JAL-1605 merge commit

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index cbdf2ef..80f1255 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -192,20 +192,20 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       // copy over the displayed feature settings
       if (fr.av != null)
       {
-        if (fr.av.featuresDisplayed != null)
+        if (fr.av.getFeaturesDisplayed() != null)
         {
           // update display settings
-          if (av.featuresDisplayed == null)
+          if (av.getFeaturesDisplayed() == null)
           {
-            av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
+            av.setFeaturesDisplayed(new Hashtable(fr.av.getFeaturesDisplayed()));
           }
           else
           {
-            av.featuresDisplayed.clear();
-            Enumeration en = fr.av.featuresDisplayed.keys();
+            av.getFeaturesDisplayed().clear();
+            Enumeration en = fr.av.getFeaturesDisplayed().keys();
             while (en.hasMoreElements())
             {
-              av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+              av.getFeaturesDisplayed().put(en.nextElement(), Boolean.TRUE);
             }
 
           }
@@ -349,11 +349,11 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       fm = g.getFontMetrics();
     }
 
-    if (av.featuresDisplayed == null || renderOrder == null
+    if (av.getFeaturesDisplayed() == null || renderOrder == null
             || newFeatureAdded)
     {
       findAllFeatures();
-      if (av.featuresDisplayed.size() < 1)
+      if (av.getFeaturesDisplayed().size() < 1)
       {
         return;
       }
@@ -388,7 +388,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       type = renderOrder[renderIndex];
 
-      if (type == null || !av.featuresDisplayed.containsKey(type))
+      if (type == null || !av.getFeaturesDisplayed().containsKey(type))
       {
         continue;
       }
@@ -682,9 +682,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
     findingFeatures = true;
 
-    if (av.featuresDisplayed == null)
+    if (av.getFeaturesDisplayed() == null)
     {
-      av.featuresDisplayed = new Hashtable();
+      av.setFeaturesDisplayed(new Hashtable());
     }
 
     allfeatures = new Vector();
@@ -717,7 +717,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       int index = 0;
       while (index < features.length)
       {
-        if (!av.featuresDisplayed.containsKey(features[index].getType()))
+        if (!av.getFeaturesDisplayed().containsKey(features[index].getType()))
         {
 
           if (featureGroups.containsKey(features[index].getType()))
@@ -742,7 +742,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
             {
               // this is a new feature type on the alignment. Mark it for
               // display.
-              av.featuresDisplayed.put(features[index].getType(),
+              av.getFeaturesDisplayed().put(features[index].getType(),
                       new Integer(getColour(features[index].getType())
                               .getRGB()));
               setOrder(features[index].getType(), 0);
@@ -1253,7 +1253,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         sf.description = lastDescriptionAdded;
 
         setColour(sf.type, fcol);
-        av.featuresDisplayed.put(sf.type, getColour(sf.type));
+        av.getFeaturesDisplayed().put(sf.type, getColour(sf.type));
 
         try
         {
@@ -1281,9 +1281,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
           ffile.parseDescriptionHTML(features[i], false);
         }
 
-        if (av.featuresDisplayed == null)
+        if (av.getFeaturesDisplayed() == null)
         {
-          av.featuresDisplayed = new Hashtable();
+          av.setFeaturesDisplayed(new Hashtable());
         }
 
         if (lastFeatureGroupAdded != null)
@@ -1293,7 +1293,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
         }
         setColour(lastFeatureAdded, fcol);
-        av.featuresDisplayed.put(lastFeatureAdded,
+        av.getFeaturesDisplayed().put(lastFeatureAdded,
                 getColour(lastFeatureAdded));
 
         findAllFeatures(false);
@@ -1386,13 +1386,13 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
   {
     if (visibleNew)
     {
-      if (av.featuresDisplayed != null)
+      if (av.getFeaturesDisplayed() != null)
       {
-        av.featuresDisplayed.clear();
+        av.getFeaturesDisplayed().clear();
       }
       else
       {
-        av.featuresDisplayed = new Hashtable();
+        av.setFeaturesDisplayed(new Hashtable());
       }
     }
     if (data == null)
@@ -1414,7 +1414,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         // interface object
         if (((Boolean) data[i][2]).booleanValue())
         {
-          av.featuresDisplayed.put(type, new Integer(getColour(type)
+          av.getFeaturesDisplayed().put(type, new Integer(getColour(type)
                   .getRGB()));
         }