JAL-2480 SequenceFeaturesI encapsulates features api

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 26f9964..067d8ae 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Help.HelpId;
@@ -60,6 +61,7 @@ import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -470,43 +472,19 @@ public class FeatureSettings extends JPanel implements
   @Override
   synchronized public void discoverAllFeatureData()
   {
-    Vector<String> allFeatures = new Vector<String>();
-    Vector<String> allGroups = new Vector<String>();
-    SequenceFeature[] tmpfeatures;
-    String group;
-    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
-    {
-      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getSequenceFeatures();
-      if (tmpfeatures == null)
-      {
-        continue;
-      }
+    Set<String> allGroups = new HashSet<String>();
+    AlignmentI alignment = af.getViewport().getAlignment();
 
-      int index = 0;
-      while (index < tmpfeatures.length)
+    for (int i = 0; i < alignment.getHeight(); i++)
+    {
+      SequenceI seq = alignment.getSequenceAt(i);
+      for (String group : seq.getFeatures().getFeatureGroups(true))
       {
-        if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
+        if (group != null && !allGroups.contains(group))
         {
-          index++;
-          continue;
-        }
-
-        if (tmpfeatures[index].getFeatureGroup() != null)
-        {
-          group = tmpfeatures[index].featureGroup;
-          if (!allGroups.contains(group))
-          {
-            allGroups.addElement(group);
-            checkGroupState(group);
-          }
+          allGroups.add(group);
+          checkGroupState(group);
         }
-
-        if (!allFeatures.contains(tmpfeatures[index].getType()))
-        {
-          allFeatures.addElement(tmpfeatures[index].getType());
-        }
-        index++;
       }
     }
 
@@ -572,7 +550,7 @@ public class FeatureSettings extends JPanel implements
 
   synchronized void resetTable(String[] groupChanged)
   {
-    if (resettingTable == true)
+    if (resettingTable)
     {
       return;
     }
@@ -591,13 +569,13 @@ public class FeatureSettings extends JPanel implements
     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
 
-      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getSequenceFeatures();
+      SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i);
+      tmpfeatures = seq.getSequenceFeatures();
       if (tmpfeatures == null)
       {
         continue;
       }
-
+      Set<String> types = seq.getFeatures().getFeatureTypes();
       int index = 0;
       while (index < tmpfeatures.length)
       {