JAL-1919 initial support for mmCIF using JMol API. Created an Abstract class - Struct...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2edbee2..e19db81 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -282,7 +282,9 @@ public class AppletFormatAdapter
         boolean isParseWithJMOL = false;
         if (isParseWithJMOL)
         {
-          alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
+          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct, inFile,
+                  type);
         }
         else
         {
@@ -293,7 +295,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("mmCIF"))
       {
-        alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
+        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
       }
       else if (format.equals("STH"))
       {
@@ -424,7 +427,8 @@ public class AppletFormatAdapter
         boolean isParseWithJMOL = false;
         if (isParseWithJMOL)
         {
-          alignFile = new jalview.ext.jmol.JmolParser(source);
+          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct, source);
         }
         else
         {
@@ -434,7 +438,8 @@ public class AppletFormatAdapter
       }
       else if (format.equals("mmCIF"))
       {
-        alignFile = new jalview.ext.jmol.JmolParser(source);
+        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {