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<?php

namespace DispatchModule\Models;

/**
 * Cppredict2Model cooperates with Cppredict2
 *
 */
class Cppredict2Model extends \BaseModule\Models\BaseModel {

    /**
     * Used as: cp_predict.py -r $cp_root
     * @var string
     */
    protected $cpRoot;

    /**
     * This is where the temporary files for cp_predict2 are created.
     * @var string
     */
    protected $tempDir;

    /**
     * Used as: cp_predict.py -t $templates
     * @var string
     */
    protected $templates;

    /**
     * Used as: cp_predict.py -m $tmap
     * @var string
     */
    protected $tmap;

    /**
     * Passed directly. Will change when further input fields are enabled.
     * @var string
     */
    protected $defaultPredictionSettings;

    /**
     * Used for debugging.
     * @var FileModel
     */
    private $logFile;

    /**
     * Debug mode
     * @var bool
     */
    private $debug;

    /**
     * Log message output for debugging purposes, incl. formatting.
     * @param string $message Log message to be saved
     */
    public function logRecord($message) {
        if ($this->debug) {
            $this->logFile->appendContent(time() . ' : Cppredict2Model : ' . $message . "\n");
        }
    }

    /**
     * Fills in the default values for running cp_predict.py
     *
     * @param bool $debug if set to true, debug mode is on
     */
    public function __construct($debug = -1) {

        if ($debug === -1) { // default => Nette debug value
            $this->debug = \Nette\Diagnostics\Debugger::isEnabled();
        } else {
            $this->debug = $debug;
        }

        $this->cpRoot = CPPREDICT_TOOLDIR . 'cp_root/';
        # If the setup.py installation procedure is found to work, we will
        # not need $this->cpRoot any more.

        $this->tempDir = TEMP_PATH . '/cppredict/';
        $this->templates = 'template-selection.aln';
        $this->tmap = 'tmap.csv';
        $this->defaultPredictionSettings = ' -p -w 10 -g 0.15 --disregard_ends';
        $this->logFile = new \BaseModule\Models\FileModel('files/cppredict/cppredict_tool.log');
        $dummyCommand = $this->buildCommand('someInput');
        $this->logRecord('  Built model with command ' . $dummyCommand);
    }

    /**
     * Builds the shell command to execute. Everything except the input FASTA
     * sequence name is known from inside Cppredict2Model, so the only argument
     * is the input FASTA name.          
     *          
     * @param string $inputSeqFasta The path to the input FASTA file, relative to $cp_root
     * 
     * @return string The command to pass to shell_exec() to run CP-predict2           
     */
    public function buildCommand($inputSeqFasta) {


        $this->logRecord('Constructing command for input: ' . $inputSeqFasta);

        # Testing with the cp_predict2 data included by default in the
        # rPredictorDB Python package.
        # $command = 'cp_predict.py';
        $command = 'cp_predict.py -r ' . $this->cpRoot;
        $command = $command . ' -t ' . $this->templates;
        $command = $command . ' -m ' . $this->tmap;
        $command = $command . $this->defaultPredictionSettings;
        $command = $command . ' --tmp_dir ' . $this->tempDir;
        $command = $command . ' -i ' . $inputSeqFasta;

        if ($this->debug) {
            $command = $command . ' -v 2>>' . $this->logFile->getFile();
        }

        $this->logRecord('Constructed command: ' . $command);

        return $command;
    }

}