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[Suggestion] add ignore obsolete functionality #8

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[Suggestion] add ignore obsolete functionality #8

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35 changes: 21 additions & 14 deletions ontologizer/src/ontologizer/ontology/OBOParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -215,6 +215,10 @@ public Set<Term> getTermMap()
return this.terms;
}

public boolean ignoreObsoleteTerms()
{
return false;
}
/**
* This puts the results of the parse of a single OBO stanza into one Term
* object and stores that in the HashSet terms.
Expand All @@ -239,20 +243,23 @@ private void enterNewTerm()
return;

}

/* Create a Term object and put it in the HashMap terms. */
Term t = new Term(currentID, currentName, currentNamespace, currentParents);
t.setObsolete(currentObsolete);
t.setDefinition(currentDefintion);
t.setAlternatives(currentAlternatives);
t.setEquivalents(currentEquivalents);
t.setSubsets(currentSubsets);
t.setSynonyms(currentSynonyms);
t.setXrefs(currentXrefs);
terms.add(t);

/* Statistics */
numberOfRelations += currentParents.size();
//Ignore term if both obsolete and we are ignoring obsoletes
if (!(ignoreObsoleteTerms() && this.currentObsolete))
{
/* Create a Term object and put it in the HashMap terms. */
Term t = new Term(currentID, currentName, currentNamespace, currentParents);
t.setObsolete(currentObsolete);
t.setDefinition(currentDefintion);
t.setAlternatives(currentAlternatives);
t.setEquivalents(currentEquivalents);
t.setSubsets(currentSubsets);
t.setSynonyms(currentSynonyms);
t.setXrefs(currentXrefs);
terms.add(t);

/* Statistics */
numberOfRelations += currentParents.size();
}
}

resetCurrentStanza();
Expand Down