Package org.pathvisio.libgpml.util

Class FileUtils

java.lang.Object
org.pathvisio.libgpml.util.FileUtils
public class FileUtils
extends java.lang.Object
Collection of static utility methods dealing with files.
Author:
unknown

  • Constructor Summary

    Constructors
    Constructor Description
    FileUtils()  

  • Method Summary

    Modifier and Type Method Description
    static void downloadFile​(java.net.URL url, java.io.File toFile)
    Downloads a remote file given by an URL to the given local file
    static java.lang.String getExtension​(java.lang.String fileName)
    Returns file name extension.
    static java.util.List<java.io.File> getFiles​(java.io.File directory, boolean recursive)
    Returns all files in a directory
    static java.util.List<java.io.File> getFiles​(java.io.File directory, java.lang.String extension, boolean recursive)
    Returns all files in a directory
    static int getNrLines​(java.lang.String fileName)
    Determines the number of lines in the given file.
    static java.io.File mapFileTree​(java.io.File f, java.io.File srcDir, java.io.File destDir)
    Maps a file from one point in the directory tree to another point.
    static java.lang.String removeExtension​(java.lang.String fname)
    Removes the file extension (everything from the last occurence of '.')
    static java.io.File replaceExtension​(java.io.File fname, java.lang.String extension)
    Replaces file extension with something else.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • FileUtils

      public FileUtils()

  • Method Details

    • getFiles

      public static java.util.List<java.io.File> getFiles​(java.io.File directory, boolean recursive)
      Returns all files in a directory
      Parameters:
      directory - The directory to get the files from
      recursive - Whether to include sub directories or not
      Returns:
      A list of files in the given directory

    • getFiles

      public static java.util.List<java.io.File> getFiles​(java.io.File directory, java.lang.String extension, boolean recursive)
      Returns all files in a directory
      Parameters:
      directory - the directory to get the files from
      extension - the extension of the files to get, without the dot so e.g. "gpml"
      recursive - whether to include subdirectories or not
      Returns:
      A list of files with given extension present in the given directory

    • getNrLines

      public static int getNrLines​(java.lang.String fileName)
      Determines the number of lines in the given file.
      Parameters:
      fileName - the file to get the number of lines from
      Returns:
      the number of lines, or -1 if unable to determine the number of lines

    • getExtension

      public static java.lang.String getExtension​(java.lang.String fileName)
      Returns file name extension.
      Parameters:
      fileName - file as a String
      Returns:
      fragment of the filename after the '.'. Returns null if there was no '.'.

    • removeExtension

      public static java.lang.String removeExtension​(java.lang.String fname)
      Removes the file extension (everything from the last occurence of '.')

    • replaceExtension

      public static java.io.File replaceExtension​(java.io.File fname, java.lang.String extension)
      Replaces file extension with something else. If there was no extension previously, the new one will simply be added.
      Parameters:
      fname - the file name to use.
      extension - the new extension to use. Should not include dot.

    • downloadFile

      public static void downloadFile​(java.net.URL url, java.io.File toFile) throws java.io.IOException
      Downloads a remote file given by an URL to the given local file
      Parameters:
      url - the URL that specifies the location of the file to download
      toFile - the local file to which the remote file will be downloaded
      Throws:
      java.io.IOException

    • mapFileTree

      public static java.io.File mapFileTree​(java.io.File f, java.io.File srcDir, java.io.File destDir)
      Maps a file from one point in the directory tree to another point. For example, with this function you can map from /home/username/input/pathways/human/metabolomic/pathway.gpml to /tmp/output/pathways/human/metabolomic/pathway.gpml
      Parameters:
      f - the file.
      srcDir - the source directory.
      destDir - the destination directory.
      Returns:
      the file.