Package fr.ens.biologie.genomique.eoulsan

Class AbstractEoulsanRuntime

java.lang.Object
fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Direct Known Subclasses:
HadoopEoulsanRuntime, LocalEoulsanRuntime
public abstract class AbstractEoulsanRuntime extends Object
This class define an abstract EoulsanRuntime.
Since:
1.0
Author:
Laurent Jourdren

  • Method Details

    • getSettings

      public Settings getSettings()
      Get Settings.
      Returns:
      a Settings object

    • getTempDirectory

      public abstract File getTempDirectory()
      Get the temporary directory.
      Returns:
      the temporary directory as a File object

    • getMode

      public abstract AbstractEoulsanRuntime.EoulsanExecMode getMode()
      Get Eoulsan mode.
      Returns:
      the Eoulsan mode

    • getInputStream

      public abstract InputStream getInputStream(String dataSource) throws IOException
      Create an InputStream to load data.
      Parameters:
      dataSource - the source of the data to load
      Returns:
      an InputStream corresponding to the source
      Throws:
      IOException - if an error occurs the InputStream

    • getRawInputStream

      public abstract InputStream getRawInputStream(String dataSource) throws IOException
      Create a raw InputStream (without decompression of input data) to load data.
      Parameters:
      dataSource - the source of the data to load
      Returns:
      an InputStream corresponding to the source
      Throws:
      IOException - if an error occurs the InputStream

    • getOutputStream

      public abstract OutputStream getOutputStream(String dataSource) throws IOException
      Create an OutputStream to load data.
      Parameters:
      dataSource - the source of the data to load
      Returns:
      an OutputStream corresponding to the source
      Throws:
      IOException - if an error occurs the OutputStream

    • createTempDir

      public File createTempDir() throws IOException
      Create a new temporary directory.
      Returns:
      the new directory
      Throws:
      IOException - if there is an error creating the temporary directory

    • createTempDir

      public File createTempDir(String prefix) throws IOException
      Create a new temporary directory.
      Parameters:
      prefix - prefix of the temporary directory
      Returns:
      the new directory
      Throws:
      IOException - if there is an error creating the temporary directory

    • createTempFile

      public File createTempFile(String prefix, String suffix) throws IOException
      Create a new temporary file.
      Parameters:
      prefix - Prefix of the temporary file
      suffix - suffix of the temporary file
      Returns:
      the new temporary file
      Throws:
      IOException - if there is an error creating the temporary directory

    • createFileInTempDir

      public File createFileInTempDir(String filename)
      Create a file in the temporary directory.
      Parameters:
      filename - The filename to create
      Returns:
      The new File