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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 java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.annotation.Nonnull;

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 {

    /**
     * @param doc1 doc1
     * @param doc2 doc2
     * @return list of diffs
     */
    @Nonnull
    public static List getDiffs(@Nonnull OBODoc doc1, @Nonnull OBODoc doc2) {
        List diffs = new ArrayList<>();
        diffs.addAll(getDiffs("Header", doc1.getHeaderFrame(), 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
    @Nonnull
    private static List getDiffsAsym(String ftype, @Nonnull Collection fl1,
        @Nonnull Collection fl2, int n, boolean isCheckFrame) {
        List diffs = new ArrayList<>();
        Map fm2 = new HashMap<>();
        for (Frame f : fl2) {
            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;
    }

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

    // FRAMES
    @SuppressWarnings("null")
    @Nonnull
    private static List getDiffsAsym(String ftype, @Nonnull Frame f1, @Nonnull Frame f2,
        int n) {
        List diffs = new ArrayList<>();
        for (Clause c : f1.getClauses()) {
            boolean isMatched = false;
            for (Clause c2 : f2.getClauses()) {
                if (c.getTag().equals(c2.getTag()) && 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;
    }

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