JAL-3509 coerce RESNUM to hidden (really) after fetching from PDB - resolved conflict...

[jalview.git] / src / jalview / io / PDBFeatureSettings.java

diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
index a422a00..6b09cd1 100644 (file)
--- a/src/jalview/io/PDBFeatureSettings.java
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -1,28 +1,52 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.api.FeatureColourI;
-import jalview.schemes.FeatureColourAdapter;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.FeatureSettingsAdapter;
-import jalview.ws.dbsources.Pdb;
 
 import java.awt.Color;
 
+import mc_view.PDBChain;
+
 public class PDBFeatureSettings extends FeatureSettingsAdapter
 {
+  // TODO find one central place to define feature names
+  private static final String FEATURE_INSERTION = "INSERTION";
+
+  private static final String FEATURE_RES_NUM = PDBChain.RESNUM_FEATURE;
 
   @Override
-  public boolean isFeatureDisplayed(String type)
+  public boolean isFeatureHidden(String type)
   {
-    return type.equalsIgnoreCase(Pdb.FEATURE_INSERTION)
-            || type.equalsIgnoreCase(Pdb.FEATURE_RES_NUM);
+    return type.equalsIgnoreCase(FEATURE_RES_NUM);
   }
 
   @Override
   public FeatureColourI getFeatureColour(String type)
   {
-    if (type.equalsIgnoreCase(Pdb.FEATURE_INSERTION))
+    if (type.equalsIgnoreCase(FEATURE_INSERTION))
     {
-      return new FeatureColourAdapter()
+      return new FeatureColour()
       {
 
         @Override
@@ -41,23 +65,22 @@ public class PDBFeatureSettings extends FeatureSettingsAdapter
   @Override
   public int compare(String feature1, String feature2)
   {
-    if (feature1.equalsIgnoreCase(Pdb.FEATURE_INSERTION))
+    if (feature1.equalsIgnoreCase(FEATURE_INSERTION))
     {
       return +1;
     }
-    if (feature2.equalsIgnoreCase(Pdb.FEATURE_INSERTION))
+    if (feature2.equalsIgnoreCase(FEATURE_INSERTION))
     {
       return -1;
     }
-    if (feature1.equalsIgnoreCase(Pdb.FEATURE_RES_NUM))
+    if (feature1.equalsIgnoreCase(FEATURE_RES_NUM))
     {
       return +1;
     }
-    if (feature2.equalsIgnoreCase(Pdb.FEATURE_RES_NUM))
+    if (feature2.equalsIgnoreCase(FEATURE_RES_NUM))
     {
       return -1;
     }
     return 0;
   }
 }
-