merge from develop

[jalview.git] / src / jalview / ext / jmol / PDBFileWithJmol.java

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 3b6f0c2..240ea7b 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -176,8 +176,14 @@ public class PDBFileWithJmol extends AlignFile implements
                   newseq[p] = cinds[seq[p]] == nonGap ? ngc : seq[p];
                   if (secstr[p] >= 'A' && secstr[p] <= 'z')
                   {
-                    asecstr[p] = new Annotation("" + secstr[p], null,
-                            secstrcode[p], Float.NaN);
+                    try
+                    {
+                      asecstr[p] = new Annotation("" + secstr[p], null,
+                              secstrcode[p], Float.NaN);
+                    } catch (ArrayIndexOutOfBoundsException e)
+                    {
+                      // skip - patch for JAL-1836
+                    }
                   }
                 }
                 String modelTitle = (String) ms