JAL-674 new constructors to pass flags about annotating sequence with data from PDB...

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index bc58c9a..e99ece0 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -41,15 +41,33 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException
   boolean processSecondaryStructure=true;
+  
+
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure)
+  {
+    super();
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+  }
+
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, String file, String protocol) throws IOException
   {
-    super(inFile, inType);
+    super(false, file, protocol);
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    doParse();
   }
 
-  public PDBfile(FileParse source) throws IOException
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, FileParse source) throws IOException
   {
-    super(source);
+    super(false, source);
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    doParse();
   }
 
   public String print()