All Downloads are FREE. Search and download functionalities are using the official Maven repository.

org.obolibrary.oboformat.model.Clause Maven / Gradle / Ivy

Go to download

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/.

The newest version!
package org.obolibrary.oboformat.model;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import javax.annotation.Nullable;

import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Clause.
 */
public class Clause {

    private static final Logger LOGGER = LoggerFactory.getLogger(Clause.class);
    private static final Set trueValues = new HashSet<>(Arrays.asList(Boolean.TRUE, "true"));
    private static final Set falseValues = new HashSet<>(Arrays.asList(Boolean.FALSE, "false"));
    @Nullable
    protected String tag;
    protected List values = new ArrayList<>();
    protected Collection xrefs = new ArrayList<>();
    protected Collection qualifierValues = new ArrayList<>();

    /**
     * @param tag tag
     */
    public Clause(OboFormatTag tag) {
        this(tag.getTag());
    }

    /**
     * @param tag tag
     */
    public Clause(@Nullable String tag) {
        this.tag = tag;
    }

    /**
     * @param tag tag
     * @param value value
     */
    public Clause(@Nullable String tag, String value) {
        this(tag);
        setValue(value);
    }

    /**
     * @param tag tag
     * @param value value
     */
    public Clause(OboFormatTag tag, String value) {
        this(tag.getTag(), value);
    }

    /**
     * Default constructor.
     *
     * @deprecated use Clause(String). Using this constructor makes the hashcode variable.
     */
    @Deprecated
    public Clause() {
        super();
    }

    private static boolean collectionsEquals(@Nullable Collection c1,
        @Nullable Collection c2) {
        if (c1 == null || c1.isEmpty()) {
            return c2 == null || c2.isEmpty();
        }
        if (c2 == null || c1.size() != c2.size()) {
            return false;
        }
        return checkContents(c1, c2);
    }

    protected static boolean checkContents(Collection c1, Collection c2) {
        // xrefs are stored as lists to preserve order, but order is not
        // important for comparisons
        Set s = new HashSet<>(c2);
        for (Object x : c1) {
            if (!s.contains(x)) {
                return false;
            }
        }
        return true;
    }

    /**
     * @param value value to set
     * @return modified clause
     */
    public Clause withValue(String value) {
        setValue(value);
        return this;
    }

    /**
     * freezing a clause signals that the clause has become quiescent, and that data structures can
     * be adjusted to increase performance, or reduce memory consumption.
     */
    void freeze() {
        freezeValues();
        freezeXrefs();
        freezeQualifiers();
    }

    void freezeValues() {
        switch (values.size()) {
            case 0:
                values = Collections.emptyList();
                break;
            case 1:
                values = Collections.singletonList(values.get(0));
                break;
            default:
                ((ArrayList) values).trimToSize();
        }
    }

    void freezeXrefs() {
        switch (xrefs.size()) {
            case 0:
                xrefs = Collections.emptyList();
                break;
            case 1:
                Xref xref = xrefs.iterator().next();
                xrefs = Collections.singletonList(xref);
                break;
            default:
                if (xrefs instanceof ArrayList) {
                    ((ArrayList) xrefs).trimToSize();
                }
        }
    }

    void freezeQualifiers() {
        switch (qualifierValues.size()) {
            case 0:
                qualifierValues = Collections.emptyList();
                break;
            case 1:
                qualifierValues = Collections.singletonList(qualifierValues.iterator().next());
                break;
            default:
                if (qualifierValues instanceof ArrayList) {
                    ((ArrayList) qualifierValues).trimToSize();
                }
        }
    }

    /**
     * @return true if no xrefs or qualifiers exist
     */
    public boolean hasNoAnnotations() {
        return xrefs.isEmpty() && qualifierValues.isEmpty();
    }

    /**
     * @return tag
     */
    @Nullable
    public String getTag() {
        return tag;
    }

    /**
     * @param tag tag
     */
    public void setTag(String tag) {
        this.tag = tag;
    }

    /**
     * @return values
     */
    public Collection getValues() {
        return values;
    }

    /**
     * @param values values
     */
    public void setValues(Collection values) {
        if (!(this.values instanceof ArrayList)) {
            switch (values.size()) {
                case 0:
                    this.values = Collections.emptyList();
                    break;
                case 1:
                    Object o = values.iterator().next();
                    this.values = Collections.singletonList(o);
                    break;
                default:
                    this.values = new ArrayList<>(values);
            }
        } else {
            this.values.clear();
            this.values.addAll(values);
        }
    }

    /**
     * @param v v
     */
    public void addValue(@Nullable Object v) {
        if (!(values instanceof ArrayList)) {
            List newValues = new ArrayList<>(values.size() + 1);
            newValues.addAll(values);
            values = newValues;
        }
        values.add(v);
    }

    /**
     * @return value
     * @throws FrameStructureException if there is no value
     */
    public Object getValue() {
        Object value = null;
        if (!values.isEmpty()) {
            value = values.get(0);
        }
        if (value == null) {
            // TODO: Throw Exceptions
            LOGGER.error("Cannot translate: {}", this);
            throw new FrameStructureException("Clause value is null: " + this);
        }
        return value;
    }

    /**
     * @param v v
     */
    public void setValue(Object v) {
        if (values instanceof ArrayList) {
            values.clear();// TODO: Remove this line after profile gathering
            values.add(v);
        } else {
            values = Collections.singletonList(v);
        }
    }

    /**
     * @param cls class
     * @param  value type
     * @return value
     */
    public  T getValue(Class cls) {
        Object value = getValue();
        return cls.cast(value);
    }

    /**
     * @return value2
     * @throws FrameStructureException if there is no value
     */
    public Object getValue2() {
        if (values.size() > 1) {
            return values.get(1);
        }
        return null;
    }

    /**
     * @param cls class
     * @param  value type
     * @return value2
     */
    public  T getValue2(Class cls) {
        Object value = getValue2();
        return cls.cast(value);
    }

    /**
     * @return xref list
     */
    public Collection getXrefs() {
        return xrefs;
    }

    /**
     * @param xrefs xref list
     */
    public void setXrefs(Collection xrefs) {
        if (!(this.xrefs instanceof ArrayList)) {
            switch (xrefs.size()) {
                case 0:
                    this.xrefs = Collections.emptyList();
                    break;
                case 1:
                    Xref xref = xrefs.iterator().next();
                    this.xrefs = Collections.singletonList(xref);
                    break;
                default:
                    this.xrefs = new ArrayList<>(xrefs);
            }
        } else {
            this.xrefs.clear();
            this.xrefs.addAll(xrefs);
        }
    }

    /**
     * @param xref xref
     */
    public void addXref(Xref xref) {
        if (!(xrefs instanceof ArrayList)) {
            List newXrefs = new ArrayList<>(xrefs.size() + 1);
            newXrefs.addAll(xrefs);
            xrefs = newXrefs;
        }
        xrefs.add(xref);
    }

    /**
     * @return qualifier values
     */
    public Collection getQualifierValues() {
        return qualifierValues;
    }

    /**
     * @param qualifierValues qualifier values
     */
    public void setQualifierValues(Collection qualifierValues) {
        if (!(this.qualifierValues instanceof ArrayList)) {
            switch (qualifierValues.size()) {
                case 0:
                    this.qualifierValues = Collections.emptyList();
                    break;
                case 1:
                    this.qualifierValues =
                        Collections.singletonList(qualifierValues.iterator().next());
                    break;
                default:
                    this.qualifierValues = new ArrayList<>(qualifierValues);
            }
        } else {
            this.qualifierValues.clear();
            this.qualifierValues.addAll(qualifierValues);
        }
    }

    /**
     * @param qv qualifier value
     */
    public void addQualifierValue(QualifierValue qv) {
        if (!(qualifierValues instanceof ArrayList)) {
            List newQualifierValues = new ArrayList<>(qualifierValues.size() + 1);
            newQualifierValues.addAll(qualifierValues);
            qualifierValues = newQualifierValues;
        }
        qualifierValues.add(qv);
    }

    @Override
    public String toString() {
        StringBuilder sb = new StringBuilder(tag);
        sb.append('(');
        for (Object ob : values) {
            sb.append(' ');
            sb.append(ob);
        }
        if (!qualifierValues.isEmpty()) {
            sb.append('{');
            for (QualifierValue qv : qualifierValues) {
                sb.append(qv);
                sb.append(' ');
            }
            sb.append('}');
        }
        if (!xrefs.isEmpty()) {
            sb.append('[');
            for (Xref x : xrefs) {
                sb.append(x);
                sb.append(' ');
            }
            sb.append(']');
        }
        sb.append(')');
        return sb.toString();
    }

    @Override
    public int hashCode() {
        return 31 * 31 * 31 * qualifierValues.hashCode() + 31 * xrefs.hashCode()
            + 31 * 31 * values.hashCode() + taghash();
    }

    private int taghash() {
        if (tag == null) {
            return 0;
        } else {
            assert tag != null;
            return tag.hashCode();
        }
    }

    private boolean tag(@Nullable String otherTag) {
        if (tag == null) {
            return otherTag == null;
        }
        assert tag != null;
        return tag.equals(otherTag);
    }

    @Override
    public boolean equals(@Nullable Object obj) {
        if (!(obj instanceof Clause)) {
            return false;
        }
        if (obj == this) {
            return true;
        }
        Clause other = (Clause) obj;
        if (!tag(other.tag)) {
            return false;
        }
        if (getValues().size() == 1 && other.getValues().size() == 1) {
            // special case for comparing booleans
            // this is a bit of a hack - ideally owl2obo would use the correct
            // types
            if (!compareValues(other)) {
                return false;
            }
        } else {
            if (!getValues().equals(other.getValues())) {
                return false;
            }
        }
        if (!collectionsEquals(xrefs, other.getXrefs())) {
            return false;
        }
        return collectionsEquals(qualifierValues, other.getQualifierValues());
    }

    protected boolean compareValues(Clause other) {
        try {
            Object v1 = getValue();
            Object v2 = other.getValue();
            if (v1 != v2 && !v1.equals(v2)) {
                return trueValues.contains(v1) && trueValues.contains(v2)
                    || falseValues.contains(v1) && falseValues.contains(v2);
            }
        } catch (FrameStructureException e) {
            // this cannot happen as it's already been tested
            LOGGER.debug(e.getMessage(), e);
        }
        return true;
    }
}
    

    

    

            

    

            



    
    






    
© 2015 - 2024 Weber Informatics LLC | Privacy Policy