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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
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
}
\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
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
toUpperCase();
\r
\r
int absStart = entry.getUniprotSequence().getContent().indexOf(
\r