Merge branch 'develop' into JAL-1483_featureBasedTreeCalc

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 009d0a2..ef48bf9 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1392,8 +1392,7 @@ public class JalviewLite extends Applet implements
       }
       else
       {
-        throw new Error(
-                "Invalid separator parameter - must be non-zero length");
+        throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
       }
     }
     int r = 255;
@@ -2077,10 +2076,12 @@ public class JalviewLite extends Applet implements
             {
               String sequence = applet.getParameter("PDBSEQ");
               if (sequence != null)
+              {
                 seqs = new SequenceI[]
                 { matcher == null ? (Sequence) newAlignFrame
                         .getAlignViewport().getAlignment()
                         .findName(sequence) : matcher.findIdMatch(sequence) };
+              }
 
             }
             else
@@ -2140,6 +2141,8 @@ public class JalviewLite extends Applet implements
                 if (seqs[i] != null)
                 {
                   ((Sequence) seqs[i]).addPDBId(pdb);
+                  StructureSelectionManager.getStructureSelectionManager(
+                          applet).registerPDBEntry(pdb);
                 }
                 else
                 {
@@ -2324,7 +2327,9 @@ public class JalviewLite extends Applet implements
     // note separator local variable intentionally masks object field
     int seplen = separator.length();
     if (list == null || list.equals("") || list.equals(separator))
+    {
       return null;
+    }
     java.util.Vector jv = new Vector();
     int cp = 0, pos;
     while ((pos = list.indexOf(separator, cp)) > cp)