protected void processAddedAliasEvent(Alias added) { // the added alias is gene name and it is not the current gene name if (geneName == null && AliasUtils.doesAliasHaveType(added, Alias.GENE_NAME_MI, Alias.GENE_NAME)){ geneName = added; } }
protected void processAddedAliasEvent(Alias added) { if (recommendedName == null && AliasUtils.doesAliasHaveType(added, Alias.COMPLEX_RECOMMENDED_NAME_MI, Alias.COMPLEX_RECOMMENDED_NAME)){ recommendedName = added; } else if (systematicName == null && AliasUtils.doesAliasHaveType(added, Alias.COMPLEX_SYSTEMATIC_NAME_MI, Alias.COMPLEX_SYSTEMATIC_NAME)){ systematicName = added; } }
/** * The source of the Alias is uniprotkb if the alias type is gene name, gene name synonym, isoform synonym, * locus name or orf name. It is unknown otherwise. * @param alias * @return the default dbsource for this alias */ public static String findDbSourceForAlias(Alias alias){ // these aliases should come from uniprotkb if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME) || AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_SYNONYM_MI, Alias.GENE_NAME_SYNONYM) || AliasUtils.doesAliasHaveType(alias, Alias.ISOFORM_SYNONYM_MI, Alias.ISOFORM_SYNONYM) || AliasUtils.doesAliasHaveType(alias, Alias.LOCUS_NAME_MI, Alias.LOCUS_NAME) || AliasUtils.doesAliasHaveType(alias, Alias.ORF_NAME_MI, Alias.ORF_NAME)){ return Xref.UNIPROTKB; } return UNKNOWN_DATABASE; }
/** * This method will return the first Alias having this typeId/type name * It will return null if there are no Alias with this type id/name * @param aliases : the collection of Alias * @param typeId : the type id to look for * @param typeName : the type name to look for * @return the first alias having this type name/id, null if no Alias with this type name/id */ public static Alias collectFirstAliasWithType(Collection<? extends Alias> aliases, String typeId, String typeName){ if (aliases == null || aliases.isEmpty()){ return null; } for (Alias alias : aliases){ if (doesAliasHaveType(alias, typeId, typeName)){ return alias; } } return null; }
/** * Remove all Alias having this method name/method id from the collection of aliases * @param aliases : the collection of Checksum * @param typeId : the method id to look for * @param typeName : the method name to look for */ public static void removeAllAliasesWithType(Collection<Alias> aliases, String typeId, String typeName){ if (aliases != null){ Iterator<Alias> aliasIterator = aliases.iterator(); while (aliasIterator.hasNext()){ if (doesAliasHaveType(aliasIterator.next(), typeId, typeName)){ aliasIterator.remove(); } } } }
/** * Extract all the aliases having a specific type. * @param aliases : the aliases to analyse * @param typeId : the alias type MI identifier * @param typeName : the alias type name * @return the selection of aliases having the specified type (typeId or typeName if no ids) */ public static Collection<Alias> collectAllAliasesHavingType(Collection<? extends Alias> aliases, String typeId, String typeName){ if (aliases == null || aliases.isEmpty()){ return Collections.EMPTY_LIST; } Collection<Alias> selectedAliases = new ArrayList<Alias>(aliases.size()); for (Alias alias : aliases){ if (doesAliasHaveType(alias, typeId, typeName)){ selectedAliases.add(alias); } } return selectedAliases; }
if (AliasUtils.doesAliasHaveType(alias, Checksum.SMILE_MI, Checksum.SMILE) || AliasUtils.doesAliasHaveType(alias, Checksum.SMILE_MI, Checksum.SMILE_SHORT)){ createChecksumFromAlias(interactor, alias); else if (AliasUtils.doesAliasHaveType(alias, Checksum.INCHI_KEY_MI, Checksum.INCHI_KEY)){ createChecksumFromAlias(interactor, alias); else if (AliasUtils.doesAliasHaveType(alias, Checksum.STANDARD_INCHI_KEY_MI, Checksum.STANDARD_INCHI_KEY)){ createChecksumFromAlias(interactor, alias); else if (AliasUtils.doesAliasHaveType(alias, Checksum.INCHI_MI, Checksum.INCHI) || AliasUtils.doesAliasHaveType(alias, Checksum.INCHI_MI, Checksum.INCHI_SHORT)){ createChecksumFromAlias(interactor, alias); else if (AliasUtils.doesAliasHaveType(alias, Checksum.ROGID_MI, Checksum.ROGID) || AliasUtils.doesAliasHaveType(alias, null, Checksum.IROGID)){ createChecksumFromAlias(interactor, alias);
/** * The source of the Alias is uniprotkb if the alias type is gene name, gene name synonym, isoform synonym, * locus name or orf name. If the participant has an modelled interaction with a source, * it will return the source shortname. It is unknown otherwise. * @param participant * @param alias * @return */ public static String findDbSourceForAlias(ModelledParticipant participant, Alias alias){ if (participant != null){ // these aliases should come from uniprotkb if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME) || AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_SYNONYM_MI, Alias.GENE_NAME_SYNONYM) || AliasUtils.doesAliasHaveType(alias, Alias.ISOFORM_SYNONYM_MI, Alias.ISOFORM_SYNONYM) || AliasUtils.doesAliasHaveType(alias, Alias.LOCUS_NAME_MI, Alias.LOCUS_NAME) || AliasUtils.doesAliasHaveType(alias, Alias.ORF_NAME_MI, Alias.ORF_NAME)){ return Xref.UNIPROTKB; } // check source else if (participant.getInteraction() != null){ ModelledInteraction interaction = participant.getInteraction(); if (interaction.getSource() != null){ return interaction.getSource().getShortName(); } } } return UNKNOWN_DATABASE; }
if (AliasUtils.doesAliasHaveType(alias, null, DISPLAY_SHORT)){ if (displayShort == null){ displayShort = alias; else if (AliasUtils.doesAliasHaveType(alias, null, DISPLAY_LONG)){ if (displayLong == null){ displayLong = alias; else if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME)){ if (geneName == null){ geneName = alias; else if (AliasUtils.doesAliasHaveType(alias, null, SHORTLABEL)){ if (shortLabel == null){ shortLabel = alias;
if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME) || AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_SYNONYM_MI, Alias.GENE_NAME_SYNONYM) || AliasUtils.doesAliasHaveType(alias, Alias.ISOFORM_SYNONYM_MI, Alias.ISOFORM_SYNONYM) || AliasUtils.doesAliasHaveType(alias, Alias.LOCUS_NAME_MI, Alias.LOCUS_NAME) || AliasUtils.doesAliasHaveType(alias, Alias.ORF_NAME_MI, Alias.ORF_NAME)){ return Xref.UNIPROTKB;
if (AliasUtils.doesAliasHaveType(alias, Alias.GENE_NAME_MI, Alias.GENE_NAME)){ this.shortName = alias.getName(); break; if (AliasUtils.doesAliasHaveType((Alias)alias, Alias.AUTHOR_ASSIGNED_NAME_MI, Alias.AUTHOR_ASSIGNED_NAME)) { this.authorAssignedName = ((Alias)alias).getName(); break;