createconversioncdsfile.ParseCLI.java Source code

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Here is the source code for createconversioncdsfile.ParseCLI.java

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package createconversioncdsfile;

import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.cli.BasicParser;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;

/**
 *
 * @author rutgero
 */
public final class ParseCLI {

    /**
     * stores the path to a protein file.
     */
    private Path protPath;
    /**
     * stores the path to a cds file.
     */
    private Path cdsPath;
    /**
     * stores the path to a transcript file.
     */
    private Path transPath;
    /**
     * stores the path to the new file.
     */
    private String newFilePath;
    /**
     * stores the path to the conversion file.
     */
    private Path conversionFilePath;

    private Pattern re = Pattern.compile("(?<=\\\\|/)\\w+\\.txt");

    /**
     * Rutger Ozinga. ParseCLI Parses the commandline input and is able to
     * return the wanted option and value.
     *
     * @param args are commandline arguments.
     * @throws org.apache.commons.cli.ParseException an exception
     */
    public ParseCLI(final String[] args) throws org.apache.commons.cli.ParseException {
        HelpFormatter helpForm = new HelpFormatter();
        Options cliOpt = new Options();
        cliOpt.addOption("h", "help", false, "Displays help");
        cliOpt.addOption("p", true, "Expects a path to a protein fasta file.");
        cliOpt.addOption("t", true, "Expects a path to a transcript fasta file.");
        cliOpt.addOption("c", true, "Expects a path to a conversion file at.");
        cliOpt.addOption("cds", true, "Expects a path to a cds file at.");
        cliOpt.addOption("o", true, "Expects a path to place the new tab separated protein file at");
        if (args.length == 0) {
            helpForm.printHelp("Please enter all the " + "options below. ", cliOpt);
            System.exit(0);
        } else {
            BasicParser parser = new BasicParser();
            CommandLine cliParser = parser.parse(cliOpt, args);
            if (cliParser.getOptions().length < 4) {
                System.out.println(
                        "Error : " + "Please enter all options in" + " order for this program to work" + "!\n");
                helpForm.printHelp("Please enter all of the  " + "option ", cliOpt);
                System.exit(0);
            } else {
                if (cliParser.hasOption("h") && cliParser.hasOption("help")) {
                    helpForm.printHelp("Command Line Help:\n", cliOpt);
                    System.exit(0);
                } else {
                    String snpFileString = cliParser.getOptionValue("p");
                    Path snpPath = Paths.get(snpFileString);
                    if (Files.exists(snpPath)) {
                        setProtPath(snpPath);
                    } else {
                        System.out.println("The entered Path does" + " not exits");
                        helpForm.printHelp("Please enter -p followed by a valid" + " path ", cliOpt);
                        System.exit(0);
                    }
                    String conversionFileString = cliParser.getOptionValue("c");
                    Path conversionPath = Paths.get(conversionFileString);
                    if (Files.exists(conversionPath)) {
                        setConversionFilePath(conversionPath);
                    } else {
                        System.out.println("The entered Path does" + " not exits");
                        helpForm.printHelp("Please enter -c followed by a valid" + " path ", cliOpt);
                        System.exit(0);
                    }
                    String cdsFileString = cliParser.getOptionValue("cds");
                    Path cdsPath = Paths.get(cdsFileString);
                    if (Files.exists(cdsPath)) {
                        setCdsPath(cdsPath);
                    } else {
                        System.out.println("The entered Path does" + " not exits");
                        helpForm.printHelp("Please enter -cds followed by a valid" + " path ", cliOpt);
                        System.exit(0);
                    }
                    String transcriptFileString = cliParser.getOptionValue("t");
                    Path transcriptPath = Paths.get(transcriptFileString);
                    if (Files.exists(transcriptPath)) {
                        setTransPath(transcriptPath);
                    } else {
                        System.out.println("The entered Path does" + " not exits");
                        helpForm.printHelp("Please enter -t followed by a valid" + " path ", cliOpt);
                        System.exit(0);
                    }
                    String newFileString = cliParser.getOptionValue("o");
                    Matcher match = re.matcher(newFileString);
                    String editedFileString = match.replaceAll("");
                    Path newPath = Paths.get(editedFileString);
                    if (Files.exists(newPath)) {
                        setNewFilePath(newFileString);
                    } else {
                        System.out.println("The entered Path does" + " not exits");
                        helpForm.printHelp("Please enter -o followed by a valid" + " path ", cliOpt);
                        System.exit(0);
                    }
                }
            }
        }
    }

    /**
     * gets the protein file path.
     *
     * @return the protein file path
     */
    public Path getProtPath() {
        return protPath;
    }

    /**
     * sets the protein file path.
     *
     * @param newProtPath the file path
     */
    public void setProtPath(final Path newProtPath) {
        this.protPath = newProtPath;
    }

    /**
     * gets the transcriptfile path.
     *
     * @return the transcript file path
     */
    public Path getTransPath() {
        return transPath;
    }

    /**
     * sets the transcript file path.
     *
     * @param newTransPath the file path
     */
    public void setTransPath(final Path newTransPath) {
        this.transPath = newTransPath;
    }

    /**
     * gets the path to the new file.
     *
     * @return newFilePath
     */
    public String getNewFilePath() {
        return newFilePath;
    }

    /**
     * sets the path to the new file.
     *
     * @param fileTranscriptPath the path to the new file.
     */
    public void setConversionFilePath(final Path fileTranscriptPath) {
        this.conversionFilePath = fileTranscriptPath;
    }

    /**
     * gets the path to the new file.
     *
     * @return newTranscriptFilePath
     */
    public Path getConversionFilePath() {
        return conversionFilePath;
    }

    /**
     * sets the path to the new file.
     *
     * @param filePath the path to the new file.
     */
    public void setNewFilePath(final String filePath) {
        this.newFilePath = filePath;
    }

    /**
     * gets the path to the cds file.
     *
     * @return cdsPath
     */
    public Path getCdsPath() {
        return cdsPath;
    }

    /**
     * sets the path to the cds file.
     *
     * @param newCdsPath the path to the cds file.
     */
    public void setCdsPath(final Path newCdsPath) {
        this.cdsPath = newCdsPath;
    }
}