ca.pfv.spmf.input.sequence_database_list_strings

Class SequenceDatabase

java.lang.Object

ca.pfv.spmf.input.sequence_database_list_strings.SequenceDatabase

public class SequenceDatabase
extends java.lang.Object

Implementation of a sequence database as list of strings. Each sequence should have a unique id. See examples in /test/ directory for the format of input files.

See Also:

Sequence

Constructor Summary

Constructors

Constructor and Description
SequenceDatabase()

Method Summary

Modifier and Type	Method and Description
void	addSequence(Sequence sequence) Add a sequence to this sequence database.
java.util.Set<java.lang.Integer>	getSequenceIDs() Get the list of sequence IDs for this database.
java.util.List<Sequence>	getSequences() Get the sequences from this sequence database.
void	loadFile(java.lang.String path) Method to load a sequence database from a text file in SPMF format.
void	printDatabase() Print this sequence database to System.out.
void	printDatabaseStats() Print some statistics about this sequence database to System.out.
int	size() Get the sequence count in this database.
java.lang.String	toString() Return a string representation of this sequence database.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceDatabase

public SequenceDatabase()

Method Detail

loadFile

public void loadFile(java.lang.String path)
              throws java.io.IOException

Method to load a sequence database from a text file in SPMF format.

Parameters:

path - the input file path.

Throws:

java.io.IOException - exception if error while reading the file.

addSequence

public void addSequence(Sequence sequence)

Add a sequence to this sequence database.

Parameters:

sequence - A sequence.

printDatabase

public void printDatabase()

Print this sequence database to System.out.

printDatabaseStats

public void printDatabaseStats()

Print some statistics about this sequence database to System.out.

toString

public java.lang.String toString()

Return a string representation of this sequence database.

Overrides:

toString in class java.lang.Object

size

public int size()

Get the sequence count in this database.

Returns:

the sequence count.

getSequences

public java.util.List<Sequence> getSequences()

Get the sequences from this sequence database.

Returns:

A list of sequences (Sequence).

getSequenceIDs

public java.util.Set<java.lang.Integer> getSequenceIDs()

Get the list of sequence IDs for this database.

Returns:

A set containing the sequence IDs of sequence in this database.