X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=8e40ef0073782056798dcb83acec939ab4dd98fc;hb=efafd3884da37ce71c4e551ba023ba104e3c0559;hp=4af6fde9b5b06282edd98ad524a9b6d4d286e028;hpb=09d3b755d9b00f5c3acb44049aedd49361dc0690;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 4af6fde..8e40ef0 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -37,6 +37,7 @@ import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -612,7 +613,7 @@ public abstract class FeatureRendererModel
    * @param type
    * @return
    */
-  protected boolean showFeatureOfType(String type)
+  public boolean showFeatureOfType(String type)
   {
     return type == null ? false : (av.getFeaturesDisplayed() == null ? true
             : av.getFeaturesDisplayed().isVisible(type));
@@ -987,10 +988,8 @@ public abstract class FeatureRendererModel
   {
     return featureGroups != null
             && sequenceFeature.featureGroup != null
-            && sequenceFeature.featureGroup.length() != 0
-            && featureGroups.containsKey(sequenceFeature.featureGroup)
-            && !featureGroups.get(sequenceFeature.featureGroup)
-                    .booleanValue();
+            && sequenceFeature.featureGroup.length() > 0 && !featureGroups
+                    .get(sequenceFeature.featureGroup).booleanValue();
   }
 
   /**
@@ -1156,6 +1155,33 @@ public abstract class FeatureRendererModel
     return filter == null ? true : filter.matches(sf);
   }
 
+  /**
+   * Answers true unless the specified group is set to hidden. Defaults to true
+   * if group visibility is not set.
+   * 
+   * @param group
+   * @return
+   */
+  public boolean isGroupVisible(String group)
+  {
+    if (!featureGroups.containsKey(group))
+    {
+      return true;
+    }
+    return featureGroups.get(group);
+  }
+
+  /**
+   * Orders features in render precedence (last in order is last to render, so
+   * displayed on top of other features)
+   * 
+   * @param order
+   */
+  public void orderFeatures(Comparator<String> order)
+  {
+    Arrays.sort(renderOrder, order);
+  }
+
   @Override
   public boolean isVisible(SequenceFeature feature)
   {
@@ -1183,5 +1209,4 @@ public abstract class FeatureRendererModel
     }
     return true;
   }
-
 }