X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=03f15d3ddccf4f1d084095d7bf38ef0b130dcf7e;hb=688e59f05f78f52d949f29cd5adc33503d98a147;hp=7cdc0e8419e24b7d2b72cf90942410616347dba0;hpb=1e1f9a1e1983144126974c77005dcab524051ae7;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 7cdc0e8..03f15d3 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -84,6 +84,23 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     featureGroups = fr.featureGroups;
     featureColours = fr.featureColours;
     transparency = fr.transparency;
+    if (av!=null && fr.av!=null && fr.av!=av)
+    {
+      if (fr.av.featuresDisplayed!=null)
+      {
+        if (av.featuresDisplayed==null)
+        {
+          av.featuresDisplayed = new Hashtable();
+        } else {
+          av.featuresDisplayed.clear();
+        }
+        Enumeration en=fr.av.featuresDisplayed.keys();
+        while (en.hasMoreElements())
+        {
+          av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+        }
+      }
+    }
   }
 
   static String lastFeatureAdded;
@@ -661,16 +678,16 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
         {
 
-          renderFeature(g, seq, seq
-                  .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
-                  .findIndex(sequenceFeatures[sfindex].begin) - 1,
+          renderFeature(g, seq,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
                   getColour(sequenceFeatures[sfindex])
                   // new Color(((Integer) av.featuresDisplayed
                   // .get(sequenceFeatures[sfindex].type)).intValue())
                   , start, end, y1);
-          renderFeature(g, seq, seq
-                  .findIndex(sequenceFeatures[sfindex].end) - 1, seq
-                  .findIndex(sequenceFeatures[sfindex].end) - 1,
+          renderFeature(g, seq,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                  seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                   getColour(sequenceFeatures[sfindex])
                   // new Color(((Integer) av.featuresDisplayed
                   // .get(sequenceFeatures[sfindex].type)).intValue())
@@ -681,9 +698,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         {
           if (showFeature(sequenceFeatures[sfindex]))
           {
-            renderFeature(g, seq, seq
-                    .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
-                    .findIndex(sequenceFeatures[sfindex].end) - 1,
+            renderFeature(g, seq,
+                    seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                    seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                     getColour(sequenceFeatures[sfindex]), start, end, y1);
           }
         }
@@ -747,6 +764,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
   }
 
   Hashtable minmax = null;
+
   /**
    * Called when alignment in associated view has new/modified features to
    * discover and display.
@@ -757,6 +775,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     lastSeq = null;
     findAllFeatures();
   }
+
   /**
    * find all features on the alignment
    */
@@ -790,8 +809,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         {
           if (getColour(features[index].getType()) == null)
           {
-            featureColours.put(features[index].getType(), ucs
-                    .createColourFromName(features[index].getType()));
+            featureColours.put(features[index].getType(),
+                    ucs.createColourFromName(features[index].getType()));
           }
 
           av.featuresDisplayed.put(features[index].getType(), new Integer(
@@ -1045,9 +1064,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       for (int i = 0; i < toset.length; i++)
       {
         Object st = featureGroups.get(toset[i]);
+        featureGroups.put(toset[i], new Boolean(visible));
         if (st != null)
         {
-          featureGroups.put(toset[i], new Boolean(visible));
           rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
         }
       }
@@ -1071,6 +1090,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     }
   }
 
+  ArrayList<String> hiddenGroups=new ArrayList<String>();
   /**
    * analyse alignment for groups and hash tables (used to be embedded in
    * FeatureSettings.setTableData)
@@ -1084,8 +1104,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       featureGroups = new Hashtable();
     }
-    Vector allFeatures = new Vector();
-    Vector allGroups = new Vector();
+    hiddenGroups =new ArrayList<String>();
+    hiddenGroups.addAll(featureGroups.keySet());
+    ArrayList allFeatures = new ArrayList();
+    ArrayList allGroups = new ArrayList();
     SequenceFeature[] tmpfeatures;
     String group;
     for (int i = 0; i < av.alignment.getHeight(); i++)
@@ -1104,9 +1126,11 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         if (tmpfeatures[index].getFeatureGroup() != null)
         {
           group = tmpfeatures[index].featureGroup;
+          // Remove group from the hiddenGroup list
+          hiddenGroups.remove(group);
           if (!allGroups.contains(group))
           {
-            allGroups.addElement(group);
+            allGroups.add(group);
 
             boolean visible = true;
             if (featureGroups.containsKey(group))
@@ -1122,7 +1146,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
         if (!allFeatures.contains(tmpfeatures[index].getType()))
         {
-          allFeatures.addElement(tmpfeatures[index].getType());
+          allFeatures.add(tmpfeatures[index].getType());
         }
         index++;
       }