score = Double.toString(((HmmerLocation) location).getEvalue()); } else if (location instanceof BlastProDomMatch.BlastProDomLocation) { score = Double.toString( ((BlastProDomMatch.BlastProDomLocation) location).getEvalue() ); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) { score = Double.toString( ((ProfileScanMatch.ProfileScanLocation) location).getScore() );
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 { final Set<BlastProDomLocation> clonedLocations = new HashSet<BlastProDomLocation>(this.getLocations().size()); for (BlastProDomLocation location : this.getLocations()) { clonedLocations.add((BlastProDomLocation) location.clone()); } return new BlastProDomMatch(this.getSignature(), clonedLocations); }
score = Double.toString(((HmmerLocation) location).getEvalue()); } else if (location instanceof BlastProDomMatch.BlastProDomLocation) { score = Double.toString( ((BlastProDomMatch.BlastProDomLocation) location).getEvalue() ); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) { score = Double.toString( ((ProfileScanMatch.ProfileScanLocation) location).getScore() );
score = Double.toString(((HmmerLocation) location).getEvalue()); } else if (location instanceof BlastProDomMatch.BlastProDomLocation) { score = Double.toString( ((BlastProDomMatch.BlastProDomLocation) location).getEvalue() ); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) { score = Double.toString( ((ProfileScanMatch.ProfileScanLocation) location).getScore() );
score = Double.toString(((HmmerLocationWithSites) location).getEvalue()); } else if (location instanceof BlastProDomMatch.BlastProDomLocation) { score = Double.toString( ((BlastProDomMatch.BlastProDomLocation) location).getEvalue() ); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) { score = Double.toString( ((ProfileScanMatch.ProfileScanLocation) location).getScore() );
score = Double.toString(((HmmerLocation) location).getEvalue()); } else if (location instanceof BlastProDomMatch.BlastProDomLocation) { score = Double.toString(((BlastProDomMatch.BlastProDomLocation) location).getEvalue()); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) { score = Double.toString(((ProfileScanMatch.ProfileScanLocation) location).getScore());
score = Double.toString(((HmmerLocationWithSites) location).getEvalue()); } else if (location instanceof BlastProDomMatch.BlastProDomLocation) { score = Double.toString(((BlastProDomMatch.BlastProDomLocation) location).getEvalue()); } else if (location instanceof ProfileScanMatch.ProfileScanLocation) { score = Double.toString(((ProfileScanMatch.ProfileScanLocation) location).getScore());
new BlastProDomMatch.BlastProDomLocation( rawMatch.getLocationStart(), rawMatch.getLocationEnd(),
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){
public Object clone() throws CloneNotSupportedException { return new BlastProDomLocation(this.getStart(), this.getEnd(), this.getScore(), this.getEvalue()); } }