X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureCommandsBase.java;h=0b5874ac58b03797eab3a294926c7ec5165bf705;hb=1affe472184986c9957f6af61a746d8c275c8580;hp=774327c153e56e8545902703f887336058c662fa;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git

diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 774327c..0b5874a 100644
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,3 +1,23 @@
+/*
+ * 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.structure;
 
 import java.awt.Color;
@@ -15,15 +35,16 @@ import java.util.Map.Entry;
  */
 public abstract class StructureCommandsBase implements StructureCommandsI
 {
-  private static final String CMD_SEPARATOR = ";";
   public static final String NAMESPACE_PREFIX = "jv_";
 
+  private static final String CMD_SEPARATOR = ";";
+
   /**
    * Returns something that separates concatenated commands
    * 
    * @return
    */
-  protected static String getCommandSeparator()
+  protected String getCommandSeparator()
   {
     return CMD_SEPARATOR;
   }
@@ -40,8 +61,9 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   }
 
   /**
-   * Helper method to add one contiguous range to the AtomSpec model for the given
-   * value (creating the model if necessary). As used by Jalview, {@code value} is
+   * Helper method to add one contiguous range to the AtomSpec model for the
+   * given value (creating the model if necessary). As used by Jalview,
+   * {@code value} is
    * <ul>
    * <li>a colour, when building a 'colour structure by sequence' command</li>
    * <li>a feature value, when building a 'set Chimera attributes from features'
@@ -68,7 +90,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
       atomSpec = new AtomSpecModel();
       map.put(value, atomSpec);
     }
-  
+
     atomSpec.addRange(model, startPos, endPos, chain);
   }
 
@@ -140,7 +162,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
           Color colour)
   {
-    String atomSpec = getAtomSpec(atomSpecModel, false);
+    String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
     return colourResidues(atomSpec, colour);
   }
 
@@ -241,4 +263,16 @@ public abstract class StructureCommandsBase implements StructureCommandsI
   {
     return null;
   }
+
+  @Override
+  public StructureCommandI listResidueAttributes()
+  {
+    return null;
+  }
+
+  @Override
+  public StructureCommandI getResidueAttributes(String attName)
+  {
+    return null;
+  }
 }