new FingerPrintsMatch.FingerPrintsLocation( rawMatch.getLocationStart(), boundedLocationEnd(protein, rawMatch),
mappingFields.add(Integer.toString(printsLocation.getMotifNumber())); mappingFields.add(Double.toString(printsLocation.getPvalue())); mappingFields.add(((FingerPrintsMatch) match).getGraphscan()); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) {
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; }
public Object clone() throws CloneNotSupportedException { return new FingerPrintsLocation(this.getStart(), this.getEnd(), this.getPvalue(), this.getScore(), this.getMotifNumber()); }
public Object clone() throws CloneNotSupportedException { final Set<FingerPrintsLocation> clonedLocations = new HashSet<FingerPrintsLocation>(this.getLocations().size()); for (FingerPrintsLocation location : this.getLocations()) { clonedLocations.add((FingerPrintsLocation) location.clone()); } return new FingerPrintsMatch(this.getSignature(), this.getEvalue(), this.getGraphscan(), clonedLocations); }
public FingerPrintsLocation(int start, int end, double pvalue, double score, int motifNumber) { super(start, end); setPvalue(pvalue); setScore(score); setMotifNumber(motifNumber); }