private void printAliases(List<Alias> aliases) { log.info("--- Ordered list of Aliases ---"); for (Alias a : aliases) { log.info(a.getDbSource() + ":" + a.getName() + "(" + a.getAliasType() + ")"); } log.info("-------------------------------"); } }
@Override protected void processAliases(Interactor mitabInteractor, Collection<InteractorAlias> aliases) { for (InteractorAlias alias : aliases){ psidev.psi.mi.tab.model.Alias aliasField = aliasConverter.intactToMitab(alias); if (aliasField != null){ mitabInteractor.getAliases().add(aliasField); // create display short which should be gene name or gene name synonym if (CvAliasType.GENE_NAME.equals(aliasField.getAliasType())){ psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, aliasField.getName(),InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); hasFoundDisplayShort = true; } } } }
String acc = alias.getName(); String sourceIdDbName = alias.getDbSource(); int firtSize = accs.size(); updateAccMap(accs, acc, idDbNameList, sourceIdDbName);
alias.setDbSource(UNIPROT); alias.setDbSource(institutionName); alias.setAliasType(type); alias.setDbSource(UNKNOWN); alias.setName(intactAlias.getName());
public boolean matches(Alias a) { return aliasTypes.indexOf( a.getAliasType() ) != -1; } }
a.setAliasType(alias.getType()); tabAliases.add(a); } else { if (shortLabel != null) { psidev.psi.mi.tab.model.Alias a = new psidev.psi.mi.tab.model.AliasImpl(UNKNOWN, shortLabel); a.setAliasType(SHORT_LABEL); tabAliases.add(a); if (fullName != null) { psidev.psi.mi.tab.model.Alias a = new psidev.psi.mi.tab.model.AliasImpl(UNKNOWN, fullName); a.setAliasType(FULL_NAME); tabAliases.add(a);
@Override protected void processAliases(Interactor mitabInteractor, Collection<InteractorAlias> aliases) { for (InteractorAlias alias : aliases){ psidev.psi.mi.tab.model.Alias aliasField = aliasConverter.intactToMitab(alias); if (aliasField != null){ mitabInteractor.getAliases().add(aliasField); // create display short which should be gene name or gene name synonym if (CvAliasType.GENE_NAME.equals(aliasField.getAliasType())){ hasFoundDisplayShort = true; psidev.psi.mi.tab.model.Alias displayShort = new AliasImpl( CvDatabase.PSI_MI, aliasField.getName(),InteractorConverter.DISPLAY_SHORT ); mitabInteractor.getAliases().add(displayShort); } } } } }
xref.setSource(alias.getDbSource()); xref.setId(alias.getName()); physicalEntity.setXref(xref);
/** * Assumes that the list of not empty. * * @param aliases a non null, non empty list of <code>CrossRefenrence</code>. * @return the identifier of the first relevant cross reference based on the current IdentifierByDatabaseComparator. */ private String pickFirstRelevantAlias(Collection<Alias> aliases, AliasComparator comparator, boolean allowNullIfNoMatch) { if (aliases == null || aliases.isEmpty()) { throw new IllegalArgumentException("You must give a non null/empty collection of aliases"); } boolean hasMatched = false; Alias picked = null; if (aliases.size() > 1) { List<Alias> orderedRefs = new ArrayList<Alias>(aliases); Collections.sort(orderedRefs, comparator); picked = orderedRefs.get(0); hasMatched = comparator.hasMatchedAny(); } else { picked = aliases.iterator().next(); hasMatched = comparator.matches(picked); } if (allowNullIfNoMatch && !hasMatched) { return null; } return picked.getName(); }
public int compare(Alias a1, Alias a2) { int idx1 = aliasTypes.indexOf(a1.getAliasType()); int idx2 = aliasTypes.indexOf(a2.getAliasType()); if( idx1 != -1 || idx2 != -1 ) { matchedAny = true; } int compare = 0; if (idx1 == -1 && idx2 == -1) { compare = 0; } else if (idx1 == -1) { compare = 1; // first is greater } else if (idx2 == -1) { compare = -1; // first is lower } else { compare = idx1 - idx2; // relative to their position in the ordered list of DBs } return compare; }
public static String joinAliasCollection(List<Alias> collection) { StringBuilder sb = new StringBuilder(); if (collection != null && !collection.isEmpty()) { Iterator<Alias> iterator = collection.iterator(); while (iterator.hasNext()) { Alias field = iterator.next(); sb.append(joinAttributes(field.getDbSource(), field.getName(), field.getAliasType())); if (iterator.hasNext()) { sb.append(FIELD_DELIMITER); } } } else { sb.append('-'); } return sb.toString(); }
String type = tabAlias.getAliasType(); String value = tabAlias.getName();
if (UNIPROT.equalsIgnoreCase(alias.getDbSource())){ if (CvAliasType.GENE_NAME.equalsIgnoreCase(alias.getAliasType())){ geneName = alias.getName(); else if (CvAliasType.LOCUS_NAME.equalsIgnoreCase(alias.getAliasType())){ locusName = alias.getName(); else if (CvAliasType.ORF_NAME.equalsIgnoreCase(alias.getAliasType())){ orf = alias.getName();
String type = tabAlias.getAliasType(); String value = tabAlias.getName();