(JAL-1050) ensure all filenames passed in to the load command are updated and their...

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3c5259e..c8466b1 100644 (file)
--- 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)
             {