ch.unibas.fittingwizard.infrastructure.RealFittabMarkerScript.java Source code

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Here is the source code for ch.unibas.fittingwizard.infrastructure.RealFittabMarkerScript.java

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/*
 * Copyright (c) 2015, Florent Hedin, Markus Meuwly, and the University of Basel
 * All rights reserved.
 *
 * The 3-clause BSD license is applied to this software.
 * see LICENSE.txt
 *
 */
package ch.unibas.fittingwizard.infrastructure;

import ch.unibas.fittingwizard.Settings;
import ch.unibas.fittingwizard.application.scripts.base.ScriptExecutionException;
import ch.unibas.fittingwizard.application.scripts.fittab.FittabScriptInput;
import ch.unibas.fittingwizard.application.scripts.fittab.FittabScriptOutput;
import ch.unibas.fittingwizard.application.scripts.fittab.IFittabScript;
import ch.unibas.fittingwizard.infrastructure.base.PythonScriptRunner;
import java.io.File;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.FilenameUtils;
import org.apache.log4j.Logger;

public class RealFittabMarkerScript implements IFittabScript {

    private final static Logger logger = Logger.getLogger(RealLRAScript.class);

    private static final String FitTabMarkerScriptNameKey = "scripts.prepare_fitting_table";
    private static final String MtpFittabExtension = "_mtpfittab.txt";

    private File moleculesDir;

    private final PythonScriptRunner runner;
    private File fitTabMarkerScriptFile;

    public RealFittabMarkerScript(File moleculesDir, Settings settings) {
        this.moleculesDir = moleculesDir;
        this.fitTabMarkerScriptFile = new File(settings.getScriptsDir(),
                settings.getValue(FitTabMarkerScriptNameKey));
        runner = new PythonScriptRunner();
    }

    @Override
    public FittabScriptOutput execute(FittabScriptInput input) {

        String moleculeName = getMoleculeName(input.getCubeFile());
        File specificMoleculeDir = new File(moleculesDir, moleculeName);

        runner.setWorkingDir(specificMoleculeDir);

        List<String> args = Arrays.asList("-cube", input.getCubeFile().getAbsoluteFile().toString(), "-vdw",
                input.getVdwFile().getAbsoluteFile().toString(), "-pun",
                input.getLpunFile().getAbsoluteFile().toString());

        File mtpFile = new File(specificMoleculeDir,
                FilenameUtils.removeExtension(input.getCubeFile().getName()) + MtpFittabExtension);

        runner.exec(fitTabMarkerScriptFile, args);

        if (!mtpFile.exists()) {
            throw new ScriptExecutionException("FittabMarker script did not create "
                    + FilenameUtils.normalize(mtpFile.getAbsolutePath()) + " output file.");
        }

        return new FittabScriptOutput(mtpFile);
    }

    private String getMoleculeName(File input) {
        return FilenameUtils.removeExtension(input.getName());
    }

}