update to print topological order

need to do bfs to achieve what eamonn would like to have

src/de/phenomics/Obo2Xls.java

@@ -5,6 +5,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.stream.Collectors;
 
 import org.apache.commons.cli.CommandLine;
@@ -130,14 +131,21 @@ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, S
 
  rowIndex = createHeaderRow(createHelper, style, rowIndex, sheet0, headersTermAdd);
 
- ArrayList<Term> termsToReport = new ArrayList<>();
+ ArrayList<Term> termsInTopologicalOrder = ontology.getTermsInTopologicalOrder();
+ HashSet<Term> termsToReport = new HashSet<>();
  if (selectedRootTerm != null) {
  termsToReport.addAll(ontologySlim.getDescendants(selectedRootTerm));
  } else {
  termsToReport.addAll(ontology.getAllTerms());
  }
 
- for (Term term : termsToReport) {
+ for (Term term : termsInTopologicalOrder) {
+
+ if (term.isObsolete())
+ continue;
+
+ if (!termsToReport.contains(term))
+ continue;
 
  Row row = sheet0.createRow((short) rowIndex++);