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<?php

namespace DispatchModule;

/**
 * BaseMatch contains default implementation of some mandatory informations
 * - serves only as a helper (reduces code duplicity)
 */
class BaseMatch {

    /**
     * Human-readable short description (name) of the used alignment tool
     * @var string
     */
    public $label;

    /**
     * Matching subsequence of query
     * @var string
     */
    public $subsequence;

    /**
     * Starting index of matching subsequence in query
     * @var int
     */
    public $queryStartPosition;

    /**
     * Stop index of matching subsequence in query
     * @var int
     */
    public $queryStopPosition;

    /**
     * Starting index of matching subsequence in db
     * @var int
     */
    public $dbStartPosition;

    /**
     * Stop index of matching subsequence in db
     * @var int
     */
    public $dbStopPosition;

    /**
     * List of all scores by the tool in format
     * 'scoreName' => 'value'
     *
     * @var array
     */
    public $scores = array();


    /**
     * Constructor used to save a name of tool
     *
     * @param string $label
     */
    public function __construct($label) {
        $this->label = $label;
        $this->setCoverage(1);
        $this->setIdentity(1);
    }

    /**
     * Sets the coverage of the match i.e. length(match)/length(query)
     * @param float $coverage coverage
     */
    public function setCoverage($coverage) {
        $this->scores["coverage"] = $coverage;
    }

    /**
     * Gets the coverage of the match
     * @return int coverage
     */
    public function getCoverage() {
        return $this->scores["coverage"];
    }

    /**
     * Sets the identity of the match i.e. #hits/length(match)
     * @param float $identity identity
     */
    public function setIdentity($identity) {
        $this->scores["identity"] = $identity;
    }

    /**
     * Gets the identity of the match
     * @return int identity
     */
    public function getIdentity() {
        return $this->scores["identity"];
    }

    /**
     * Gets the bit-score of the match
     * @return int bit-score
     */
    public function getScore() {
        if (is_null($this->scores["identity"]) || empty($this->scores["identity"])) {
            if (is_null($this->scores["coverage"]) || empty($this->scores["coverage"])) {
                return 1;
            } else {
                return $this->scores["coverage"];
            }
        } else if (is_null($this->scores["coverage"]) || empty($this->scores["coverage"])) {
            return $this->scores["identity"];
        } else {
            return $this->scores["coverage"] * $this->scores["identity"];
        }
    }

}