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A java library for converting obo format documents to OWL, and for converting (a subset of) OWL to obo format. This version has been slightly modified to be included directly in the OWL API. The upstream code for this module and its authors can be found at https://code.google.com/p/oboformat/.

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package org.obolibrary.oboformat.diff;

import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.obolibrary.oboformat.model.Clause;
import org.obolibrary.oboformat.model.Frame;
import org.obolibrary.oboformat.model.OBODoc;
import org.obolibrary.oboformat.model.Xref;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;

/**
 * Diffs two OBO Documents. Performs structural diffing only - does not use
 * reasoning (use OWLDiff or similar tools for this)
 *
 * @author cjm
 */
public class OBODocDiffer {

    private OBODocDiffer() {
    }

    /**
     * @param doc1 doc1
     * @param doc2 doc2
     * @return list of diffs
     */
    public static List getDiffs(OBODoc doc1, OBODoc doc2) {
        List diffs = new ArrayList<>();
        diffs.addAll(getDiffs("Header", verifyNotNull(doc1.getHeaderFrame()),
            verifyNotNull(doc2.getHeaderFrame())));
        diffs.addAll(getDiffs("Term", doc1.getTermFrames(), doc2.getTermFrames()));
        diffs.addAll(getDiffs("Typedef", doc1.getTypedefFrames(), doc2.getTypedefFrames()));
        diffs.addAll(getDiffs("Instance", doc1.getInstanceFrames(), doc2.getInstanceFrames()));
        return diffs;
    }

    // FRAME LISTS
    private static List getDiffsAsym(String ftype, Collection fl1,
        Collection fl2, int n,
        boolean isCheckFrame) {
        List diffs = new ArrayList<>();
        Map fm2 = new HashMap<>();
        fl2.forEach(f -> fm2.put(f.getId(), f));
        for (Frame f1 : fl1) {
            if (fm2.containsKey(f1.getId())) {
                Frame f2 = fm2.get(f1.getId());
                if (isCheckFrame) {
                    // we only need to do this once
                    diffs.addAll(getDiffs(ftype, f1, f2));
                }
            } else {
                diffs.add(new Diff(ftype, "cannot find frame", f1, n));
            }
        }
        return diffs;
    }

    private static List getDiffs(String ftype, Collection fl1, Collection fl2) {
        List diffs = getDiffsAsym(ftype, fl1, fl2, 1, true);
        diffs.addAll(getDiffsAsym(ftype, fl1, fl2, 2, false));
        return diffs;
    }

    // FRAMES
    private static List getDiffsAsym(String ftype, Frame f1, Frame f2, int n) {
        List diffs = new ArrayList<>();
        for (Clause c : f1.getClauses()) {
            boolean isMatched = false;
            for (Clause c2 : f2.getClauses()) {
                if (sameTag(c, c2)) {
                    if (c.equals(c2)) {
                        isMatched = true;
                        if (OboFormatTag.TAG_XREF.getTag().equals(c.getTag())) {
                            String a1 = c.getValue(Xref.class).getAnnotation();
                            String a2 = c2.getValue(Xref.class).getAnnotation();
                            isMatched = a1 == null && a2 == null || a1 != null && a1.equals(a2);
                        }
                        break;
                    }
                }
            }
            if (!isMatched) {
                diffs.add(new Diff(ftype, "cannot_match_clause", f1, f2, c, n));
            }
        }
        return diffs;
    }

    private static boolean sameTag(Clause tag1, Clause tag2) {
        String tag = tag1.getTag();
        if (tag == null) {
            return tag2.getTag() == null;
        }
        return tag.equals(tag2.getTag());
    }

    private static List getDiffs(String ftype, Frame f1, Frame f2) {
        List diffs = getDiffsAsym(ftype, f1, f2, 1);
        diffs.addAll(getDiffsAsym(ftype, f2, f1, 2));
        return diffs;
    }
}