JAL-629 implementation of --tempfac options

[jalview.git] / src / mc_view / PDBfile.java

diff --git a/src/mc_view/PDBfile.java b/src/mc_view/PDBfile.java
index 54bdca9..2a89e61 100755 (executable)
--- a/src/mc_view/PDBfile.java
+++ b/src/mc_view/PDBfile.java
@@ -20,6 +20,13 @@
  */
 package mc_view;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -28,12 +35,6 @@ import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.util.MessageManager;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 public class PDBfile extends StructureFile
 {
   private static String CALC_ID_PREFIX = "JalviewPDB";
@@ -51,7 +52,9 @@ public class PDBfile extends StructureFile
           DataSourceType sourceType) throws IOException
   {
     super(false, dataObject, sourceType);
+    Console.debug("***** PDBfile constructor");
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    Console.debug("***** About to doParse() 1");
     doParse();
   }
 
@@ -60,6 +63,7 @@ public class PDBfile extends StructureFile
   {
     super(false, source);
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    Console.debug("***** About to doParse() 2");
     doParse();
   }