com.compomics.util.experiment.identification
Class FastaIndex

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.identification.FastaIndex
All Implemented Interfaces:
Serializable, Cloneable

public class FastaIndex
extends ExperimentObject

This class contains the index of a fasta file

Author:
marc
See Also:
Serialized Form

Constructor Summary
FastaIndex(HashMap<String,Long> indexes, String fileName, boolean isDecoy, int nTarget)
          Constructor
 
Method Summary
 String getFileName()
          Returns the file name of the inspected fasta file
 Long getIndex(String accession)
          Returns the index of the accession of interest
 HashMap<String,Long> getIndexes()
          Returns a map of all indexes of the fasta file (accession -> index)
 int getNTarget()
          Returns the number of target sequences in the database
 boolean isDecoy()
          Returns a boolean indicating whether the database contains decoy sequences
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FastaIndex

public FastaIndex(HashMap<String,Long> indexes,
                  String fileName,
                  boolean isDecoy,
                  int nTarget)
Constructor

Parameters:
indexes - The indexes of the inspected fasta file
fileName - The fasta file name
Method Detail

getIndexes

public HashMap<String,Long> getIndexes()
Returns a map of all indexes of the fasta file (accession -> index)

Returns:
a map of all indexes of the fasta file (accession -> index)

getIndex

public Long getIndex(String accession)
Returns the index of the accession of interest

Parameters:
accession - the accession of interest
Returns:
the index of the accession of interest

getFileName

public String getFileName()
Returns the file name of the inspected fasta file

Returns:
the file name of the inspected fasta file

isDecoy

public boolean isDecoy()
Returns a boolean indicating whether the database contains decoy sequences

Returns:
a boolean indicating whether the database contains decoy sequences

getNTarget

public int getNTarget()
Returns the number of target sequences in the database

Returns:
the number of target sequences in the database


Copyright © 2011. All Rights Reserved.