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- -compbio.metadata -
-Class Limit<T>

-
-java.lang.Object
-  extended by 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
- booleanequals(Object obj) - -
-           
- intgetAvgSeqLength() - -
-           
-static intgetAvgSequenceLength(List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- StringgetPreset() - -
-           
- intgetSeqNumber() - -
-           
- inthashCode() - -
-           
- booleanisDefault() - -
-           
- booleanisExceeded(List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
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