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9c1a032
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apparent bug in JpredFile parser where annotation was not being removed from alignmen...
author
jprocter
<Jim Procter>
Thu, 10 May 2007 13:59:37 +0000
(13:59 +0000)
committer
jprocter
<Jim Procter>
Thu, 10 May 2007 13:59:37 +0000
(13:59 +0000)
src/jalview/io/JPredFile.java
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diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
30cd181
..
dabd47a
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-237,8
+237,9
@@
public class JPredFile
name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
}
name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
}
+ if (QuerySeqPosition==-1)
+ QuerySeqPosition = ids.size();
ids.addElement(name);
ids.addElement(name);
-
noSeqs++;
}
else
noSeqs++;
}
else
@@
-278,7
+279,7
@@
public class JPredFile
") has an unexpected number of columns");
}
") has an unexpected number of columns");
}
- if (newSeq.getName().startsWith("QUERY") &&
+ if ((newSeq.getName().startsWith("QUERY") || newSeq.getName().startsWith("align;"))&&
(QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
(QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();