Merge branch 'develop' into task/JAL-2196pdbeProperties

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 0bc6a73..2fe386b 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.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.io;
 
 import jalview.analysis.AlignSeq;
@@ -15,7 +35,6 @@ import jalview.structure.StructureImportSettings;
 import java.awt.Color;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
@@ -77,8 +96,8 @@ public abstract class StructureFile extends AlignFile
 
   }
 
-  public StructureFile(boolean parseImmediately, String dataObject, String type)
-          throws IOException
+  public StructureFile(boolean parseImmediately, String dataObject,
+          String type) throws IOException
   {
     super(parseImmediately, dataObject, type);
   }
@@ -92,7 +111,6 @@ public abstract class StructureFile extends AlignFile
   {
   }
 
-  @SuppressWarnings("rawtypes")
   protected SequenceI postProcessChain(PDBChain chain)
   {
     SequenceI pdbSequence = chain.sequence;
@@ -100,10 +118,9 @@ public abstract class StructureFile extends AlignFile
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
     entry.setType(getStructureFileType());
-    entry.setProperty(new Hashtable());
     if (chain.id != null)
     {
-      entry.setChainCode(String.valueOf(chain.id));
+      entry.setChainCode(chain.id);
     }
     if (inFile != null)
     {