X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;fp=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=d3b19fa23403a47d4bacd916c5555779933c7603;hb=b8810711642d8473325c8a3d3e76cc5c3c9b5bbd;hp=5366cb41d795d00bdbe95c15a863826454f1ddd8;hpb=936d4dc095734df2b1e9f3bf9e0bd29b9c86434c;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5366cb4..d3b19fa 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -123,6 +123,21 @@ public class AppletFormatAdapter
 
   public static String CLASSLOADER = "ClassLoader";
 
+  /**
+   * add jalview-derived non-secondary structure annotation from PDB structure
+   */
+  boolean annotFromStructure = false;
+
+  /**
+   * add secondary structure from PDB data with built-in algorithms
+   */
+  boolean localSecondaryStruct = false;
+
+  /**
+   * process PDB data with web services
+   */
+  boolean serviceSecondaryStruct = false;
+
   AlignFile afile = null;
 
   String inFile;
@@ -236,7 +251,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(true,true,inFile, type);
+        afile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
         // Uncomment to test Jmol data based PDB processing: JAL-1213
         // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
       }
@@ -357,7 +373,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(true,true,source);
+        afile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {