Source of file MzMlMerge.php

<?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\Utility\Misc;

/**

 * Performs the merging of two or more MzML files into a single MzML file.

 * Note this class is built for speed and does not correctly validate all fields.

 *

 * @author Andrew Collins

 */

class MzMlMerge

{

    private $timeOffset;

    private $indexOffset;

    private $idOffset;

    private $spectrumIdRef = array();

    private $dataFiles = array();

    private $outputFiles = array();

    private $fractionOffsets = array();

    private $spectrumCount = array();

    /**

     * The number of seconds that should be used as padding between scans.

     * This should be high enough that image recognition alignment tools can identify a distinct boundary

     * 

     * @var integer

     */

    private $paddingBetweenScans = 600;

    /**

     * Sets the output path for a specified replicate

     *

     * @param int $replicate

     *            The replicate ID

     * @param string $path

     *            The path to write to

     */

    public function setOutputPath($replicate, $path)

    {

        $this->outputFiles[$replicate] = $path;

    }

    /**

     * Adds a data file for processing.

     * The index is the fraction order which should be consistent across replicates

     *

     * @param int $replicate            

     * @param string $file            

     * @param int $index            

     */

    public function addDataFile($replicate, $index, $file)

    {

        $this->dataFiles[$replicate][$index] = array(

            'path' => $file,

            'endTime' => - 1,

            'endIndex' => - 1,

            'endScans' => - 1,

            'spectra' => 0

        );

    }

    public function analyseData()

    {

        // TODO: Validate input and output

        // Perform first pass on each data file to identify start, stop RT

        foreach ($this->dataFiles as $replicate => $fractions) {

            foreach ($fractions as $index => $file) {

                $this->dataFiles[$replicate][$index] = $this->analyseFile($file);

            }

        }

        // Set replicate start time

        foreach ($this->dataFiles as $replicate => $fractions) {

            foreach ($fractions as $index => $file) {

                if (! isset($this->fractionOffsets[$index]) || $file['endTime'] > $this->fractionOffsets[$index]) {

                    $this->fractionOffsets[$index] = $file['endTime'];

                }

                if (! isset($this->spectrumCount[$replicate])) {

                    $this->spectrumCount[$replicate] = 0;

                }

                $this->spectrumCount[$replicate] += $file['spectra'];

            }

        }

        // Push forward

        $sum = 0;

        foreach ($this->fractionOffsets as $index => $time) {

            // Add time to force seperation in alignment tools

            $this->fractionOffsets[$index] = $sum;

            $sum += $time + $this->paddingBetweenScans;

        }

        return $this->dataFiles;

    }

    public function getFractionOffsets()

    {

        return $this->fractionOffsets;

    }

    private function analyseFile($file)

    {

        $reader = fopen($file['path'], 'r');

        $isSpectrumList = false;

        while (! feof($reader)) {

            $line = fgets($reader);

            if (stripos($line, '<spectrumList') !== false) {

                $isSpectrumList = true;

                if (preg_match('/<spectrumList(?=.*count="([0-9.]+)")/', $line, $matches)) {

                    $file['spectra'] = $matches[1];

                }

                continue;

            }

            if (! $isSpectrumList) {

                continue;

            }

            if (stripos($line, '</spectrumList') !== false) {

                break;

            }

            if (preg_match('/<spectrum(?=.*(index="([0-9.]+)"))(?=.*(id=".*(scan=([0-9]+)).*?"))/', $line, $matches)) {

                $index = $matches[2];

                if ($index > $file['endIndex']) {

                    $file['endIndex'] = $index;

                }

                $scan = $matches[5];

                if ($scan > $file['endScans']) {

                    $file['endScans'] = $scan;

                }

            }

            if (preg_match('/accession="MS:1000016"(?=.*(value="([0-9.]+))")(?=.*unitAccession="([A-Z0-9:]+)")/', $line, 

                $matches)) {

                $scanTime = $matches[2];

                if ($matches[3] == 'UO:0000031') {

                    $scanTime *= 60;

                }

                if ($scanTime > $file['endTime']) {

                    $file['endTime'] = $scanTime;

                }

                if ($matches[3] == 'UO:0000031') {

                    $scanTime /= 60;

                }

            }

        }

        return $file;

    }

    /**

     * Merges the MzML files specified in the constructor into a single MzML file and writes the data to the output file specified in the constructor

     */

    public function merge()

    {

        // TODO: verify analysis phase run

        foreach ($this->dataFiles as $replicate => $fractions) {

            $firstFile = current($fractions);

            // Write header

            $this->writeHeader($firstFile['path'], $this->spectrumCount[$replicate], $this->outputFiles[$replicate]);

            // Resets vars

            $this->spectrumIdRef = array();

            $this->timeOffset = 0;

            $this->indexOffset = 0;

            $this->idOffset = 0;

            foreach ($fractions as $fractionIndex => $file) {

                $this->writeSpectrum($file['path'], $this->outputFiles[$replicate], 

                    $this->fractionOffsets[$fractionIndex]);

            }

            $this->writeFooter($firstFile['path'], $this->outputFiles[$replicate]);

        }

    }

    private function writeHeader($file, $spectrumCount, $outputFile)

    {

        $reader = fopen($file, 'r');

        $writer = fopen($outputFile, 'w');

        while (! feof($reader)) {

            $line = fgets($reader);

            if (preg_match('/<spectrumList(?=.*count="([0-9.]+)")/', $line, $matches)) {

                $line = str_replace($matches[1], $spectrumCount, $line);

            }

            fwrite($writer, $line);

            if (stripos($line, '<spectrumList') !== false) {

                break;

            }

        }

        fclose($reader);

        fclose($writer);

    }

    private function writeFooter($file, $outputFile)

    {

        $reader = fopen($file, 'r');

        $writer = fopen($outputFile, 'a');

        $isPastSpectrumList = false;

        while (! feof($reader)) {

            $line = fgets($reader);

            if (stripos($line, '</spectrumList') !== false) {

                $isPastSpectrumList = true;

            }

            if ($isPastSpectrumList) {

                fwrite($writer, $line);

            }

        }

        fclose($reader);

        fclose($writer);

    }

    private function writeSpectrum($file, $outputFile, $timeOffset)

    {

        $reader = fopen($file, 'r');

        $writer = fopen($outputFile, 'a');

        $isSpectrumList = false;

        // Local offsets

        $localIndexOffset = $this->indexOffset;

        $localIdOffset = $this->idOffset;

        while (! feof($reader)) {

            $line = fgets($reader);

            if (stripos($line, '<spectrumList') !== false) {

                $isSpectrumList = true;

                continue;

            }

            if (! $isSpectrumList) {

                continue;

            }

            if (stripos($line, '</spectrumList') !== false) {

                break;

            }

            if (preg_match('/<spectrum(?=.*(index="([0-9.]+)"))(?=.*(id=".*(scan=([0-9]+)).*?"))/', $line, $matches)) {

                $index = $matches[2];

                $index += $localIndexOffset;

                if ($index > $this->indexOffset) {

                    $this->indexOffset = $index;

                }

                $scan = $matches[5];

                $scan += $localIdOffset;

                if ($scan > $this->idOffset) {

                    $this->idOffset = $scan;

                }

                $line = str_replace($matches[1], 'index="' . $index . '"', $line);

                $idChunk = str_replace($matches[4], 'scan=' . $scan, $matches[3]);

                $this->spectrumIdRef[substr($matches[3], 4, - 1)] = substr($idChunk, 4, - 1);

                $line = str_replace($matches[3], $idChunk, $line);

            }

            if (preg_match('/<precursor(?=.*(spectrumRef="(.*?)"))/', $line, $matches)) {

                $line = str_replace($matches[2], $this->spectrumIdRef[$matches[2]], $line);

            }

            if (preg_match('/accession="MS:1000016"(?=.*(value="([0-9.]+))")(?=.*unitAccession="([A-Z0-9:]+)")/', $line, 

                $matches)) {

                $scanTime = $matches[2];

                if ($matches[3] == 'UO:0000031') {

                    $scanTime *= 60;

                }

                $scanTime += $timeOffset;

                if ($matches[3] == 'UO:0000031') {

                    $scanTime /= 60;

                }

                $line = str_replace($matches[2], $scanTime, $line);

            }

            fwrite($writer, $line);

        }

        fclose($reader);

        fclose($writer);

    }

}