Merge branch 'JAL-1483_29dev' into develop

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

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 32ffdbf..c87803c 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -73,10 +73,10 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     this.type = type;
     fr = frenderer;
-    float mm[] = ((float[][]) fr.minmax.get(type))[0];
+    float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
     min = mm[0];
     max = mm[1];
-    oldcs = fr.featureColours.get(type);
+    oldcs = fr.getFeatureColours().get(type);
     if (oldcs instanceof GraduatedColor)
     {
       cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
@@ -130,7 +130,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     {
       // cancel
       reset();
-      PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+      PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
       frame.setVisible(false);
     }
   }
@@ -289,7 +289,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     threshline.value = (float) slider.getValue() / 1000f;
     cs.setThresh(threshline.value);
     changeColour();
-    PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+    PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     // ap.paintAlignment(false);
   }
 
@@ -402,16 +402,16 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       }
     }
 
-    fr.featureColours.put(type, acg);
+    fr.setColour(type, acg);
     cs = acg;
-    PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+    PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     // ap.paintAlignment(false);
   }
 
   void reset()
   {
-    fr.featureColours.put(type, oldcs);
-    PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+    fr.setColour(type, oldcs);
+    PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     // ap.paintAlignment(true);
 
   }
@@ -433,7 +433,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     }
     else
     {
-      PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+      PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     }
     // ap.paintAlignment(true);
   }