Merge: 497958b 68dcaa7

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2e94782..505f609 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -126,6 +126,21 @@ 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;
@@ -239,7 +254,8 @@ 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);
       }
@@ -364,7 +380,8 @@ 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"))
       {