JAL-2015 JAL-1956 rollout of FeatureColourI in place of

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

diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index 064d58b..79217ea 100644 (file)
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -20,9 +20,9 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.GraphLine;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -33,7 +33,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.util.Hashtable;
 
 import javax.swing.BorderFactory;
 import javax.swing.JCheckBox;
@@ -52,16 +51,16 @@ public class FeatureColourChooser extends JalviewDialog
   // FeatureSettings fs;
   FeatureRenderer fr;
 
-  private GraduatedColor cs;
+  private FeatureColourI cs;
 
-  private Object oldcs;
+  private FeatureColourI oldcs;
 
   /**
    * 
    * @return the last colour setting selected by user - either oldcs (which may
    *         be a java.awt.Color) or the new GraduatedColor
    */
-  public Object getLastColour()
+  public FeatureColourI getLastColour()
   {
     if (cs == null)
     {
@@ -70,8 +69,6 @@ public class FeatureColourChooser extends JalviewDialog
     return cs;
   }
 
-  Hashtable oldgroupColours;
-
   AlignmentPanel ap;
 
   boolean adjusting = false;
@@ -127,7 +124,7 @@ public class FeatureColourChooser extends JalviewDialog
       }
     });
 
-    float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
+    float mm[] = fr.getMinMax().get(type)[0];
     min = mm[0];
     max = mm[1];
 
@@ -139,32 +136,32 @@ public class FeatureColourChooser extends JalviewDialog
     scaleFactor = (max == min) ? 1f : 100f / (max - min);
 
     oldcs = fr.getFeatureColours().get(type);
-    if (oldcs instanceof GraduatedColor)
+    if (!oldcs.isSimpleColour())
     {
-      if (((GraduatedColor) oldcs).isAutoScale())
+      if (oldcs.isAutoScaled())
       {
         // update the scale
-        cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+        cs = new FeatureColour((FeatureColour) oldcs, min, max);
       }
       else
       {
-        cs = new GraduatedColor((GraduatedColor) oldcs);
+        cs = new FeatureColour((FeatureColour) oldcs);
       }
     }
     else
     {
       // promote original color to a graduated color
-      Color bl = Color.black;
-      if (oldcs instanceof Color)
+      Color bl = oldcs.getColour();
+      if (bl == null)
       {
-        bl = (Color) oldcs;
+        bl = Color.BLACK;
       }
       // original colour becomes the maximum colour
-      cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
+      cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
       cs.setColourByLabel(false);
     }
-    minColour.setBackground(oldminColour = cs.getMinColor());
-    maxColour.setBackground(oldmaxColour = cs.getMaxColor());
+    minColour.setBackground(oldminColour = cs.getMinColour());
+    maxColour.setBackground(oldmaxColour = cs.getMaxColour());
     adjusting = true;
 
     try
@@ -174,18 +171,15 @@ public class FeatureColourChooser extends JalviewDialog
     {
     }
     // update the gui from threshold state
-    thresholdIsMin.setSelected(!cs.isAutoScale());
+    thresholdIsMin.setSelected(!cs.isAutoScaled());
     colourByLabel.setSelected(cs.isColourByLabel());
-    if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+    if (cs.hasThreshold())
     {
       // initialise threshold slider and selector
-      threshold
-              .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
-                      : 2);
+      threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
-      threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
-              "Threshold", Color.black);
+      threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 
     }
 
@@ -395,50 +389,50 @@ public class FeatureColourChooser extends JalviewDialog
       return;
     }
 
-    int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
+    boolean aboveThreshold = false;
+    boolean belowThreshold = false;
     if (threshold.getSelectedIndex() == 1)
     {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+      aboveThreshold = true;
     }
     else if (threshold.getSelectedIndex() == 2)
     {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+      belowThreshold = true;
     }
+    boolean hasThreshold = aboveThreshold || belowThreshold;
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
 
-    GraduatedColor acg;
+    FeatureColourI acg;
     if (cs.isColourByLabel())
     {
-      acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
+      acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
     }
     else
     {
-      acg = new GraduatedColor(oldminColour = minColour.getBackground(),
+      acg = new FeatureColour(oldminColour = minColour.getBackground(),
               oldmaxColour = maxColour.getBackground(), min, max);
 
     }
 
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    if (!hasThreshold)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
       thresholdIsMin.setEnabled(false);
     }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
-            && threshline == null)
+    else if (threshline == null)
     {
       // todo visual indication of feature threshold
-      threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
-              "Threshold", Color.black);
+      threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
     }
 
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    if (hasThreshold)
     {
       adjusting = true;
-      acg.setThresh(threshline.value);
+      acg.setThreshold(threshline.value);
 
       float range = (max - min) * scaleFactor;
 
@@ -453,18 +447,18 @@ public class FeatureColourChooser extends JalviewDialog
       adjusting = false;
     }
 
-    acg.setThreshType(aboveThreshold);
-    if (thresholdIsMin.isSelected()
-            && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    acg.setAboveThreshold(aboveThreshold);
+    acg.setBelowThreshold(belowThreshold);
+    if (thresholdIsMin.isSelected() && hasThreshold)
     {
       acg.setAutoScaled(false);
-      if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+      if (aboveThreshold)
       {
-        acg = new GraduatedColor(acg, threshline.value, max);
+        acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
       }
       else
       {
-        acg = new GraduatedColor(acg, min, threshline.value);
+        acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
       }
     }
     else
@@ -554,7 +548,7 @@ public class FeatureColourChooser extends JalviewDialog
   public void valueChanged()
   {
     threshline.value = slider.getValue() / scaleFactor;
-    cs.setThresh(threshline.value);
+    cs.setThreshold(threshline.value);
     changeColour();
     ap.paintAlignment(false);
   }