.getSource() == ok)
     {
-      changeColour();
       frame.setVisible(false);
     }
     else if (evt.getSource() == cancel)
@@ -328,6 +358,7 @@ public class AnnotationColourChooser extends Panel implements
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == currentColours)
@@ -345,18 +376,19 @@ public class AnnotationColourChooser extends Panel implements
     changeColour();
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
     {
-      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
       if (currentColours.getState()
               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
         changeColour();
       }
 
-      currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+      currentAnnotation.threshold.value = slider.getValue() / 1000f;
       ap.paintAlignment(false);
     }
   }
@@ -455,8 +487,6 @@ public class AnnotationColourChooser extends Panel implements
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), aboveThreshold);
     }
     else
     {
@@ -481,21 +511,21 @@ public class AnnotationColourChooser extends Panel implements
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
 
-        if (sg.cs == null)
+        if (sg.getColourScheme() == null)
         {
           continue;
         }
 
         if (currentColours.getState())
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  aboveThreshold);
+          sg.setColourScheme(new AnnotationColourGradient(
+                  currentAnnotation, sg.getColourScheme(), aboveThreshold));
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  aboveThreshold);
+          sg.setColourScheme(new AnnotationColourGradient(
+                  currentAnnotation, minColour.getBackground(), maxColour
+                          .getBackground(), aboveThreshold));
         }
 
       }
@@ -516,12 +546,12 @@ public class AnnotationColourChooser extends Panel implements
         Object cs = oldgroupColours.get(sg);
         if (cs instanceof ColourSchemeI)
         {
-          sg.cs = (ColourSchemeI) cs;
+          sg.setColourScheme((ColourSchemeI) cs);
         }
         else
         {
           // probably the "null" string we set it to if it was null originally.
-          sg.cs = null;
+          sg.setColourScheme(null);
         }
       }
     }
@@ -529,23 +559,28 @@ public class AnnotationColourChooser extends Panel implements
 
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }