java.lang.Object
com.compomics.util.experiment.io.biology.protein.FastaSummary

public class FastaSummary
extends Object
This class parses a FASTA file and gathers summary statistics.
Author:
Marc Vaudel, Harald Barsnes
  • Field Details

  • Constructor Details

    • FastaSummary

      public FastaSummary()
      Empty default constructor.
    • FastaSummary

      public FastaSummary​(String name, String description, String version, File fastaFile, TreeMap<String,​Integer> speciesOccurrence, HashMap<ProteinDatabase,​Integer> databaseType, int nSequences, int nTarget, long lastModified)
      Constructor.
      Parameters:
      name - the database name
      description - the database description
      version - the database version
      fastaFile - the FASTA file
      speciesOccurrence - the occurrence of every species
      databaseType - the occurrence of every database type
      nSequences - the number of sequences
      nTarget - the number of target sequences
      lastModified - the last time the file was modified
  • Method Details

    • getSummary

      public static FastaSummary getSummary​(String fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler) throws IOException
      Gathers summary data on the FASTA file content.
      Parameters:
      fastaFile - path to a FASTA file
      fastaParameters - the parameters to use to parse the file
      waitingHandler - a handler to allow canceling the import and displaying progress
      Returns:
      returns FASTA parameters inferred from the file
      Throws:
      IOException - exception thrown if an error occurred while iterating the file
    • getSummary

      public static FastaSummary getSummary​(String fastaFile, FastaParameters fastaParameters, boolean alwaysCreateNew, WaitingHandler waitingHandler) throws IOException
      Gathers summary data on the FASTA file content.
      Parameters:
      fastaFile - path to a FASTA file
      fastaParameters - the parameters to use to parse the file
      alwaysCreateNew - if true, a new summary file will be created even if one already exists
      waitingHandler - a handler to allow canceling the import and displaying progress
      Returns:
      returns FASTA parameters inferred from the file
      Throws:
      IOException - exception thrown if an error occurred while iterating the file
    • saveSummary

      public static void saveSummary​(String fastaFile, FastaSummary fastaSummary) throws IOException
      Saves the summary in the user folder.
      Parameters:
      fastaFile - the FASTA file
      fastaSummary - the summary
      Throws:
      IOException - exception thrown if an error occurred while writing the file
    • getTypeAsString

      public String getTypeAsString()
      Returns a string with the different database types found.
      Returns:
      a string with the different database types found
    • getName

      public String getName()
      Returns the name of the database.
      Returns:
      the name for the database
    • setName

      public void setName​(String name)
      Sets a new name for the database.
      Parameters:
      name - a new name for the database
    • getVersion

      public String getVersion()
      Returns the database version.
      Returns:
      the database version
    • setVersion

      public void setVersion​(String version)
      Sets the database version.
      Parameters:
      version - the database version
    • getDescription

      public String getDescription()
      Returns the description for this database.
      Returns:
      the description for this database
    • setDescription

      public void setDescription​(String description)
      Sets the description for this database.
      Parameters:
      description - the description for this database
    • containsDecoys

      public boolean containsDecoys()
      Returns true if the FASTA file contains decoys.
      Returns:
      true if the FASTA file contains decoys