Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 46a67c4..d0834e6 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -20,9 +20,12 @@
  */
 package jalview.appletgui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.GraphLine;
 import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.Colour;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 
 import java.awt.Checkbox;
@@ -60,9 +63,9 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
   // AlignmentPanel ap;
 
-  GraduatedColor cs;
+  FeatureColourI cs;
 
-  Object oldcs;
+  FeatureColourI oldcs;
 
   Hashtable oldgroupColours;
 
@@ -91,29 +94,30 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     this.type = type;
     fr = frenderer;
-    float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
+    float mm[] = fr.getMinMax().get(type)[0];
     min = mm[0];
     max = mm[1];
     oldcs = fr.getFeatureColours().get(type);
-    if (oldcs instanceof GraduatedColor)
+    if (oldcs.isGraduatedColour())
     {
-      cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+      cs = new FeatureColour((FeatureColour) oldcs, min, max);
     }
     else
     {
       // promote original color to a graduated color
       Color bl = Color.black;
-      if (oldcs instanceof Color)
+      if (oldcs.isSimpleColour())
       {
-        bl = (Color) oldcs;
+        bl = ColorUtils.getColor(oldcs.getColour());
       }
       // original colour becomes the maximum colour
-      cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
+      cs = new FeatureColour(new Colour(Color.white), new Colour(bl),
+              mm[0], mm[1]);
     }
-    minColour.setBackground(cs.getMinColor());
-    maxColour.setBackground(cs.getMaxColor());
-    minColour.setForeground(cs.getMinColor());
-    maxColour.setForeground(cs.getMaxColor());
+    minColour.setBackground(ColorUtils.getColor(cs.getMinColour()));
+    maxColour.setBackground(ColorUtils.getColor(cs.getMaxColour()));
+    minColour.setForeground(ColorUtils.getColor(cs.getMinColour()));
+    maxColour.setForeground(ColorUtils.getColor(cs.getMaxColour()));
     colourFromLabel.setState(cs.isColourByLabel());
     adjusting = true;
 
@@ -123,10 +127,8 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     } catch (Exception ex)
     {
     }
-    threshold
-            .select(cs.getThreshType() == AnnotationColourGradient.NO_THRESHOLD ? 0
-                    : cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
-                            : 2);
+    threshold.select(cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2
+            : 0));
 
     adjusting = false;
     changeColour();
@@ -192,11 +194,11 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     jPanel4.setBackground(Color.white);
     threshold.addItemListener(this);
     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"));
     thresholdValue.addActionListener(this);
     slider.setBackground(Color.white);
     slider.setEnabled(false);
@@ -259,6 +261,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
   private GraphLine threshline;
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)
@@ -286,6 +289,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     maxColour.setEnabled(!colourFromLabel.getState());
@@ -293,27 +297,28 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     changeColour();
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
     {
-      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
       valueChanged();
     }
   }
 
   protected void valueChanged()
   {
-    threshline.value = (float) slider.getValue() / 1000f;
-    cs.setThresh(threshline.value);
+    threshline.value = slider.getValue() / 1000f;
+    cs.setThreshold(threshline.value);
     changeColour();
     PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     // ap.paintAlignment(false);
   }
 
-  public void minColour_actionPerformed(Color newCol)
+  public void minColour_actionPerformed(Color c)
   {
-    if (newCol == null)
+    if (c == null)
     {
       UserDefinedColours udc = new UserDefinedColours(this,
               minColour.getBackground(), owner,
@@ -321,8 +326,8 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     }
     else
     {
-      minColour.setBackground(newCol);
-      minColour.setForeground(newCol);
+      minColour.setBackground(c);
+      minColour.setForeground(c);
       minColour.repaint();
       changeColour();
     }
@@ -369,8 +374,9 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
-    GraduatedColor acg = new GraduatedColor(minColour.getBackground(),
-            maxColour.getBackground(), min, max);
+    FeatureColour acg = new FeatureColour(new Colour(
+            minColour.getBackground()), new Colour(
+            maxColour.getBackground()), min, max);
 
     acg.setColourByLabel(colourFromLabel.getState());
     maxColour.setEnabled(!colourFromLabel.getState());
@@ -393,7 +399,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      acg.setThresh(threshline.value);
+      acg.setThreshold(threshline.value);
 
       float range = max * 1000f - min * 1000f;
 
@@ -406,17 +412,17 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       adjusting = false;
     }
 
-    acg.setThreshType(aboveThreshold);
+    acg.setAboveThreshold(true);
     if (thresholdIsMin.getState()
             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
       {
-        acg = new GraduatedColor(acg, threshline.value, max);
+        acg = new FeatureColour(acg, threshline.value, max);
       }
       else
       {
-        acg = new GraduatedColor(acg, min, threshline.value);
+        acg = new FeatureColour(acg, min, threshline.value);
       }
     }
 
@@ -434,14 +440,17 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     if (evt.getSource() == minColour || evt.getSource() == maxColour)
@@ -456,10 +465,12 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     // ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }