compbio.metadata
Class Limit<T>

java.lang.Object
  compbio.metadata.Limit<T>

Type Parameters:

T - the type of an executable for which this limit is defined.

public class Limit<T>
extends Object

A value object containing a maximum number of sequences and a maximum average sequence length for a preset. Also contains static method for determining the number of sequence and their average length in the List

Version:

1.0 January 2010

Author:

pvtroshin

See Also:

LimitsManager

Constructor Summary

Limit(int seqNumber, int seqLength, String preset)
Instantiate the limit

Limit(int seqNumber, int seqLength, String preset, boolean isDefault)

Method Summary

boolean	equals(Object obj)
int	getAvgSeqLength()
static int	getAvgSequenceLength(List<FastaSequence> data) Calculates an average sequence length of the dataset
String	getPreset()
int	getSeqNumber()
int	hashCode()
boolean	isDefault()
boolean	isExceeded(List<FastaSequence> data) Checks if the number of sequences or their average length in the dataset exceeds this limit.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Limit

public Limit(int seqNumber,
             int seqLength,
             String preset)

Instantiate the limit

Parameters:

seqNumber - the maximum number of sequences allowed for calculation. Required

seqLength - the average length of the sequence, optional

preset - the name of preset if any, optional

Throws:

IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative

Limit

public Limit(int seqNumber,
             int seqLength,
             String preset,
             boolean isDefault)

Method Detail

getPreset

public String getPreset()

getAvgSeqLength

public int getAvgSeqLength()

Returns:

the allowed average sequence length

getSeqNumber

public int getSeqNumber()

Returns:

the maximum number of sequences allowed

isDefault

public boolean isDefault()

Returns:

true is this is a default limit to be used, false otherwise

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

isExceeded

public boolean isExceeded(List<FastaSequence> data)

Checks if the number of sequences or their average length in the dataset exceeds this limit.

Parameters:

data - the dataset to measure

Returns:

true if a limit is exceeded (what is the dataset is larger then the limit), false otherwise. First check the number of sequences in the dataset and if it exceeds the limit return true irrespective of the average length. If the number of sequences in the dataset is less than the limit and average length is defined, then check whether the total number of letters (number of sequence multiplied by the average sequence length) is greater then the total number of letters in the dataset. Returns true if the total number of letters in the dataset is greater than the limit, false otherwise.

getAvgSequenceLength

public static int getAvgSequenceLength(List<FastaSequence> data)

Calculates an average sequence length of the dataset

Parameters:

data -

Returns:

an average sequence length in the input dataset