UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(idXref.getPrimaryId().toLowerCase()); sb.append(polymer.getSequence()); usedSequence = true; sb.append(interactor.getShortLabel());
public StringBuilder append(UniquenessStringBuilder usb) { return sb.append(usb.toString()); }
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(createUniquenessString(component.getInteractor())); sb.append(component.getStoichiometry()); sb.append(createUniquenessString(component.getCvBiologicalRole())); sb.append(createUniquenessString(expRole)); sb.append(createUniquenessString(feature)); sb.append(createUniquenessString(partDetMethod)); sb.append(createUniquenessString(experimentalPreparation)); sb.append(createUniquenessString(annotation)); sb.append(createUniquenessString(component.getExpressedIn()));
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(createUniquenessString(component.getInteractor())); sb.append(component.getStoichiometry()); sb.append(createUniquenessString(component.getCvBiologicalRole())); sb.append(createUniquenessString(expRole)); sb.append(createUniquenessString(feature)); sb.append(createUniquenessString(partDetMethod)); sb.append(createUniquenessString(experimentalPreparation)); sb.append(createUniquenessString(annotation)); sb.append(createUniquenessString(component.getExpressedIn()));
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(createUniquenessString(component)); sb.append(createUniquenessString(experiment)); sb.append(createUniquenessString(interaction.getCvInteractionType())); sb.append(createUniquenessString(annotation)); InteractorXref idMsdXref = XrefUtils.getIdentityXref(interaction, CvDatabase.MSD_PDB_MI_REF); InteractorXref idWwXref = XrefUtils.getIdentityXref(interaction, CvDatabase.WWPDB_MI_REF); if (idPdbXref != null) sb.append(idPdbXref.getPrimaryId()); if (idMsdXref != null) sb.append(idMsdXref.getPrimaryId()); if (idWwXref != null) sb.append(idWwXref.getPrimaryId());
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(createUniquenessString(component)); sb.append(createUniquenessString(experiment)); sb.append(createUniquenessString(interaction.getCvInteractionType())); sb.append(createUniquenessString(annotation)); InteractorXref idMsdXref = XrefUtils.getIdentityXref(interaction, CvDatabase.MSD_PDB_MI_REF); InteractorXref idWwXref = XrefUtils.getIdentityXref(interaction, CvDatabase.WWPDB_MI_REF); if (idPdbXref != null) sb.append(idPdbXref.getPrimaryId()); if (idMsdXref != null) sb.append(idMsdXref.getPrimaryId()); if (idWwXref != null) sb.append(idWwXref.getPrimaryId());
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(idXref.getPrimaryId().toLowerCase()); sb.append(polymer.getSequence()); usedSequence = true; sb.append(interactor.getShortLabel());
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(experiment.getShortLabel()); sb.append(createUniquenessString(experiment.getCvIdentification())); sb.append(createUniquenessString(experiment.getCvInteraction())); sb.append(createUniquenessString(experiment.getBioSource())); sb.append(createUniquenessString(annotation));
UniquenessStringBuilder sb = new UniquenessStringBuilder(); sb.append(experiment.getShortLabel()); sb.append(createUniquenessString(experiment.getCvIdentification())); sb.append(createUniquenessString(experiment.getCvInteraction())); sb.append(createUniquenessString(experiment.getBioSource())); sb.append(createUniquenessString(annotation));
protected UniquenessStringBuilder createUniquenessString(Feature feature) { if (keyExists(feature)) { UniquenessStringBuilder builder = getKey(feature); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(feature)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(feature, sb); if (feature == null) return sb; // short label // We need to add the short label for the feature because in mutations in the same amino acid is the only way to // distinguish between two features when the AC is not assigned yet. sb.append(feature.getShortLabel()); // feature type sb.append(createUniquenessString(feature.getCvFeatureType())); // feature identification sb.append(createUniquenessString(feature.getCvFeatureIdentification())); // ranges List<Range> ranges = new ArrayList<Range>(feature.getRanges()); Collections.sort(ranges, new RangeComparator()); for (Range range : ranges) { sb.append(createUniquenessString(range)); } return sb; }
protected UniquenessStringBuilder createUniquenessString(Feature feature) { if (keyExists(feature)) { UniquenessStringBuilder builder = getKey(feature); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(feature)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(feature, sb); if (feature == null) return sb; // short label // We need to add the short label for the feature because in mutations in the same amino acid is the only way to // distinguish between two features when the AC is not assigned yet. sb.append(feature.getShortLabel()); // feature type sb.append(createUniquenessString(feature.getCvFeatureType())); // feature identification sb.append(createUniquenessString(feature.getCvFeatureIdentification())); // ranges List<Range> ranges = new ArrayList<Range>(feature.getRanges()); Collections.sort(ranges, new RangeComparator()); for (Range range : ranges) { sb.append(createUniquenessString(range)); } return sb; }
protected UniquenessStringBuilder createUniquenessString(Range range) { if (keyExists(range)) { UniquenessStringBuilder builder = getKey(range); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(range)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(range, sb); if (range == null) return sb; // type from sb.append(createUniquenessString(range.getFromCvFuzzyType())); // interval from sb.append(range.getFromIntervalStart() + "-" + range.getFromIntervalEnd()); // type to sb.append(createUniquenessString(range.getToCvFuzzyType())); // interval end sb.append(range.getToIntervalStart() + "-" + range.getToIntervalEnd()); return sb; }
protected UniquenessStringBuilder createUniquenessString(Range range) { if (keyExists(range)) { UniquenessStringBuilder builder = getKey(range); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(range)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(range, sb); if (range == null) return sb; // type from sb.append(createUniquenessString(range.getFromCvFuzzyType())); // interval from sb.append(range.getFromIntervalStart() + "-" + range.getFromIntervalEnd()); // type to sb.append(createUniquenessString(range.getToCvFuzzyType())); // interval end sb.append(range.getToIntervalStart() + "-" + range.getToIntervalEnd()); return sb; }
protected UniquenessStringBuilder createUniquenessString(CvObject cvObject) { if (keyExists(cvObject)) { UniquenessStringBuilder builder = getKey(cvObject); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(cvObject)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(cvObject, sb); if (cvObject == null) return sb; // psi-mi String miIdentifier = cvObject.getIdentifier(); if (miIdentifier != null) { sb.append(miIdentifier); } else { sb.append(cvObject.getShortLabel()); } return sb; }
protected UniquenessStringBuilder createUniquenessString(BioSource bioSource) { if (keyExists(bioSource)) { UniquenessStringBuilder builder = getKey(bioSource); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(bioSource)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(bioSource, sb); if (bioSource == null) return sb; // tax id sb.append(bioSource.getTaxId()); // tissue sb.append(createUniquenessString(bioSource.getCvTissue())); // cell type sb.append(createUniquenessString(bioSource.getCvCellType())); return sb; }
protected UniquenessStringBuilder createUniquenessString(CvObject cvObject) { if (keyExists(cvObject)) { UniquenessStringBuilder builder = getKey(cvObject); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(cvObject)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(cvObject, sb); if (cvObject == null) return sb; // psi-mi String miIdentifier = cvObject.getIdentifier(); if (miIdentifier != null) { sb.append(miIdentifier); } else { sb.append(cvObject.getShortLabel()); } return sb; }
protected UniquenessStringBuilder createUniquenessString(Annotation annotation) { if (keyExists(annotation)) { UniquenessStringBuilder builder = getKey(annotation); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(annotation)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(annotation, sb); if (annotation == null) return sb; sb.append(createUniquenessString(annotation.getCvTopic())); sb.append(annotation.getAnnotationText()); return sb; }
protected UniquenessStringBuilder createUniquenessString(Annotation annotation) { if (keyExists(annotation)) { UniquenessStringBuilder builder = getKey(annotation); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(annotation)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(annotation, sb); if (annotation == null) return sb; sb.append(createUniquenessString(annotation.getCvTopic())); sb.append(annotation.getAnnotationText()); return sb; }
protected UniquenessStringBuilder createUniquenessString(BioSource bioSource) { if (keyExists(bioSource)) { UniquenessStringBuilder builder = getKey(bioSource); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(bioSource)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(bioSource, sb); if (bioSource == null) return sb; // tax id sb.append(bioSource.getTaxId()); // tissue sb.append(createUniquenessString(bioSource.getCvTissue())); // cell type sb.append(createUniquenessString(bioSource.getCvCellType())); return sb; }
public StringBuilder append(UniquenessStringBuilder usb) { return sb.append(usb.toString()); }