Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 97b246f..d39ab38 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -74,9 +74,10 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
-  public StructureFile(String inFile, String type) throws IOException
+  public StructureFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -104,9 +105,9 @@ public abstract class StructureFile extends AlignFile
   }
 
   public StructureFile(boolean parseImmediately, String dataObject,
-          String type) throws IOException
+          DataSourceType sourceType) throws IOException
   {
-    super(parseImmediately, dataObject, type);
+    super(parseImmediately, dataObject, sourceType);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -200,7 +201,7 @@ public abstract class StructureFile extends AlignFile
                 new Object[] {});
         AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
                 new Class[] { FileParse.class }).invoke(annotate3d,
-                new Object[] { new FileParse(getDataName(), type) }));
+                new Object[] { new FileParse(getDataName(), dataSourceType) }));
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
@@ -309,10 +310,8 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
-        final Constructor constructor = cl
-                .getConstructor(new Class[] { FileParse.class });
-        final Object[] args = new Object[] { new FileParse(getDataName(),
-                type) };
+        final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
+        final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
 
         StructureImportSettings.setShowSeqFeatures(false);
         StructureImportSettings.setVisibleChainAnnotation(false);