Merge branch 'JAL-1422_srs_r281' into develop

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 829eed7..0035914 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -24,7 +24,6 @@ import java.awt.*;
 
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
-import jalview.ext.jmol.PDBFileWithJmol;
 import jalview.io.FileParse;
 
 public class PDBfile extends jalview.io.AlignFile
@@ -237,10 +236,17 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
   {
-    PDBFileWithJmol jmf = new PDBFileWithJmol(new FileParse(getDataName(),type));
-    Alignment al = new Alignment(jmf.getSeqsAsArray());
-    jmf.addAnnotations(al);
-    replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+    try {
+      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+      if (cl!=null)
+      {
+        Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+        Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+        cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+        replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+      }
+    } catch (ClassNotFoundException q)
+    {}
   }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");