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;
}