JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 4cbb985..40b2cac 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -133,7 +133,7 @@ public class SliderPanel extends GSliderPanel
     conservationSlider.setTitle("Conservation Colour Increment  (" + source
             + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       sp.setAllGroupsCheckEnabled(true);
     }
@@ -209,7 +209,7 @@ public class SliderPanel extends GSliderPanel
 
     PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       pid.setAllGroupsCheckEnabled(true);
     }
@@ -266,12 +266,12 @@ public class SliderPanel extends GSliderPanel
     }
 
     ColourSchemeI toChange = null;
-    Vector allGroups = null;
+    List<SequenceGroup> allGroups = null;
     int groupIndex = 0;
 
     if (allGroupsCheck.isSelected())
     {
-      allGroups = ap.av.alignment.getGroups();
+      allGroups = ap.av.getAlignment().getGroups();
       groupIndex = allGroups.size() - 1;
     }
     else