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 CrossReference toCrossReference(O cvObject) {
if (cvObject == null) {
throw new IllegalArgumentException("CvObject must not be null. ");
}
// name of the cv is the fullname
String text =
cvObject.getFullName() != null ? cvObject.getFullName() : cvObject.getShortLabel();
String identity = cvObject.getIdentifier();
if (identity == null) {
throw new NullPointerException(
cvObject.getClass().getSimpleName() + "(" + text + ") didn't have an identity");
}
final CvObjectXref idXref =
findMatchingIdentityXref(
cvObject.getXrefs(),
identity); // XrefUtils.getIdentityXref(cvObject, CvDatabase.PSI_MI_MI_REF);
if (idXref != null) {
try {
CrossReference ref = crossRefConverter.createCrossReference(idXref, false);
ref.setText(text);
return ref;
} catch (Exception e) {
throw new RuntimeException("An exception occured while building a cv object : " + text, e);
}
} else {
CrossReference ref =
new CrossReferenceImpl(CrossReferenceConverter.DATABASE_UNKNOWN, identity, text);
return ref;
}
}
private void processSpecies(CyRow row, CrossReference ref) {
if (ref != null) {
final String name = ref.getText();
final String speciesID = ref.getIdentifier();
row.set(TAXNOMY, speciesID);
row.set(TAXNOMY_NAME, name);
}
}
public int compare(CrossReference cr1, CrossReference cr2) {
int idx1 = texts.indexOf(cr1.getText());
int idx2 = texts.indexOf(cr2.getText());
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 text
}
return compare;
}
public boolean matches(CrossReference cr) {
return texts.indexOf(cr.getText()) != -1;
}
