protected boolean isBait(Participant participant) { if (participant == null) { throw new IllegalArgumentException("Participant must not be null."); } if (participant.hasExperimentalRoles()) { for (ExperimentalRole role : participant.getExperimentalRoles()) { // search for bait log.debug("Checking if participant (id:" + participant.getId() + ") is a bait."); if (XrefUtils.hasPsiId(role.getXref(), BAIT_MI_REF)) { log.debug("Yes it is."); return true; } log.debug("No it is not."); } } return false; }
public static Participant createParticipant(Interactor interactor, BiologicalRole biologicalRole, ExperimentalRole experimentalRole) { Participant participant = new Participant(); assignNextId(participant); participant.setInteractor(interactor); participant.setBiologicalRole(biologicalRole); participant.getExperimentalRoles().add(experimentalRole); return participant; }
protected String displayParticipant(Participant p) { // fetch role String role = ""; for (ExperimentalRole aRole : p.getExperimentalRoles()) { if (role.length() > 0) { role += "&"; } if (aRole.hasNames()) { role += aRole.getNames().getShortLabel(); } else { role += "?"; } } // fetch interactor String interactor = p.getInteractor().getNames().getShortLabel(); return interactor + ":" + role; }
private String displayParticipant( Participant p ) { // fetch role String role = ""; for ( ExperimentalRole aRole : p.getExperimentalRoles() ) { if ( role.length() > 0 ) { role += "&"; } if ( aRole.hasNames() ) { role += aRole.getNames().getShortLabel(); } else { role += "?"; } } // fetch interactor String interactor = p.getInteractor().getNames().getShortLabel(); return interactor + ":" + role; }
for (ExperimentalRole role : participant.getExperimentalRoles()) { if(exp==null || role.getExperiments().contains(exp) || role.getExperiments().isEmpty()) {
Collection<ExperimentalRole> xmlExpRoles = xmlParticipant.getExperimentalRoles();
if (participant.getExperimentalRoles().size() > 1) { throw new UnsupportedConversionException("Cannot convert participants with more than one experimental role: "+participant); if (participant.getExperimentalRoles().isEmpty()) { if (log.isWarnEnabled()) log.warn("Participant without experimental roles: " + participant); roles = participant.getExperimentalRoles();
if (participant.getExperimentalRoles().size() > 1) { throw new UnsupportedConversionException("Cannot convert participants with more than one experimental role: "+participant); if (participant.getExperimentalRoles().isEmpty()) { if (log.isWarnEnabled()) log.warn("Participant without experimental roles: " + participant); roles = participant.getExperimentalRoles();
participant.getExperimentalRoles().add( expRole );
participant.getExperimentalRoles().add(experimentalRole);
for ( ExperimentalRole er : participant.getExperimentalRoles() ) { if ( er.hasExperimentRefs() ) {
jParticipant.getExperimentalRoleList().getExperimentalRoles() ) { mParticipant.getExperimentalRoles().add( experimentalRoleConverter.fromJaxb( jExperimentalRole ) );
jParticipant.getExperimentalRoleList().getExperimentalRoles() ) { mParticipant.getExperimentalRoles().add( experimentalRoleConverter.fromJaxb( jExperimentalRole ) );
for ( ExperimentalRole mExperimentalRole : mParticipant.getExperimentalRoles() ) { jParticipant.getExperimentalRoleList().getExperimentalRoles().add( experimentalRoleConverter.toJaxb( mExperimentalRole ) );
for ( ExperimentalRole mExperimentalRole : mParticipant.getExperimentalRoles() ) { jParticipant.getExperimentalRoleList().getExperimentalRoles().add( experimentalRoleConverter.toJaxb( mExperimentalRole ) );