Package eu.isas.searchgui.cmd

Class FastaCLI

java.lang.Object
eu.isas.searchgui.cmd.FastaCLI
public class FastaCLI extends Object
This class allows the user to work on the database in command line.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    FastaCLI(String[] args)
    Construct a new FastaCLI runnable from a list of arguments.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    call()
    Calling this method will run the configured FastaCLI process.
    File
    generateTargetDecoyDatabase(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Appends decoy sequences to the given target database file.
    String
    getJarFilePath()
    Returns the path to the jar file.
    static String
    getLogFileMessage()
    Returns the "see the log file" message.
    static void
    main(String[] args)
    Starts the launcher by calling the launch method.
    void
    writeDbProperties(com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters)
    Writes the database properties to System.out.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • FastaCLI

      public FastaCLI(String[] args)
      Construct a new FastaCLI runnable from a list of arguments.
      Parameters:
      args - the command line arguments

  • Method Details

    • call

      public void call()
      Calling this method will run the configured FastaCLI process.

    • writeDbProperties

      public void writeDbProperties(com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters)
      Writes the database properties to System.out.
      Parameters:
      fastaSummary - the summary information on the FASTA file
      fastaParameters - the FASTA parsing parameters

    • generateTargetDecoyDatabase

      public File generateTargetDecoyDatabase(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Appends decoy sequences to the given target database file.
      Parameters:
      fastaParameters - the FASTA parsing parameters
      waitingHandler - the waiting handler
      Returns:
      the file created
      Throws:
      IOException - exception thrown whenever an error happened while reading or writing a FASTA file

    • main

      public static void main(String[] args)
      Starts the launcher by calling the launch method. Use this as the main class in the jar file.
      Parameters:
      args - the command line arguments

    • getLogFileMessage

      public static String getLogFileMessage()
      Returns the "see the log file" message. With the path if available.
      Returns:
      the "see the log file" message

    • getJarFilePath

      public String getJarFilePath()
      Returns the path to the jar file.
      Returns:
      the path to the jar file