Package fr.ens.biologie.genomique.eoulsan.data

Class DataFile

java.lang.Object
fr.ens.biologie.genomique.eoulsan.data.DataFile
All Implemented Interfaces:
Serializable, Comparable<DataFile>
public class DataFile extends Object implements Comparable<DataFile>, Serializable
This class define a DataFile.
Since:
1.0
Author:
Laurent Jourdren
See Also:

  • Field Details

  • Constructor Details

    • DataFile

      public DataFile(String source)
      Public constructor.
      Parameters:
      source - the source of the DataFile

    • DataFile

      public DataFile(DataFile parentFile, String filename)
      Public constructor.
      Parameters:
      parentFile - the parent file of the DataFile
      filename - the filename of the DataFile

    • DataFile

      public DataFile(File parentFile, String filename)
      Public constructor.
      Parameters:
      parentFile - the parent file of the DataFile
      filename - the filename of the DataFile

    • DataFile

      public DataFile(Path parentPath, String filename)
      Public constructor.
      Parameters:
      parentPath - the parent file of the DataFile
      filename - the filename of the DataFile

    • DataFile

      public DataFile(File file)
      Public constructor.
      Parameters:
      file - the source file of the DataFile

    • DataFile

      public DataFile(Path path)
      Public constructor.
      Parameters:
      path - the source path of the DataFile

    • DataFile

      public DataFile(URI uri)
      Public constructor.
      Parameters:
      uri - the URI of the DataFile

  • Method Details

    • getSource

      public String getSource()
      Get the source of this DataFile.
      Returns:
      a String with the source of this DataFile

    • getName

      public String getName()
      Get the name of this DataFile.
      Returns:
      a String with the name of this DataFile

    • getBasename

      public String getBasename()
      Get the base name of this DataFile without all its extensions. The result is computed with the output of the getName() method.
      Returns:
      a String with the base name of this DataFile

    • getExtension

      public String getExtension()
      Get the extension of this DataFile without compression extension. The result is computed with the output of the getName() method.
      Returns:
      a String with the extension of this DataFile. The result String is empty if there is no extension

    • getFullExtension

      public String getFullExtension()
      Get the base name of this DataFile with all its extensions (include compression extension). The result is computed with the output of the getName() method.
      Returns:
      a String with the base name of this DataFile. The result String is empty if there is no extension

    • getCompressionExtension

      public String getCompressionExtension()
      Get the compression extension of this DataFile. The result is computed with the output of the getName() method.
      Returns:
      a String with the compression extension of this DataFile. The result String is empty if there is no compression extension

    • getCompressionType

      public fr.ens.biologie.genomique.kenetre.io.CompressionType getCompressionType()
      Get the compression Type of this DataFile. The result is computed with the output of the getName() method.
      Returns:
      a CompressionType object

    • getDataFormat

      public DataFormat getDataFormat()
      Get the DataFormat of the DataFile. The result is computed with the output of the getName() method. This is an alias for getDataFormatFromFilename() of the DataFormatRegistry.
      Returns:
      the DataFormat of the DataFile

    • getParent

      public DataFile getParent() throws IOException
      Get the parent of this DataFile.
      Returns:
      the parent DataFile
      Throws:
      IOException - if an error occurs while the parent

    • getProtocol

      public DataProtocol getProtocol() throws IOException
      Get the protocol of this DataFile.
      Returns:
      a DataProtocol
      Throws:
      IOException - if the protocol is unknown

    • getMetaData

      public DataFileMetadata getMetaData() throws IOException
      Get the metadata for this DataFile.
      Returns:
      a DataFileMetadata with all metadata information about this DataFile
      Throws:
      IOException - if the protocol is unknown or if the DataFile does not exists

    • getProtocolPrefixInSource

      public String getProtocolPrefixInSource()
      Get the prefix of the protocol in the source name of the DataFile.
      Returns:
      the prefix of the protocol

    • isLocalFile

      public boolean isLocalFile()
      Test if the DataFile use the defaultProtocol.
      Returns:
      true if the DataFile use the default protocol

    • toFile

      public File toFile()
      Convert the DataFile object to File object if the underlying protocol allow it. Only local protocol can return a value.
      Returns:
      a File object or null if the underlying protocol does not allow it

    • toPath

      public Path toPath()
      Convert the DataFile object to Path object if the underlying protocol allow it.
      Returns:
      a Path object or null if the underlying protocol does not allow it

    • toUri

      public URI toUri()
      Convert the DataFile object to an URI.
      Returns:
      an URI object or null if the DataFile cannot be converted into URI

    • toRealDataFile

      public DataFile toRealDataFile()
      Convert the the DataFile to a DataFile where all the indirection has been solved. This method use the JDK Path.toRealPath() method. This method has only an effect for local DataFiles.
      Returns:
      a DataFile

    • toAbsoluteDataFile

      public DataFile toAbsoluteDataFile()
      Convert the the DataFile to a absolute DataFile. This method use the JDK File.getAbsoluteFile() method. This method has only an effect for local DataFiles.
      Returns:
      a DataFile

    • create

      public OutputStream create() throws IOException
      Create an OutputStream for the DataFile. If the DataFile is declared as compressed by its content type or its extension, the output stream will be automatically compress data.
      Returns:
      an OutputStream object
      Throws:
      IOException - if an error occurs while creating the DataFile

    • rawCreate

      public OutputStream rawCreate() throws IOException
      Create an OutputStream for the DataFile. The output stream will not automatically compress data.
      Returns:
      an OutputStream object
      Throws:
      IOException - if an error occurs while creating the DataFile

    • open

      public InputStream open() throws IOException
      Create an InputStream for the DataFile. If the DataFile is compressed, the input stream will be automatically uncompress.
      Returns:
      an InputStream object
      Throws:
      IOException - if an error occurs while opening the DataFile

    • rawOpen

      public InputStream rawOpen() throws IOException
      Create an InputStream for the DataFile. The input stream will not automatically uncompress data.
      Returns:
      an InputStream object
      Throws:
      IOException - if an error occurs while opening the DataFile

    • copyTo

      public void copyTo(DataFile dest) throws IOException
      Copy this DataFile in a other DataFile.
      Parameters:
      dest - destination DataFile
      Throws:
      IOException - if an error occurs while copying the DataFile

    • exists

      public boolean exists()
      Check if this DataFile exists.
      Returns:
      true if this DataFile exists

    • exists

      public boolean exists(boolean followLink)
      Check if this DataFile exists.
      Parameters:
      followLink - follow the link target if the file is a symbolic link
      Returns:
      true if this DataFile exists

    • mkdir

      public void mkdir() throws IOException
      Create a directory with the path of the DataFile.
      Throws:
      IOException - if an error occurs while creating the directory

    • mkdirs

      public void mkdirs() throws IOException
      Create a directory and its parents if not exists with the path of the DataFile.
      Throws:
      IOException - if an error occurs while creating the directory

    • symlink

      public void symlink(DataFile link) throws IOException
      Create a symbolic link that target is the current file.
      Parameters:
      link - symbolic file
      Throws:
      IOException - if an error occurs while creating the symbolic link

    • symlink

      public void symlink(DataFile link, boolean relativize) throws IOException
      Create a symbolic link that target is the current file.
      Parameters:
      link - symbolic file
      relativize - relativize the link target path
      Throws:
      IOException - if an error occurs while creating the symbolic link

    • delete

      public void delete() throws IOException
      Delete the DataFile.
      Throws:
      IOException - if an error occurs while deleting the DataFile

    • delete

      public void delete(boolean recursive) throws IOException
      Delete the DataFile.
      Parameters:
      recursive - recursive deletion
      Throws:
      IOException - if an error occurs while deleting the DataFile

    • list

      public List<DataFile> list() throws IOException
      List the content of a directory.
      Returns:
      a List with the content of the directory
      Throws:
      IOException - if an error occurs while listing the directory

    • renameTo

      public void renameTo(DataFile dest) throws IOException
      Rename the DataFile.
      Parameters:
      dest - destination DataFile
      Throws:
      IOException - if an error occurs while renaming the DataFile

    • compareTo

      public int compareTo(DataFile o)
      Specified by:
      compareTo in interface Comparable<DataFile>

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object