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

Go to download
Show more of this group Show more artifacts with this name
Show all versions of owlapi-oboformat Show documentation
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 static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;

import java.util.ArrayList;
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.obo2owl.OboInOwlCardinalityTools;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;

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

    /**
     * The clauses.
     */
    protected Collection clauses = new ArrayList<>();
    /**
     * The id.
     */
    @Nullable
    protected String id;
    /**
     * The type.
     */
    @Nullable
    protected FrameType type;

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

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

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

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

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

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

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

    /**
     * @param tag the tag
     * @return null if no value set, otherwise first value
     */
    @Nullable
    public Clause getClause(@Nullable String tag) {
        if (tag == null) {
            return null;
        }
        for (Clause cl : clauses) {
            if (tag.equals(cl.getTag())) {
                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(OboFormatTag tag) {
        return getClause(tag.getTag());
    }

    /**
     * @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() {
        StringBuilder sb = new StringBuilder("Frame(");
        sb.append(id);
        sb.append(' ');
        clauses.forEach(cl -> sb.append(cl).append(' '));
        sb.append(')');
        return sb.toString();
    }

    /**
     * @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(OboFormatTag tag) {
        return getTagValue(tag.getTag());
    }

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

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

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