From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 10 Oct 2014 15:23:40 +0000 (+0100)
Subject: JAL-674 new constructors to pass flags about annotating sequence with data from PDB... 
X-Git-Tag: Jalview_2_9~169^2~34
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1000a9e49d7f7c295348025621e0f8d11817d200;p=jalview.git

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index bc58c9a..e99ece0 100755
--- 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()