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:
java.io.Serializable, java.lang.Cloneable

public class FastaIndex
extends ExperimentObject

This class contains the index of a FASTA file.

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
FastaIndex(java.util.HashMap<java.lang.String,java.lang.Long> indexes, java.lang.String fileName, boolean isDecoy, int nTarget)
          Constructor.
 
Method Summary
 java.lang.String getFileName()
          Returns the file name of the inspected FASTA file.
 java.lang.Long getIndex(java.lang.String accession)
          Returns the index of the accession of interest.
 java.util.HashMap<java.lang.String,java.lang.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(java.util.HashMap<java.lang.String,java.lang.Long> indexes,
                  java.lang.String fileName,
                  boolean isDecoy,
                  int nTarget)
Constructor.

Parameters:
indexes - The indexes of the inspected FASTA file
fileName - The FASTA file name
isDecoy - If the FASTA file contains decoys or nor
nTarget - Number of target sequences found in the database
Method Detail

getIndexes

public java.util.HashMap<java.lang.String,java.lang.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 java.lang.Long getIndex(java.lang.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 java.lang.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


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