public void mapEdgeColumn(final EncoreInteraction interaction, final CyRow row) {
final Set<String> exp = interaction.getExperimentToPubmed().keySet();
row.set(DETECTION_METHOD_ID, new ArrayList<String>(exp));
final List<CrossReference> pubIDs = interaction.getPublicationIds();
final List<String> pubIdList = new ArrayList<String>();
final List<String> pubDBList = new ArrayList<String>();
for (CrossReference pub : pubIDs) {
pubIdList.add(pub.getIdentifier());
pubDBList.add(pub.getDatabase());
}
if (pubIdList.isEmpty() == false) row.set(PUB_ID, pubIdList);
if (pubDBList.isEmpty() == false) row.set(PUB_DB, pubDBList);
// Interaction (use UniqueID)
row.set(CyEdge.INTERACTION, interaction.getMappingIdDbNames());
final List<Confidence> scores = interaction.getConfidenceValues();
for (Confidence c : scores) {
String type = c.getType();
String value = c.getValue();
if (row.getTable().getColumn(type) == null)
row.getTable().createColumn(type, Double.class, true);
try {
double doubleVal = Double.parseDouble(value);
row.set(type, doubleVal);
} catch (NumberFormatException e) {
// logger.warn("Invalid number string: " + value);
// Ignore invalid number
}
}
}
public void mapNodeColumn(
final EncoreInteraction interaction, final CyRow sourceRow, final CyRow targetRow) {
final Map<String, String> accsSource = interaction.getInteractorAccsA();
processNames(sourceRow, accsSource);
final Map<String, List<String>> otherSource = interaction.getOtherInteractorAccsA();
processOtherNames(sourceRow, otherSource);
final Collection<CrossReference> speciesSource = interaction.getOrganismsA();
// Add Species names
if (speciesSource.size() != 0) {
CrossReference speciesSourceFirst = speciesSource.iterator().next();
processSpecies(sourceRow, speciesSourceFirst);
}
// Try to find human-readable gene name
guessHumanReadableName(sourceRow);
if (targetRow == null) {
return;
}
// If target exists...
final Map<String, String> accsTarget = interaction.getInteractorAccsB();
processNames(targetRow, accsTarget);
final Map<String, List<String>> otherTarget = interaction.getOtherInteractorAccsB();
processOtherNames(targetRow, otherTarget);
final Collection<CrossReference> speciesTarget = interaction.getOrganismsB();
if (speciesTarget.size() != 0) {
CrossReference speciesTargetFirst = speciesTarget.iterator().next();
processSpecies(targetRow, speciesTargetFirst);
}
guessHumanReadableName(targetRow);
}
