X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=ab220f0ade10e31ae6b683fa89ab484a17b2e763;hb=4a3198610bf947684199326eeb41fefa0a74d9e4;hp=26c202c91c941e996d89e75a7c838cbc0620e7fa;hpb=8a5e0bc033d75200f22202146b5dc448b2b70a39;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 26c202c..ab220f0 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -42,7 +42,6 @@ import MCview.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
-
   private String id;
 
   private PDBEntry.Type dbRefType;
@@ -69,9 +68,10 @@ 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
@@ -99,9 +99,9 @@ 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
@@ -195,7 +195,7 @@ 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)
@@ -304,10 +304,8 @@ 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);
@@ -408,7 +406,8 @@ public abstract class StructureFile extends AlignFile
    * make a friendly ID string.
    * 
    * @param dataName
-   * @return truncated dataName to after last '/'
+   * @return truncated dataName to after last '/' and pruned .extension if
+   *         present
    */
   protected String safeName(String dataName)
   {
@@ -417,6 +416,9 @@ public abstract class StructureFile extends AlignFile
     {
       dataName = dataName.substring(p + 1);
     }
+    if(dataName.indexOf(".") > -1){
+      dataName = dataName.substring(0, dataName.lastIndexOf("."));
+    }
     return dataName;
   }