From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 28 Aug 2015 15:31:33 +0000 (+0100)
Subject: JAL-1836 temporary workaround for negative resNumIns in PDB file
X-Git-Tag: Release_2_10_0~517^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fac668afe0509dd43d360b921f5ba4eda8601887;p=jalview.git

JAL-1836 temporary workaround for negative resNumIns in PDB file
---

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 3b6f0c2..240ea7b 100644
--- 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