Null sequence check

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b3ccf5e..99ba120 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -191,10 +191,13 @@ public class SequenceFetcher
           ) + ":" + textfield.getText(),\r
           "fasta", "raw");\r
 \r
-      for (int i = 0; i < reply.length; i++)\r
-        result.append(reply[i] + "\n");\r
+      if(reply!=null)\r
+      {\r
+        for (int i = 0; i < reply.length; i++)\r
+          result.append(reply[i] + "\n");\r
 \r
-      parseResult(result.toString());\r
+        parseResult(result.toString());\r
+      }\r
     }\r
     else if (database.getSelectedItem().equals("PDB"))\r
     {\r
@@ -203,11 +206,12 @@ public class SequenceFetcher
       while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
       {\r
         StringBuffer respart = getPDBFile(query.toUpperCase());\r
-        result.append(respart);\r
-\r
+        if(respart!=null)\r
+          result.append(respart);\r
       }\r
 \r
-      if (result != null)\r
+\r
+      if (result.length()>0)\r
         parseResult(result.toString());\r
     }\r
 \r
@@ -395,6 +399,11 @@ public class SequenceFetcher
                                       + "=" + sequences[i].getStart()\r
                                       + "-" + sequences[i].getEnd());\r
               sequences[i].getDatasetSequence().addPDBId(entry);\r
+\r
+              // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
+              // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
+              DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
+              sequences[i].getDatasetSequence().addDBRef(dbentry);\r
             }\r
             else\r
             {\r