X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;fp=src%2Fjalview%2Fio%2FStructureFile.java;h=fc0e207c7c302648c9e29d2f318532ba73c9d205;hb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;hp=97e11eb05db197b43cb7ce699922e845e76aaf73;hpb=1811f4469c23e9cce0a72649e17b634f60f9fbe0;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 97e11eb..fc0e207 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -8,6 +8,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureImportSettings;
 
@@ -25,7 +26,7 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
-  private String dbRefType;
+  private PDBEntry.Type dbRefType;
 
   /**
    * set to true to add derived sequence annotations (temp factor read from
@@ -70,7 +71,7 @@ public abstract class StructureFile extends AlignFile
     this.visibleChainAnnotation = StructureImportSettings
             .isVisibleChainAnnotation();
     this.predictSecondaryStructure = StructureImportSettings
-            .isPredictSecondaryStructure();
+            .isProcessSecondaryStructure();
     this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
 
@@ -116,8 +117,6 @@ public abstract class StructureFile extends AlignFile
     DBRefEntry sourceDBRef = new DBRefEntry();
     sourceDBRef.setAccessionId(getId());
     sourceDBRef.setSource(DBRefSource.PDB);
-    sourceDBRef.setStartRes(pdbSequence.getStart());
-    sourceDBRef.setEndRes(pdbSequence.getEnd());
     pdbSequence.setSourceDBRef(sourceDBRef);
     pdbSequence.addPDBId(entry);
     pdbSequence.addDBRef(sourceDBRef);
@@ -273,7 +272,7 @@ public abstract class StructureFile extends AlignFile
         StructureImportSettings.setShowSeqFeatures(false);
         StructureImportSettings.setVisibleChainAnnotation(false);
         StructureImportSettings
-                .setPredictSecondaryStructure(predictSecondaryStructure);
+                .setProcessSecondaryStructure(predictSecondaryStructure);
         StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
@@ -401,13 +400,18 @@ public abstract class StructureFile extends AlignFile
     this.chains = chains;
   }
 
-  public String getDbRefType()
+  public Type getDbRefType()
   {
     return dbRefType;
   }
 
   public void setDbRefType(String dbRefType)
   {
+    this.dbRefType = Type.valueOf(dbRefType);
+  }
+
+  public void setDbRefType(Type dbRefType)
+  {
     this.dbRefType = dbRefType;
   }