com.act.biointerpretation.networkanalysis.NetworkEdge.java Source code

Introduction

Here is the source code for com.act.biointerpretation.networkanalysis.NetworkEdge.java

Source

/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program is free software: you can redistribute it and/or modify  *
*  it under the terms of the GNU General Public License as published by  *
*  the Free Software Foundation, either version 3 of the License, or     *
*  (at your option) any later version.                                   *
*                                                                        *
*  This program is distributed in the hope that it will be useful,       *
*  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
*  GNU General Public License for more details.                          *
*                                                                        *
*  You should have received a copy of the GNU General Public License     *
*  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
*                                                                        *
*************************************************************************/

package com.act.biointerpretation.networkanalysis;

import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.collections4.CollectionUtils;

import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

/**
 * Represents an edge, or reaction, in the metabolism network
 */
public class NetworkEdge {

    @JsonProperty("substrates")
    private List<Integer> substrates;

    @JsonProperty("products")
    private List<Integer> products;

    @JsonProperty("reaction_ids")
    Set<Integer> reactionIds;

    @JsonProperty("projector_names")
    Set<String> projectorNames;

    @JsonProperty("orgs")
    Set<String> orgs;

    @JsonCreator
    public NetworkEdge(@JsonProperty("substrates") List<Integer> substrates,
            @JsonProperty("products") List<Integer> products,
            @JsonProperty("reaction_ids") Set<Integer> reactionIds,
            @JsonProperty("projector_names") Set<String> projectorNames, @JsonProperty("orgs") Set<String> orgs) {
        if (substrates == null || products == null) {
            throw new IllegalArgumentException("Cannot create network edge with null substrates or products.");
        }
        this.substrates = substrates;
        this.products = products;
        this.reactionIds = reactionIds;
        this.projectorNames = projectorNames;
        this.orgs = orgs;
    }

    public NetworkEdge(List<Integer> substrates, List<Integer> products) {
        this(substrates, products, new HashSet<Integer>(), new HashSet<String>(), new HashSet<String>());
    }

    /**
     * Merges another edge into this one by adding the auxiliary data from the other edge to this edge.
     * This includes reaction IDs and projector names associated with the other edge.
     * Ensures that the edges have the same chemicals; throws IllegalArgumentException otherwise.
     *
     * @param edge The edge whose data should be added.
     * @return This edge for chaining.
     * @throws IllegalArgumentException if the other edge has different chemicals from this one.
     */
    public NetworkEdge merge(NetworkEdge edge) {
        if (!hasSameSubstratesAndProducts(edge)) {
            throw new IllegalArgumentException("Can only merge two edges with the same chemicals.");
        }
        this.reactionIds.addAll(edge.getReactionIds());
        this.projectorNames.addAll(edge.getProjectorNames());
        return this;
    }

    /**
     * Tests if this edge should be considered the same as another. Returns true if substrate and product are the same,
     * regardless of auxiliary data. This takes into account both the identity and cardinality of each chemical in the lists.
     *
     * @param edge The edge to compare to.
     * @return True if same.
     */
    public boolean hasSameSubstratesAndProducts(NetworkEdge edge) {
        return CollectionUtils.isEqualCollection(this.getSubstrates(), edge.getSubstrates())
                && CollectionUtils.isEqualCollection(this.getProducts(), edge.getProducts());
    }

    public List<Integer> getSubstrates() {
        return substrates;
    }

    public List<Integer> getProducts() {
        return products;
    }

    public Set<Integer> getReactionIds() {
        return Collections.unmodifiableSet(reactionIds);
    }

    public NetworkEdge addReactionId(Integer reactionId) {
        this.reactionIds.add(reactionId);
        return this;
    }

    public Set<String> getProjectorNames() {
        return Collections.unmodifiableSet(projectorNames);
    }

    public NetworkEdge addProjectorName(String projectorName) {
        this.projectorNames.add(projectorName);
        return this;
    }

    public Set<String> getOrgs() {
        return this.orgs;
    }

    public void addOrg(String org) {
        this.orgs.add(org);
    }
}