edu.rit.compbio.seq

Class ProteinDatabase

java.lang.Object

edu.rit.compbio.seq.ProteinDatabase

public class ProteinDatabase
extends java.lang.Object

Class ProteinDatabase encapsulates a protein sequence database stored in a file. Class ProteinDatabase is used to read ProteinSequence objects from the database.

A protein sequence database file consists of one or more protein sequences stored in FASTA format. A FASTA format protein sequence consists of one description line and one or more sequence lines. The description line consists of an initial '>' character followed by zero or more characters (the protein's description). A sequence line consists of one or more characters 'A' through 'Z', 'a' through 'z', '*', or '-'. For further information, see class ProteinSequence.

Along with the protein sequence database file, there is a protein sequence index file. The index file tells where each protein is located in the database file. Class ProteinDatabase's constructor requires both the database file and the index file to be supplied as arguments.

Class ProteinDatabase includes a main program that reads a protein sequence database file and creates the requisite protein sequence index file. If the n argument is specified, the program creates an index file for just the first n sequences in the database. If the n argument is omitted, the program creates an index file for all the sequences in the database.

Usage: java edu.rit.compbio.seq.ProteinDatabase databasefile indexfile [ n ]
databasefile = Input protein sequence database file
indexfile = Output protein sequence index file
n = Number of sequences in the index (default: all)

Constructor Summary

Constructors

Constructor and Description
ProteinDatabase(java.io.File theDatabaseFile, java.io.File theIndexFile) Construct a new protein sequence database.

Method Summary

Modifier and Type	Method and Description
void	close() Close this protein sequence database.
long	getDatabaseLength() Get the sum of the lengths of the protein sequences in this protein sequence database.
long	getProteinCount() Get the number of protein sequences in this protein sequence database.
ProteinSequence	getProteinSequence(long i) Get the protein sequence at the given index in this protein sequence database.
static void	main(java.lang.String[] args) Main program that reads a protein sequence database file and creates the requisite protein sequence index file.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinDatabase

public ProteinDatabase(java.io.File theDatabaseFile,
                       java.io.File theIndexFile)
                throws java.io.IOException

Construct a new protein sequence database.

Parameters:

theDatabaseFile - Protein sequence database file.

theIndexFile - Protein sequence index file.

Throws:

java.lang.NullPointerException - (unchecked exception) Thrown if theDatabaseFile is null. Thrown if theIndexFile is null.

java.io.IOException - Thrown if an I/O error occurred.

Method Detail

getDatabaseLength

public long getDatabaseLength()

Get the sum of the lengths of the protein sequences in this protein sequence database.

Returns:

Total protein sequence length.

getProteinCount

public long getProteinCount()

Get the number of protein sequences in this protein sequence database.

Returns:

Number of protein sequences, N.

getProteinSequence

public ProteinSequence getProteinSequence(long i)
                                   throws java.io.IOException

Get the protein sequence at the given index in this protein sequence database.

Parameters:

i - Index in the range 0 ≤ i ≤ N−1.

Returns:

Protein sequence.

Throws:

java.lang.IndexOutOfBoundsException - (unchecked exception) Thrown if i is out of bounds.

java.io.IOException - Thrown if an I/O error occurred.

close

public void close()
           throws java.io.IOException

Close this protein sequence database.

Throws:

java.io.IOException - Thrown if an I/O error occurred.

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Main program that reads a protein sequence database file and creates the requisite protein sequence index file. If the n argument is specified, the program creates an index file for just the first n sequences in the database. If the n argument is omitted, the program creates an index file for all the sequences in the database.

Usage: java edu.rit.compbio.seq.ProteinDatabase databasefile indexfile [ n ]
databasefile = Input protein sequence database file
indexfile = Output protein sequence index file
n = Number of sequences in the index (default: all)

Throws:

java.lang.Exception