JAL-629 implementation of --tempfac options

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 94a832b..c816f6d 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -20,10 +20,17 @@
  */
 package jalview.io;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.List;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -31,13 +38,6 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureImportSettings;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.List;
-import java.util.Vector;
-
 import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
@@ -71,7 +71,13 @@ public abstract class StructureFile extends AlignFile
   public StructureFile(Object inFile, DataSourceType sourceType)
           throws IOException
   {
-    super(inFile, sourceType);
+    this(inFile, sourceType, null);
+  }
+
+  public StructureFile(Object inFile, DataSourceType sourceType,
+          AlignmentAnnotation.TFType tempfacType) throws IOException
+  {
+    super(inFile, sourceType, tempfacType);
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -342,10 +348,10 @@ public abstract class StructureFile extends AlignFile
     }
     StructureImportSettings.setShowSeqFeatures(true);
   }
-  
+
   /**
-   * Answers the first PDBChain found matching the given id, or null if none 
-   * is found
+   * Answers the first PDBChain found matching the given id, or null if none is
+   * found
    * 
    * @param id
    * @return