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 4a6a1c2..322c6b8 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -15,7 +15,6 @@ 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;
 
@@ -92,7 +91,6 @@ public abstract class StructureFile extends AlignFile
   {
   }
 
-  @SuppressWarnings("rawtypes")
   protected SequenceI postProcessChain(PDBChain chain)
   {
     SequenceI pdbSequence = chain.sequence;
@@ -100,10 +98,9 @@ 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)
     {
@@ -285,11 +282,10 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
-        final Constructor constructor = cl.getConstructor(new Class[] {
-            boolean.class, boolean.class, boolean.class, FileParse.class });
-        final Object[] args = new Object[] { visibleChainAnnotation,
-            predictSecondaryStructure, externalSecondaryStructure,
-            new FileParse(getDataName(), type) };
+        final Constructor constructor = cl
+                .getConstructor(new Class[] { FileParse.class });
+        final Object[] args = new Object[] { new FileParse(getDataName(),
+                type) };
 
         StructureImportSettings.setShowSeqFeatures(false);
         StructureImportSettings.setVisibleChainAnnotation(false);