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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.model;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.obolibrary.obo2owl.OboInOwlCardinalityTools;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;

/** The Class Frame. */
public class Frame {

    /** The Enum FrameType. */
    public enum FrameType {
        /** HEADER. */
        HEADER, /** TERM. */
        TERM, /** TYPEDEF. */
        TYPEDEF, /** INSTANCE. */
        INSTANCE, /** ANNOTATION. */
        ANNOTATION
    }

    /** The clauses. */
    protected Collection clauses;
    /** The id. */
    protected String id;
    /** The type. */
    protected FrameType type;

    /** Instantiates a new frame. */
    public Frame() {
        init();
    }

    /**
     * Instantiates a new frame.
     * 
     * @param type
     *        the type
     */
    public Frame(FrameType type) {
        init();
        this.type = type;
    }

    /** Init clauses. */
    protected final void init() {
        clauses = new ArrayList<>();
    }

    /**
     * freezing a frame signals that a frame has become quiescent, and that data structures can be adjusted to
     * increase performance or reduce memory consumption. If a frozen frame is subsequently modified it will be thawed
     * as necessary.
     */
    public void freeze() {
        if (clauses.isEmpty()) {
            clauses = Collections.emptyList();
            return;
        }

        for (Clause clause : clauses) {
            clause.freeze();
        }

        if (clauses.size() == 1) {
            clauses = Collections.singletonList(clauses.iterator().next());
            return;
        }

        if (clauses instanceof ArrayList) {
            ArrayList arrayList = (ArrayList) clauses;
            arrayList.trimToSize();
        }

    }

    /**
     * @return the type
     */
    public FrameType getType() {
        return type;
    }

    /**
     * @param type
     *        the new type
     */
    public void setType(FrameType type) {
        this.type = type;
    }

    /**
     * @return the id
     */
    public String getId() {
        return id;
    }

    /**
     * @param id
     *        the new id
     */
    public void setId(String id) {
        this.id = id;
    }

    /**
     * @return the clauses
     */
    public Collection getClauses() {
        return clauses;
    }

    /**
     * @param tag
     *        the tag
     * @return the clauses for tag
     */
    @Nonnull
    public Collection getClauses(String tag) {
        Collection cls = new ArrayList<>();
        for (Clause cl : clauses) {
            if (cl.getTag().equals(tag)) {
                cls.add(cl);
            }
        }
        return cls;
    }

    /**
     * @param tag
     *        the tag
     * @return the clauses for tag
     */
    @Nonnull
    public Collection getClauses(@Nonnull OboFormatTag tag) {
        return getClauses(tag.getTag());
    }

    /**
     * @param tag
     *        the tag
     * @return null if no value set, otherwise first value
     */
    @Nullable
    public Clause getClause(String tag) {
        for (Clause cl : clauses) {
            if (cl.getTag().equals(tag)) {
                return cl;
            }
            // TODO - throw exception if more than one clause of this type?
        }
        return null;
    }

    /**
     * @param tag
     *        the tag
     * @return the clause for tag
     */
    @Nullable
    public Clause getClause(@Nonnull OboFormatTag tag) {
        return getClause(tag.getTag());
    }

    /**
     * @param clauses
     *        the new clauses
     */
    public void setClauses(Collection clauses) {
        this.clauses = clauses;
    }

    /**
     * @param cl
     *        the clause
     */
    public void addClause(Clause cl) {
        if (!(clauses instanceof ArrayList)) {
            Collection tmp  = new ArrayList<>(clauses.size()+1);
            tmp.addAll(clauses);
            clauses = tmp;
        }
        clauses.add(cl);
    }

    @Override
    public String toString() {
        StringBuffer sb = new StringBuffer();
        sb.append("Frame(");
        sb.append(id);
        sb.append(' ');
        for (Clause cl : clauses) {
            sb.append(cl);
        }
        sb.append(')');
        String string = sb.toString();
        assert string != null;
        return string;
    }

    /**
     * @param tag
     *        the tag
     * @return the tag value for tag
     */
    @Nullable
    public Object getTagValue(String tag) {
        Clause clause = getClause(tag);
        if (clause == null) {
            return null;
        }
        return clause.getValue();
    }

    /**
     * @param tag
     *        the tag
     * @return the tag value for tag
     */
    @Nullable
    public Object getTagValue(@Nonnull OboFormatTag tag) {
        return getTagValue(tag.getTag());
    }

    /**
     * @param 
     *        the generic type
     * @param tag
     *        the tag
     * @param cls
     *        the cls
     * @return the tag value for tag and class
     */
    @SuppressWarnings("null")
    @Nullable
    public  T getTagValue(String tag, @Nonnull Class cls) {
        if (getClause(tag) == null) {
            return null;
        }
        Object value = getClause(tag).getValue();
        if (value != null && value.getClass().isAssignableFrom(cls)) {
            return cls.cast(value);
        }
        return null;
    }

    /**
     * @param 
     *        the generic type
     * @param tag
     *        the tag
     * @param cls
     *        the cls
     * @return the tag value for tag and class
     */
    @Nullable
    public  T getTagValue(@Nonnull OboFormatTag tag, @Nonnull Class cls) {
        return getTagValue(tag.getTag(), cls);
    }

    /**
     * @param tag
     *        the tag
     * @return the tag values for tag
     */
    @Nonnull
    public Collection