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

Class AnnotationDataProtocol

java.lang.Object
fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
All Implemented Interfaces:
DataProtocol
public class AnnotationDataProtocol extends DeprecatedDataProtocol
This class define a annotation protocol.
Since:
1.1
Author:
Laurent Jourdren

  • Field Details

  • Constructor Details

    • AnnotationDataProtocol

      public AnnotationDataProtocol()
      Public constructor.

  • Method Details

    • getName

      public String getName()
      Description copied from interface: DataProtocol
      Get Protocol name.
      Returns:
      the name of the protocol

    • getSourceFilename

      public String getSourceFilename(String source)
      Description copied from interface: DataProtocol
      Get the name of the filename that correspond to the source.
      Specified by:
      getSourceFilename in interface DataProtocol
      Parameters:
      source - the source
      Returns:
      a String with the filename

    • getDataFileParent

      public DataFile getDataFileParent(DataFile src)
      Description copied from interface: DataProtocol
      Get the parent source of the source.
      Specified by:
      getDataFileParent in interface DataProtocol
      Parameters:
      src - source to use
      Returns:
      a String with the source of the parent or null if there is parent

    • putData

      public OutputStream putData(DataFile src, DataFileMetadata md) throws IOException
      Description copied from interface: DataProtocol
      Create an OutputStream from the source.
      Specified by:
      putData in interface DataProtocol
      Parameters:
      src - source to use
      md - metadata for the stream to write
      Returns:
      an OutputStream
      Throws:
      IOException - if an error occurs while creating the OutputStream

    • putData

      public void putData(DataFile src, DataFile dest) throws IOException
      Description copied from interface: DataProtocol
      Copy data from a source to a destination source
      Specified by:
      putData in interface DataProtocol
      Parameters:
      src - source source
      dest - destination source
      Throws:
      IOException - if an error occurs while copying data

    • getSourceAsFile

      public File getSourceAsFile(DataFile src)
      Description copied from interface: DataProtocol
      Get the underlying File object for the DataFile if the protocol allow it.
      Specified by:
      getSourceAsFile in interface DataProtocol
      Parameters:
      src - source DataFile
      Returns:
      a File object or null if the protocol does not allow it

    • getSourceAsPath

      public Path getSourceAsPath(DataFile src)
      Description copied from interface: DataProtocol
      Get the underlying File object for the DataFile if the protocol allow it.
      Specified by:
      getSourceAsPath in interface DataProtocol
      Parameters:
      src - source DataFile
      Returns:
      a File object or null if the protocol does not allow it

    • mkdir

      public void mkdir(DataFile dir) throws IOException
      Description copied from interface: DataProtocol
      Create a directory.
      Specified by:
      mkdir in interface DataProtocol
      Parameters:
      dir - directory to create
      Throws:
      IOException - if an error occurs while creating the directory

    • mkdirs

      public void mkdirs(DataFile dir) throws IOException
      Description copied from interface: DataProtocol
      Create a directory and its parents if not exists.
      Specified by:
      mkdirs in interface DataProtocol
      Parameters:
      dir - directory to create
      Throws:
      IOException - if an error occurs while creating the directory

    • canMkdir

      public boolean canMkdir()
      Description copied from interface: DataProtocol
      Test if the mkdir() and mkdirs() methods are available with this protocol.
      Specified by:
      canMkdir in interface DataProtocol
      Returns:
      true if mkdir() and mkdirs() are available

    • symlink

      public void symlink(DataFile target, DataFile link) throws IOException
      Description copied from interface: DataProtocol
      Create a symbolic link.
      Specified by:
      symlink in interface DataProtocol
      Parameters:
      target - target file
      link - symbolic link file
      Throws:
      IOException - if an error occurs while creating the symbolic link

    • canSymlink

      public boolean canSymlink()
      Description copied from interface: DataProtocol
      Test if the symlink() method is available with this protocol.
      Specified by:
      canSymlink in interface DataProtocol
      Returns:
      true if symlink() is available

    • delete

      public void delete(DataFile file, boolean recursive) throws IOException
      Description copied from interface: DataProtocol
      Delete a file.
      Specified by:
      delete in interface DataProtocol
      Parameters:
      file - file to delete
      recursive - recursive deletion
      Throws:
      IOException - if an error occurs while deleting the file

    • canDelete

      public boolean canDelete()
      Description copied from interface: DataProtocol
      Test if the delete() method is available with this protocol.
      Specified by:
      canDelete in interface DataProtocol
      Returns:
      true if delete() is available

    • list

      public List<DataFile> list(DataFile file) throws IOException
      Description copied from interface: DataProtocol
      List a directory.
      Specified by:
      list in interface DataProtocol
      Parameters:
      file - directory to list
      Returns:
      a list of DataFile objects
      Throws:
      IOException - if an error occurs while listing the directory

    • canList

      public boolean canList()
      Description copied from interface: DataProtocol
      Test if the list() method is available with this protocol.
      Specified by:
      canList in interface DataProtocol
      Returns:
      true if list() is available

    • canRename

      public boolean canRename()
      Description copied from interface: DataProtocol
      Test if the renameTo() method is available with this protocol.
      Specified by:
      canRename in interface DataProtocol
      Returns:
      true if renameTo() is available

    • rename

      public void rename(DataFile oldName, DataFile newName) throws IOException
      Description copied from interface: DataProtocol
      Rename a file.
      Specified by:
      rename in interface DataProtocol
      Parameters:
      oldName - the file to rename
      newName - the destination file
      Throws:
      IOException - if an error occurs while renaming the directory