public String getSystematicName() { return this.systematicName != null ? this.systematicName.getName() : null; }
public String getGeneName() { return this.geneName != null ? this.geneName.getName() : null; }
public String getRecommendedName() { return this.recommendedName != null ? this.recommendedName.getName() : null; }
/** * Use DefaultAliasComparator to know if two aliases are equals. * @param alias1 * @param alias2 * @return true if the two aliases are equal */ public static boolean areEquals(Alias alias1, Alias alias2){ if (alias1 == alias2){ return true; } else if (alias1 == null || alias2 == null){ return false; } else { CvTerm type1 = alias1.getType(); CvTerm type2 = alias2.getType(); if (!DefaultCvTermComparator.areEquals(type1, type2)){ return false; } // check identifiers which cannot be null String name1 = alias1.getName(); String name2 = alias2.getName(); return name1.equals(name2); } } }
/** * * @param alias * @return the hashcode consistent with the equals method for this comparator */ public static int hashCode(Alias alias){ if (unambiguousAliasComparator == null){ unambiguousAliasComparator = new UnambiguousAliasComparator(); } if (alias == null){ return 0; } int hashcode = 31; CvTerm type = alias.getType(); hashcode = 31*hashcode + UnambiguousCvTermComparator.hashCode(type); String name = alias.getName(); hashcode = 31*hashcode + name.hashCode(); return hashcode; } }
public void writeAlias(Alias alias) throws IOException { if (alias != null){ // write db first escapeAndWriteString(MitabUtils.findDbSourceForAlias(alias)); // write xref separator writer.write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ writer.write("("); escapeAndWriteString(alias.getType().getShortName()); writer.write(")"); } } }
public void writeAlias(ModelledParticipant participant, Alias alias) throws IOException { if (alias != null){ // write db first escapeAndWriteString(MitabUtils.findDbSourceForAlias(participant, alias)); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } }
public void writeAlias(ParticipantEvidence participant, Alias alias) throws IOException { if (alias != null){ // write db first escapeAndWriteString(MitabUtils.findDbSourceForAlias(participant, alias)); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } }
@Override public void writeAlias(Alias alias) throws IOException { if (alias instanceof MitabAlias){ MitabAlias mitabAlias = (MitabAlias) alias; // write db first escapeAndWriteString(mitabAlias.getDbSource()); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } else{ super.writeAlias(alias); } }
@Override public void writeAlias(Alias alias) throws IOException { if (alias instanceof MitabAlias){ MitabAlias mitabAlias = (MitabAlias) alias; // write db first escapeAndWriteString(mitabAlias.getDbSource()); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } else{ super.writeAlias(alias); } }
@Override public void writeAlias(Alias alias) throws IOException { if (alias instanceof MitabAlias){ MitabAlias mitabAlias = (MitabAlias) alias; // write db first escapeAndWriteString(mitabAlias.getDbSource()); // write xref separator getWriter().write(MitabUtils.XREF_SEPARATOR); // write name escapeAndWriteString(alias.getName()); // write type if (alias.getType() != null){ getWriter().write("("); escapeAndWriteString(alias.getType().getShortName()); getWriter().write(")"); } } else { super.writeAlias(alias); } }