import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
// alippline
String aliaseq = (String) dhit.get("aliaseq"), alimodel = (String) dhit
.get("alimodel"), ppline = (String) dhit.get("alippline");
- AlignmentAnnotation alipp = parsePosteriorProb(ppline);
//
int found = 0;
for (SequenceI hitseq : hits)
if (hitseq.getStart() == alisqfrom && hitseq.getEnd() == alisqto)
{
found++; // annotated a sequence
+ AlignmentAnnotation alipp = parsePosteriorProb(ppline);
AlignmentAnnotation pval = new AlignmentAnnotation("p-value",
"hmmer3 pvalue", pvalue);
AlignmentAnnotation eval = new AlignmentAnnotation("e-value",
hitseq.addAlignmentAnnotation(eval);
alipp.createSequenceMapping(hitseq, hitseq.getStart(), false);
hitseq.addAlignmentAnnotation(alipp);
+ hitseq.addSequenceFeature(new SequenceFeature(
+ "Pfam Domain Architecture", (hmmrhit.get("archindex"))
+ + " "
+ + (String) hmmrhit.get("arch"), 0, 0, Integer
+ .valueOf((String) hmmrhit.get("archScore")),
+ "HMMER3"));
alipp.setScore(Double.valueOf("" + dhit.get("bitscore")));
alipp.adjustForAlignment();
resultAl.addAnnotation(pval);