Source of file PrecursorIon.php

Size: 4,068 Bytes - Last Modified: 2019-05-10T12:24:09+01:00

src/Core/Spectra/PrecursorIon.php

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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetIdentifier
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetIdentifier
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetIdentifier
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetTitle
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetTitle
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetTitle
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Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansValid
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansInvalid
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansInvalid
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansInvalid
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansValid
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansValid
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanSetScansValid
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Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanGetSetFragmentIons
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearFragmentIons
141
Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanGetSetFragmentIons
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearFragmentIons
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Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanGetSetFragmentIons
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearFragmentIons
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearFragmentIons
159
Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearFragmentIons
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Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanGetSetIdentifications
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearIdentifications
170
Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanGetSetIdentifications
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearIdentifications
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Covered by 2 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanGetSetIdentifications
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearIdentifications
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Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearIdentifications
188
Covered by 1 test(s):
  • pgb_liv\php_ms\Test\Unit\PrecursorIonTest::testCanClearIdentifications
189190
<?php
/**
 * Copyright 2016 University of Liverpool
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
namespace pgb_liv\php_ms\Core\Spectra;

use pgb_liv\php_ms\Core\Identification;

/**
 * Precursor Ion class.
 *
 * @author Andrew Collins
 */
class PrecursorIon implements IonInterface
{
    use IonTrait;

    /**
     * The unique identifier for this object
     *
     * @var string
     */
    private $identifier;

    /**
     * The title for this object
     *
     * @var string
     */
    private $title;

    /**
     * The scan number for this precursor
     *
     * @var int
     */
    private $scan;

    /**
     * A list of fragment ions associated with this precursor ion
     *
     * @var FragmentIon[]
     */
    private $fragmentIons = array();

    /**
     * A list of identifications associated with precursor ion
     *
     * @var Identification[]
     */
    private $identifications;

    /**
     * Sets the unique identifier for this object
     *
     * @param string $identifier
     */
    public function setIdentifier($identifier)
    {
        $this->identifier = $identifier;
    }

    /**
     * Gets the unique identifier for this object
     *
     * @return string
     */
    public function getIdentifier()
    {
        return $this->identifier;
    }

    /**
     * Sets the title name for this precursor
     *
     * @param string $title
     */
    public function setTitle($title)
    {
        $this->title = $title;
    }

    /**
     * Gets the title name for this precursor
     *
     * @return string
     */
    public function getTitle()
    {
        return $this->title;
    }

    /**
     * Sets the scan number for this precursor
     *
     * @param int|float $scan
     *            Scan number to set
     * @throws \InvalidArgumentException
     */
    public function setScan($scan)
    {
        if (! (is_int($scan) || is_float($scan))) {
            throw new \InvalidArgumentException(
                'Argument 1 must be of type int or float. Value is of type ' . gettype($scan));
        }

        $this->scan = $scan;
    }

    /**
     * Gets the scan number for this precursor
     *
     * @return int
     */
    public function getScan()
    {
        return $this->scan;
    }

    /**
     * Adds a fragment ion to this precursor
     *
     * @param FragmentIon $ion
     *            Fragment ion object to add
     */
    public function addFragmentIon(FragmentIon $ion)
    {
        $this->fragmentIons[] = $ion;
    }

    /**
     * Gets the fragment ions for this precursor
     *
     * @return FragmentIon[]
     */
    public function getFragmentIons()
    {
        return $this->fragmentIons;
    }

    /**
     * Clears the fragment ion list stored by this instance.
     */
    public function clearFragmentIons()
    {
        $this->fragmentIons = array();
    }

    /**
     * Adds an identification to this precursor
     *
     * @param Identification $identification
     *            Identification object to add
     */
    public function addIdentification(Identification $identification)
    {
        $this->identifications[] = $identification;
    }

    /**
     * Gets the list of identifications for this spectra object
     *
     * @return Identification[]
     */
    public function getIdentifications()
    {
        return $this->identifications;
    }

    /**
     * Clears the identification list stored by this instance.
     */
    public function clearIdentifications()
    {
        $this->identifications = array();
    }
}