umcg.genetica.io.Gpio Maven / Gradle / Ivy

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/*
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package umcg.genetica.io;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.channels.FileChannel;
import java.text.DecimalFormat;
import java.util.ArrayList;

/**
 *
 * @author harmjan
 */
public class Gpio {

    public static String[] getListOfFiles(String dir, String extension, String containsThis, String doesntContainThis) {

        File loc = new File(dir);
        String[] fileList = loc.list();

        ArrayList al = new ArrayList();

        for (String fileloc : fileList) {
            File file = new File(fileloc);
            if (!file.isDirectory()) {
                String fileName = file.getName();
                int mid = fileName.lastIndexOf(".");

                if (mid >= 0) {
                    String fname = fileName.substring(0, mid);
                    if (fname.contains(containsThis)) {
                        if (doesntContainThis.isEmpty() || !fname.contains(doesntContainThis)) {
                            String ext = fileName.substring(mid + 1, fileName.length());
                            if (ext.toLowerCase().equals(extension)) {
                                al.add(loc.getAbsolutePath() + Gpio.getFileSeparator() + fileName);
                            }
                        }
                    }
                }
            }
        }

        String[] output = al.toArray(new String[0]);
        return output;
    }

    public static String[] getListOfFiles(String dir, String extension, String containsThis) {
        return getListOfFiles(dir, extension, containsThis, "");
    }

    public static String[] getListOfFiles(String dir, String extension) {
        return getListOfFiles(dir, extension, "", "");
    }

    public static void createDir(String dirName) throws IOException {
        if (!dirName.endsWith(Gpio.getFileSeparator())) {
            dirName += Gpio.getFileSeparator();
        }
        if (!exists(dirName)) {

            // Create one directory
            boolean success = (new File(dirName)).mkdirs();
            if (success) {
                System.out.println("Directory: " + dirName + " created");
            }

        }
    }

    public static boolean isDir(String dir) {
        File loc = new File(dir);
        if (loc.isDirectory()) {
            return true;
        } else {
            return false;
        }
    }

    public static boolean exists(String dir) {
		return existsAndReadable(new File(dir));
    }
	
	public static boolean existsAndReadable(File file){
		return file.exists() && file.canRead();
	}
	
	public static boolean createOuputDir(File dir) throws IOException {
		
		if(!dir.exists()){
			if(!dir.mkdirs()){
				throw new IOException("Failed to create output dir at: " + dir.getAbsolutePath());
			}
		}
		return dir.canRead() && dir.canWrite();
		
	}

    public static void copyFile(File sourceFile, File destFile) throws IOException {
        if (!destFile.exists()) {
            destFile.createNewFile();
        }

        FileChannel source = null;
        FileChannel destination = null;
        try {
            source = new FileInputStream(sourceFile).getChannel();
            destination = new FileOutputStream(destFile).getChannel();
            destination.transferFrom(source, 0, source.size());
        } finally {
            if (source != null) {
                source.close();
            }
            if (destination != null) {
                destination.close();
            }
        }
    }

    public static String[] getListOfFiles(String dir) {
        File loc = new File(dir);
        String[] fileList = loc.list();
        return fileList;
    }

    public static long getFileSize(String fileName) {
        File f = new File(fileName);
        long size = f.length();
        return size;
    }

    public static String humanizeFileSize(long s) {
        String output = "";
        DecimalFormat df = new DecimalFormat("##.##");
        if (s == 0) {
            output = "0b";
        } else if (s > 1099511627776l) {
            double nrtb = (double) s / 1099511627776l;
            output = df.format(nrtb) + " TB";
        } else if (s > 1073741824) {
            double nrtb = (double) s / 1073741824;
            output = df.format(nrtb) + " GB";
        } else if (s > 1048576) {
            double nrtb = (double) s / 1048576;
            output = df.format(nrtb) + " MB";
        } else if (s > 1024) {
            double nrtb = (double) s / 1024;
            output = df.format(nrtb) + " KB";
        }
        return output;
    }

    public static void moveFile(String fileIn, String fileOut) throws IOException {
        // File (or directory) to be moved
        File f1 = new File(fileIn);
        File f2 = new File(fileOut);
        Gpio.copyFile(f1, f2);
        f1.delete();
    }

    public static boolean canRead(String fileName) {
        File f = new File(fileName);
        return f.canRead();
    }

    public static boolean canWrite(String fileName) {
        File f = new File(fileName);
        return f.canWrite();
    }

    public static boolean canExecute(String fileName) {
        File f = new File(fileName);
        return f.canExecute();
    }

    public static String getParentDir(String file) {
        File f = new File(file);
        
        return (f.getParent());
    }
    
    public static String getFileName(String file) {
        File f = new File(file);
        return (f.getName());
    }

    public static String getFileSeparator() {
        return System.getProperty("file.separator");
    }

    public static String formatAsDirectory(String loc) {
        if (!loc.endsWith(getFileSeparator())) {
            loc += getFileSeparator();
        }
        return loc;
    }

    public static void copyFile(String filein, String fileout) throws IOException {
        copyFile(new File(filein), new File(fileout));
    }
}