How to use

Hmmer3Match

in

uk.ac.ebi.interpro.scan.model

public Object clone() throws CloneNotSupportedException {
  final Set<Hmmer3Location> clonedLocations = new HashSet<Hmmer3Location>(this.getLocations().size());
  for (Hmmer3Location location : this.getLocations()) {
    clonedLocations.add((Hmmer3Location) location.clone());
  }
  return new Hmmer3Match(this.getSignature(), this.getScore(), this.getEvalue(), clonedLocations);
}

private String getSeqEvalue(Match match, Location location) {
  //get the seevalue
  String seqEvalue = null;
  if (match instanceof PantherMatch) {
    seqEvalue = Double.toString(((PantherMatch) match).getEvalue());
  } else if (match instanceof Hmmer3Match) {
    seqEvalue = Double.toString(((Hmmer3Match) match).getEvalue());
  } else if (match instanceof Hmmer2Match) {
    seqEvalue = Double.toString(((Hmmer2Match) match).getEvalue());
  } else if (match instanceof Hmmer3MatchWithSites) {
    seqEvalue = Double.toString(((Hmmer3MatchWithSites) match).getEvalue());
  } else if (location instanceof RPSBlastMatch.RPSBlastLocation) {
    seqEvalue = Double.toString(((RPSBlastMatch.RPSBlastLocation) location).getEvalue());
  } else  if (location instanceof BlastProDomMatch.BlastProDomLocation) {
    seqEvalue = Double.toString(((BlastProDomMatch.BlastProDomLocation) location).getEvalue());
  } else if (match instanceof FingerPrintsMatch) {
    seqEvalue = Double.toString(((FingerPrintsMatch) match).getEvalue());
  } else if (match instanceof SuperFamilyHmmer3Match) {
    seqEvalue = Double.toString(((SuperFamilyHmmer3Match) match).getEvalue());
  }
  return seqEvalue;
}
private String getScore(Location location){

private String getSeqScore(Match match, Location location){
  String seqScore = null;
  if (match instanceof PantherMatch) {
    seqScore = Double.toString( ((PantherMatch) match).getScore());
  }  else if (match instanceof Hmmer3Match) {
    seqScore = Double.toString( ((Hmmer3Match) match).getScore());
  } else if (match instanceof Hmmer2Match) {
    seqScore = Double.toString(((Hmmer2Match) match).getScore());
  } else if (match instanceof Hmmer3MatchWithSites) {
    seqScore = Double.toString(((Hmmer3MatchWithSites) match).getScore());
  } else if (location instanceof RPSBlastMatch.RPSBlastLocation) {
    seqScore = Double.toString(((RPSBlastMatch.RPSBlastLocation) location).getScore());
  } else  if (location instanceof BlastProDomMatch.BlastProDomLocation) {
    seqScore = Double.toString(((BlastProDomMatch.BlastProDomLocation) location).getScore());
  } else if (location instanceof FingerPrintsMatch.FingerPrintsLocation) {
    seqScore = Double.toString( ((FingerPrintsMatch.FingerPrintsLocation) location).getScore());
  } else if (location instanceof ProfileScanMatch.ProfileScanLocation)  {
    seqScore = Double.toString( ((ProfileScanMatch.ProfileScanLocation) location).getScore());
  } else if (location instanceof TMHMMMatch.TMHMMLocation) {
    seqScore = Double.toString( ((TMHMMMatch.TMHMMLocation) location).getScore());
  } else if (location instanceof SignalPMatch.SignalPLocation) {
    seqScore = Double.toString( ((SignalPMatch.SignalPLocation) location).getScore());
  }
  return seqScore;
}

matchLocationCount += match.getLocations().size();

private static Hmmer3Match getMatch(Signature signature, String modelId, Map<String, Set<Hmmer3RawMatch>> matchesByModel) {
  Set<Hmmer3Match.Hmmer3Location> locations = new HashSet<Hmmer3Match.Hmmer3Location>();
  double score = 0, evalue = 0;
  for (Hmmer3RawMatch m : matchesByModel.get(modelId)) {
    // Score and evalue should be the same (repeated for each location)
    score = m.getScore();
    evalue = m.getEvalue();
    locations.add(getLocation(m));
  }
  return new Hmmer3Match(signature, score, evalue, locations);
}