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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
fdf0cec
..
6fd0a4a
100755
(executable)
--- a/
src/jalview/ws/JPredClient.java
+++ b/
src/jalview/ws/JPredClient.java
@@
-57,6
+57,7
@@
public class JPredClient
wsInfo = setWebService();
\r
\r
SequenceI seq = msf[0];
\r
wsInfo = setWebService();
\r
\r
SequenceI seq = msf[0];
\r
+
\r
altitle = "JNet prediction on " + seq.getName() +
\r
" using alignment from " + title;
\r
\r
altitle = "JNet prediction on " + seq.getName() +
\r
" using alignment from " + title;
\r
\r
@@
-65,8
+66,10
@@
public class JPredClient
AlignSeq.extractGaps("-. ", seq.getSequence()) +
\r
"\n");
\r
SequenceI aln[] = new SequenceI[msf.length];
\r
AlignSeq.extractGaps("-. ", seq.getSequence()) +
\r
"\n");
\r
SequenceI aln[] = new SequenceI[msf.length];
\r
- for (int i=0,j=msf.length; i<j;i++)
\r
- aln[i] = new jalview.datamodel.Sequence(msf[i]);
\r
+ for (int i=0,j=msf.length; i<j;i++) {
\r
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);
\r
+ }
\r
+
\r
SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
\r
\r
if (!locateWebService())
\r
SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
\r
\r
if (!locateWebService())
\r
@@
-173,7
+176,8
@@
public class JPredClient
msf[0].getSequence()));
\r
\r
this.msa = new vamsas.objects.simple.Msfalignment();
\r
msf[0].getSequence()));
\r
\r
this.msa = new vamsas.objects.simple.Msfalignment();
\r
- msa.setMsf(jalview.io.PileUpfile.print(msf));
\r
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
\r
+ msa.setMsf(pileup.print(msf));
\r
}
\r
\r
public void run()
\r
}
\r
\r
public void run()
\r
@@
-402,16
+406,17
@@
public class JPredClient
{
\r
al = new Alignment(new FormatAdapter().readFile(
\r
result.getAligfile(), "Paste", format));
\r
{
\r
al = new Alignment(new FormatAdapter().readFile(
\r
result.getAligfile(), "Paste", format));
\r
+ SequenceI sqs[] = new SequenceI[al.getHeight()];
\r
for (int i=0, j=al.getHeight(); i<j; i++) {
\r
for (int i=0, j=al.getHeight(); i<j; i++) {
\r
- SequenceI sq = al.getSequenceAt(i);
\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
\r
- sq, (Hashtable) SequenceInfo.get(sq.getName())))
\r
+ sqs[i] = al.getSequenceAt(i);
\r
+ }
\r
+ if (!jalview.analysis.SeqsetUtils.deuniquify(
\r
+ (Hashtable) SequenceInfo,sqs))
\r
{
\r
throw (new Exception(
\r
{
\r
throw (new Exception(
\r
- "Couldn't recover sequence properties for JNet "
\r
- +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
\r
+ "Couldn't recover sequence properties for alignment."));
\r
}
\r
}
\r
- }
\r
+
\r
noMsa = false;
\r
FirstSeq = 0;
\r
}
\r
noMsa = false;
\r
FirstSeq = 0;
\r
}
\r
@@
-434,6
+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
@@
-455,6
+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
@@
-498,7
+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
@@
-506,7
+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
@@
-539,8
+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