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){