Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

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

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 8de751a..9456986 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -85,7 +85,7 @@ public class AnnotationColourChooser extends Panel implements
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
+      oldgroupColours = new HashMap<>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
         oldgroupColours.put(sg, sg.getColourScheme());
@@ -180,8 +180,8 @@ public class AnnotationColourChooser extends Panel implements
     // TODO remove duplication with gui.AnnotationRowFilter
     // TODO add 'per sequence only' option / parameter
 
-    annotationLabels = new HashMap<AlignmentAnnotation, String>();
-    Vector<String> list = new Vector<String>();
+    annotationLabels = new HashMap<>();
+    Vector<String> list = new Vector<>();
     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
     if (anns == null)
     {
@@ -350,7 +350,7 @@ public class AnnotationColourChooser extends Panel implements
     {
       try
       {
-        float f = new Float(thresholdValue.getText()).floatValue();
+        float f = Float.valueOf(thresholdValue.getText()).floatValue();
         slider.setValue((int) (f * 1000));
         adjustmentValueChanged(null);
       } catch (NumberFormatException ex)
@@ -376,7 +376,7 @@ public class AnnotationColourChooser extends Panel implements
     else if (evt.getSource() == cancel)
     {
       reset();
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
       frame.setVisible(false);
     }
 
@@ -417,7 +417,7 @@ public class AnnotationColourChooser extends Panel implements
       }
 
       currentAnnotation.threshold.value = slider.getValue() / 1000f;
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -559,7 +559,7 @@ public class AnnotationColourChooser extends Panel implements
 
     // update colours in linked windows
     ap.alignmentChanged();
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   void reset()
@@ -572,7 +572,7 @@ public class AnnotationColourChooser extends Panel implements
         sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override
@@ -588,7 +588,7 @@ public class AnnotationColourChooser extends Panel implements
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override