Any character non aa or nucleotide is a space

[jalview.git] / src / jalview / io / DBRefFetcher.java

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index d26ef6d..bd3c733 100644 (file)
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -181,7 +181,7 @@ public class DBRefFetcher implements Runnable
             for(int j=0; j<uprefs.length; j++)\r
             {\r
               addSeqId(sequence, uprefs[j].getAccessionId());\r
-              queryString.append(uprefs[i].getAccessionId()+";");\r
+              queryString.append(uprefs[j].getAccessionId()+";");\r
             }\r
           }\r
           else\r
@@ -305,7 +305,8 @@ public class DBRefFetcher implements Runnable
         System.out.println("Adding dbref to " + sequence.getName() + " : " +\r
                            entry.getAccession().elementAt(0).toString());\r
 \r
-        String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence()).\r
+        String nonGapped = AlignSeq.extractGaps("-. ",\r
+                                                sequence.getSequenceAsString()).\r
             toUpperCase();\r
 \r
         int absStart = entry.getUniprotSequence().getContent().indexOf(\r