From c11ccf600bdcfa62302eeeb4898ff431eea6de14 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 Apr 2007 14:06:19 +0000
Subject: [PATCH] adds annotation for display (with flag to set
 alignmentAnnotation as hidden initially)

---
 src/MCview/PDBfile.java |   16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 6fdd978..227bcf7 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -31,6 +31,10 @@ public class PDBfile
   public Vector chains;
   public String id;
 
+  /**
+   * set to true to add chain alignment annotation as visible annotation.
+   */
+  boolean VisibleChainAnnotation=false;
   public PDBfile(String inFile, String inType)
       throws IOException
   {
@@ -128,7 +132,17 @@ public class PDBfile
           entry.setFile(inFile.getAbsolutePath());
         }
         dataset.addPDBId(entry);
-        getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
+        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
+        seqs.addElement(chainseq);
+        AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+        if (chainannot!=null)
+        {
+          for (int ai=0; ai<chainannot.length; ai++)
+          {
+            chainannot[ai].visible=VisibleChainAnnotation;
+            annotations.addElement(chainannot[ai]);
+          }
+        }
       }
     }
     catch (OutOfMemoryError er)
-- 
1.7.10.2