Package fr.ens.biologie.genomique.eoulsan.core

Class FileNaming

java.lang.Object
fr.ens.biologie.genomique.eoulsan.core.FileNaming
Direct Known Subclasses:
WorkflowFileNaming
public class FileNaming extends Object
This class contains methods to create workflow data file names.
Since:
2.0
Author:
Laurent Jourdren

  • Method Details

    • getStepId

      public String getStepId()
      Get Step Id.
      Returns:
      the step Id

    • getPortName

      public String getPortName()
      Get the port name.
      Returns:
      the port name

    • getDataName

      public String getDataName()
      Get the data name.
      Returns:
      the data name

    • getSampleNumber

      public int getSampleNumber()
      Get the sample number related to the data. This value is only use when generate compatible filenames.
      Returns:
      the number of the sample related to the file or -1 if not known

    • getFormat

      public DataFormat getFormat()
      Get the format.
      Returns:
      the format

    • getFileIndex

      public int getFileIndex()
      Get the file index.
      Returns:
      the file index

    • getPart

      public int getPart()
      Get the file part.
      Returns:
      the file part

    • getCompression

      public fr.ens.biologie.genomique.kenetre.io.CompressionType getCompression()
      Get the compression.
      Returns:
      the compression

    • setStepId

      public void setStepId(String stepId)
      Set the step id.
      Parameters:
      stepId - the step id

    • setPortName

      public void setPortName(String portName)
      Set the port name.
      Parameters:
      portName - the port name

    • setDataName

      public void setDataName(String dataName)
      Set the data name.
      Parameters:
      dataName - the data name

    • setSampleNumber

      public void setSampleNumber(int sampleNumber)
      Set the sample number related to the data. This value is only use when generate compatible filenames.
      Parameters:
      sampleNumber - the number of the sample related to the file or -1 if not known

    • setFormat

      public void setFormat(DataFormat format)
      Set the format.
      Parameters:
      format - the format

    • setFileIndex

      public void setFileIndex(int fileIndex)
      Set the file index.
      Parameters:
      fileIndex - the file index

    • setPart

      public void setPart(int part)
      Set the part number.
      Parameters:
      part - the part number

    • setCompression

      public void setCompression(fr.ens.biologie.genomique.kenetre.io.CompressionType compression)
      Set the compression
      Parameters:
      compression - the compression type

    • filePrefix

      public String filePrefix()
      Return the file prefix.
      Returns:
      a string with the file prefix

    • fileSuffix

      public String fileSuffix()
      Return the file suffix.
      Returns:
      q string with the file suffix

    • fileMiddle

      public String fileMiddle()
      Return the middle string of the filename.
      Returns:
      a string with the middle string of the filename

    • filename

      public String filename()
      Return the filename.
      Returns:
      a string with the filename

    • glob

      public String glob()
      Get a glob for the filename.
      Returns:
      a glob in a string

    • compatibilityFilename

      public String compatibilityFilename()
      Return the filename using Eoulsan 1.x naming.
      Returns:
      a string with the filename using Eoulsan 1.x naming

    • filePrefix

      public static String filePrefix(String stepId, String portName, DataFormat format)
      Create the prefix of a filename.
      Parameters:
      stepId - step id
      portName - port name
      format - format of the file
      Returns:
      a String with the prefix of the file

    • filePrefix

      public static String filePrefix(String stepId, String portName, String formatPrefix)
      Create the prefix of a filename.
      Parameters:
      stepId - step id
      portName - port name
      formatPrefix - format prefix of the file
      Returns:
      a String with the prefix of the file

    • fileMiddle

      public static String fileMiddle(String dataName, int fileIndex, int part)
      Create the middle of a filename.
      Parameters:
      dataName - data name
      fileIndex - file index
      part - file part
      Returns:
      a String with the suffix of a file

    • fileSuffix

      public static String fileSuffix(DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)
      Create the suffix of a file.
      Parameters:
      format - format of the file
      compression - file compression
      Returns:
      a String with the suffix of a file

    • fileSuffix

      public static String fileSuffix(String extension, String compression)
      Create the suffix of a file.
      Parameters:
      extension - file extension
      compression - file compression
      Returns:
      a String with the suffix of a file

    • filename

      public static String filename(String stepId, String portName, DataFormat format, String dataName, int fileIndex, int part, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)
      Create the filename from several parameters.
      Parameters:
      stepId - the step id
      portName - the port name
      format - the format
      dataName - the data name
      fileIndex - the file index
      part - the part
      compression - the compression type
      Returns:
      a string with the filename

    • parse

      public static FileNaming parse(Path file)
      Create a FileNaming object from a File object.
      Parameters:
      file - the file
      Returns:
      a new FileNaming object

    • parse

      public static FileNaming parse(File file)
      Create a FileNaming object from a File object.
      Parameters:
      file - the file
      Returns:
      a new FileNaming object

    • parse

      public static FileNaming parse(DataFile file)
      Create a FileNaming object from a DataFile object.
      Parameters:
      file - the file
      Returns:
      a new FileNaming object

    • parse

      public static FileNaming parse(String filename)
      Create a FileNaming object from a filename.
      Parameters:
      filename - the filename
      Returns:
      a new FileNaming object

    • isStepIdValid

      public static boolean isStepIdValid(String stepId)
      Test if a step id is valid.
      Parameters:
      stepId - the step id to check
      Returns:
      true if the step id is valid

    • isFormatPrefixValid

      public static boolean isFormatPrefixValid(String formatPrefix)
      Test if a format prefix id is valid.
      Parameters:
      formatPrefix - the format prefix to check
      Returns:
      true if the format prefix is valid

    • isPortNameValid

      public static boolean isPortNameValid(String portName)
      Test if a port name is valid.
      Parameters:
      portName - port name to check
      Returns:
      true if the port name is valid

    • isDataNameValid

      public static boolean isDataNameValid(String dataName)
      Test if a data name is valid.
      Parameters:
      dataName - data name to check
      Returns:
      true if the data name is valid

    • isFilenameValid

      public static boolean isFilenameValid(DataFile file)
      Test if a filename is valid.
      Parameters:
      file - the file to test.
      Returns:
      true if the filename is valid

    • isFilenameValid

      public static boolean isFilenameValid(File file)
      Test if a filename is valid.
      Parameters:
      file - the file to test.
      Returns:
      true if the filename is valid

    • isFilenameValid

      public static boolean isFilenameValid(Path file)
      Test if a filename is valid.
      Parameters:
      file - the file to test.
      Returns:
      true if the filename is valid

    • isFilenameValid

      public static boolean isFilenameValid(String filename)
      Test if a filename is valid.
      Parameters:
      filename - the file to test.
      Returns:
      true if the filename is valid

    • dataEquals

      public static boolean dataEquals(Path file1, Path file2)
      Test if two files are related to the same data.
      Parameters:
      file1 - the first file
      file2 - the second file
      Returns:
      true if the two files are related to the same data

    • dataEquals

      public static boolean dataEquals(File file1, File file2)
      Test if two files are related to the same data.
      Parameters:
      file1 - the first file
      file2 - the second file
      Returns:
      true if the two files are related to the same data

    • dataEquals

      public static boolean dataEquals(DataFile file1, DataFile file2)
      Test if two files are related to the same data.
      Parameters:
      file1 - the first file
      file2 - the second file
      Returns:
      true if the two files are related to the same data

    • dataEquals

      public static boolean dataEquals(String filename1, String filename2)
      Test if two filenames are related to the same data.
      Parameters:
      filename1 - the first filename
      filename2 - the second filename
      Returns:
      true if the two files are related to the same data