JAL-747 - warning dialog if Jalview can't resolve filename for a structure in a Jmol...

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e639844..1a9bc03 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2602,22 +2602,32 @@ public class Jalview2XML
                   jmoldat[1] = ids[p].getStructureState(s).getContent();
                 }
               }
-              Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
-                      .get(ids[p].getFile());
-              if (seqstrmaps == null)
+              if (ids[p].getFile() != null)
               {
-                ((Hashtable) jmoldat[2]).put(
-                        new File(ids[p].getFile()).toString(),
-                        seqstrmaps = new Object[]
-                        { pdbFile, ids[p].getId(), new Vector(),
-                            new Vector() });
+                Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
+                        .get(ids[p].getFile());
+                if (seqstrmaps == null)
+                {
+                  ((Hashtable) jmoldat[2]).put(
+                          new File(ids[p].getFile()).toString(),
+                          seqstrmaps = new Object[]
+                          { pdbFile, ids[p].getId(), new Vector(),
+                              new Vector() });
+                }
+                if (!((Vector) seqstrmaps[2]).contains(seq))
+                {
+                  ((Vector) seqstrmaps[2]).addElement(seq);
+                  // ((Vector)seqstrmaps[3]).addElement(n) :
+                  // in principle, chains
+                  // should be stored here : do we need to
+                  // TODO: store and recover seq/pdb_id :
+                  // chain mappings
+                }
               }
-              if (!((Vector) seqstrmaps[2]).contains(seq))
+              else
               {
-                ((Vector) seqstrmaps[2]).addElement(seq);
-                // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains
-                // should be stored here : do we need to
-                // TODO: store and recover seq/pdb_id : chain mappings
+                errorMessage=("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+                warn(errorMessage);
               }
             }
           }