{\r
jalview.bin.Cache.log.debug("Getting associated alignment.");\r
// we ignore the returned alignment if we only predicted on a single sequence\r
- String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
+ String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),\r
"Paste");\r
\r
if (jalview.io.FormatAdapter.formats.contains(format))\r
}\r
}\r
\r
+ al.setDataset(null);\r
\r
AlignmentAnnotation annot;\r
Annotation[] annotations = null;\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
{\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
"JNet Output", annotations);\r
}\r
\r
- al.addAnnotation(annot);\r
+ al.addAnnotation(annot, seqRef);\r
\r
if (noMsa)\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