compbio.data.sequence
Class Score

java.lang.Object
  compbio.data.sequence.Score

@Immutable
public class Score
extends Object

A value class for AACon annotation results storage

Author:

pvtroshin

Constructor Summary

Score(ConservationMethod method, List<Float> scores)
Instantiate the Score

Method Summary

boolean	equals(Object obj)
ConservationMethod	getMethod() Returns the ConservationMethod
List<Float>	getScores() The column scores for the alignment
int	hashCode()
String	toString()
static void	write(Set<Score> scores, OutputStream output) Outputs the List of Score objects into the Output stream.

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Score

public Score(ConservationMethod method,
             List<Float> scores)

Instantiate the Score

Parameters:

method - the ConservationMethod with which scores were calculated

scores - the actual conservation values for each column of the alignment

Method Detail

getMethod

public ConservationMethod getMethod()

Returns the ConservationMethod

Returns:

the ConservationMethod

getScores

public List<Float> getScores()

The column scores for the alignment

Returns:

the column scores for the alignment

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

write

public static void write(Set<Score> scores,
                         OutputStream output)
                  throws IOException

Outputs the List of Score objects into the Output stream. The output format is as follows:

 #MethodName <space separated list of values>
 	  
 For example:
 	 
 #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
 #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
 
 

The maximum precision for values is 3 digits, but can be less.

Parameters:

scores - the list of scores to output

output - the stream to output the data to

Throws:

IOException - if the OutputStream cannot be written into

NullPointerException - if the output stream is null