Package com.compomics.util.experiment.io.biology.protein

Class FastaParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.io.biology.protein.FastaParameters
All Implemented Interfaces:
Serializable
public class FastaParameters extends ExperimentObject
The parameters used to parse a FASTA file.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Field Details

    • DECOY_FLAGS

      public static final String[] DECOY_FLAGS
      The decoy flags used to infer the FASTA parameters.

    • DECOY_SEPARATORS

      public static final char[] DECOY_SEPARATORS
      The decoy separators used to infer the FASTA parameters.

  • Constructor Details

    • FastaParameters

      public FastaParameters()
      Empty default constructor.

  • Method Details

    • isTargetDecoy

      public boolean isTargetDecoy()
      Returns a boolean indicating whether the FASTA file should be processed as target-decoy or only target.
      Returns:
      a boolean indicating whether the FASTA file should be processed as target-decoy or only target

    • setTargetDecoy

      public void setTargetDecoy(boolean targetDecoy)
      Sets whether the FASTA file should be processed as target-decoy or only target.
      Parameters:
      targetDecoy - whether the FASTA file should be processed as target-decoy or only target

    • getDecoyFlag

      public String getDecoyFlag()
      Returns the decoy flag.
      Returns:
      the decoy flag

    • setDecoyFlag

      public void setDecoyFlag(String decoyFlag)
      Sets the decoy flag.
      Parameters:
      decoyFlag - the decoy flag

    • isDecoySuffix

      public boolean isDecoySuffix()
      Returns a boolean indicating whether the decoy flag is a suffix or a prefix.
      Returns:
      a boolean indicating whether the decoy flag is a suffix or a prefix

    • setDecoySuffix

      public void setDecoySuffix(boolean decoySuffix)
      Sets whether the decoy flag is a suffix or a prefix.
      Parameters:
      decoySuffix - whether the decoy flag is a suffix or a prefix

    • getTargetDecoyFileNameSuffix

      public String getTargetDecoyFileNameSuffix()
      Returns the target-decoy file name suffix.
      Returns:
      the targetDecoyFileNameSuffix

    • setTargetDecoyFileNameSuffix

      public void setTargetDecoyFileNameSuffix(String targetDecoyFileNameSuffix)
      Set the target-decoy file name suffix.
      Parameters:
      targetDecoyFileNameSuffix - the targetDecoyFileNameSuffix to set

    • isSameAs

      public boolean isSameAs(FastaParameters fastaParameters)
      Returns a boolean indicating whether the parsing parameters are the same as the given parameters.
      Parameters:
      fastaParameters - the other parameters
      Returns:
      a boolean indicating whether the parsing parameters are the same as the given parameters

    • inferParameters

      public static FastaParameters inferParameters(String fastaFilePath, WaitingHandler waitingHandler) throws IOException
      Infers the parameters used to parse the file.
      Parameters:
      fastaFilePath - path to a FASTA file
      waitingHandler - a handler to allow canceling the import
      Returns:
      returns FASTA parameters inferred from the file
      Throws:
      IOException - exception thrown if an error occurred while iterating the file

    • equals

      public boolean equals(FastaParameters fastaParameters)

    • getShortDescription

      public String getShortDescription()
      Returns a short description of the parameters.
      Returns:
      a short description of the parameters