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Add Annotation to specific sequence
[jalview.git]
/
src
/
jalview
/
ws
/
JPredClient.java
diff --git
a/src/jalview/ws/JPredClient.java
b/src/jalview/ws/JPredClient.java
index
f503f91
..
6fd0a4a
100755
(executable)
--- a/
src/jalview/ws/JPredClient.java
+++ b/
src/jalview/ws/JPredClient.java
@@
-439,6
+439,7
@@
public class JPredClient
}
\r
}
\r
\r
}
\r
}
\r
\r
+ al.setDataset(null);
\r
\r
AlignmentAnnotation annot;
\r
Annotation[] annotations = null;
\r
\r
AlignmentAnnotation annot;
\r
Annotation[] annotations = null;
\r
@@
-460,6
+461,8
@@
public class JPredClient
// JBPNote Should also rename the query sequence sometime...
\r
i = 0;
\r
\r
// JBPNote Should also rename the query sequence sometime...
\r
i = 0;
\r
\r
+ SequenceI seqRef = al.getSequenceAt(FirstSeq);
\r
+
\r
while (i < preds.length)
\r
{
\r
String id = preds[i].getName().toUpperCase();
\r
while (i < preds.length)
\r
{
\r
String id = preds[i].getName().toUpperCase();
\r
@@
-503,7
+506,8
@@
public class JPredClient
{
\r
annot = new AlignmentAnnotation(preds[i].getName(),
\r
"JNet Output", annotations, 0f,
\r
{
\r
annot = new AlignmentAnnotation(preds[i].getName(),
\r
"JNet Output", annotations, 0f,
\r
- 10f, 1);
\r
+ 10f,
\r
+ AlignmentAnnotation.BAR_GRAPH);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-511,7
+515,7
@@
public class JPredClient
"JNet Output", annotations);
\r
}
\r
\r
"JNet Output", annotations);
\r
}
\r
\r
- al.addAnnotation(annot);
\r
+ al.addAnnotation(annot, seqRef);
\r
\r
if (noMsa)
\r
{
\r
\r
if (noMsa)
\r
{
\r
@@
-544,8
+548,7
@@
public class JPredClient
}
\r
catch (Exception ex)
\r
{
\r
}
\r
catch (Exception ex)
\r
{
\r
- jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
\r
- jalview.bin.Cache.log.debug("Exception: ",ex);
\r
+ jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r