From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 12 Feb 2012 15:18:34 +0000 (+0000)
Subject: (JAL-1050) ensure all filenames passed in to the load command are updated and their... 
X-Git-Tag: Archived_Release_2_7~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3492dd1b00c0cd49ea8dc14a5a2d717ac3ff9e8a;p=jalview.git

(JAL-1050) ensure all filenames passed in to the load command are updated and their pdb associations added to the Jmol view.
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3c5259e..c8466b1 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2730,6 +2730,8 @@ public class Jalview2XML
               {
                 newFileLoc = new StringBuffer();
               }
+              do {
+                // look for next filename in load statement
               newFileLoc.append(state.substring(cp,
                       ncp = (state.indexOf("\"", ncp + 1) + 1)));
               String oldfilenam = state.substring(ncp,
@@ -2746,6 +2748,7 @@ public class Jalview2XML
               newFileLoc.append("\"");
               cp = ecp + 1; // advance beyond last \" and set cursor so we can
                             // look for next file statement.
+              } while ((ncp=state.indexOf("/*file*/",cp))>-1);
             }
             if (cp > 0)
             {