compbio.data.sequence

Class Score

java.lang.Object

compbio.data.sequence.Score

All Implemented Interfaces:

java.lang.Comparable<Score>

@Immutable
public class Score
extends java.lang.Object
implements java.lang.Comparable<Score>

A value class for AACon annotation results storage. The objects of this type are immutable

Author:

pvtroshin

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	method
(package private) static java.text.NumberFormat	NUMBER_FORMAT
private java.util.TreeSet<Range>	ranges
private java.util.ArrayList<java.lang.Float>	scores

Constructor Summary

Constructors

Modifier	Constructor and Description
private	Score()
	Score(java.lang.Enum<?> method, java.util.ArrayList<java.lang.Float> scores) Instantiate the Score
	Score(java.lang.Enum<?> method, java.util.ArrayList<java.lang.Float> scores, java.util.TreeSet<Range> ranges)
	Score(java.lang.Enum<?> method, float[] scores)
	Score(java.lang.Enum<?> method, java.util.TreeSet<Range> ranges)

Method Summary

Modifier and Type	Method and Description
int	compareTo(Score o)
boolean	equals(java.lang.Object obj)
java.lang.String	getMethod() Returns the ConservationMethod
java.util.TreeSet<Range>	getRanges() Return Ranges if any Collections.EMPTY_SET otherwise
java.util.ArrayList<java.lang.Float>	getScores() The column scores for the alignment
int	hashCode()
void	setRanges(java.util.TreeSet<Range> ranges)
private java.util.ArrayList<java.lang.Float>	toList(float[] values)
java.lang.String	toString()
static void	write(java.util.TreeSet<Score> scores, java.io.Writer writer) Outputs the List of Score objects into the Output stream.

Methods inherited from class java.lang.Object

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

Field Detail

NUMBER_FORMAT

static final java.text.NumberFormat NUMBER_FORMAT

method

private final java.lang.String method

ranges

private java.util.TreeSet<Range> ranges

scores

private java.util.ArrayList<java.lang.Float> scores

Constructor Detail

Score

private Score()

Score

public Score(java.lang.Enum<?> method,
             java.util.ArrayList<java.lang.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

Score

public Score(java.lang.Enum<?> method,
             java.util.ArrayList<java.lang.Float> scores,
             java.util.TreeSet<Range> ranges)

Parameters:

method - the ConservationMethod with which scores were calculated

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

ranges - The set of ranges i.e. parts of the sequence with specific function, usually can be calculated based on scores

Score

public Score(java.lang.Enum<?> method,
             java.util.TreeSet<Range> ranges)

Score

public Score(java.lang.Enum<?> method,
             float[] scores)

Method Detail

toList

private java.util.ArrayList<java.lang.Float> toList(float[] values)

getMethod

public java.lang.String getMethod()

Returns the ConservationMethod

Returns:

the ConservationMethod

getScores

public java.util.ArrayList<java.lang.Float> getScores()

The column scores for the alignment

Returns:

the column scores for the alignment

getRanges

public java.util.TreeSet<Range> getRanges()

Return Ranges if any Collections.EMPTY_SET otherwise

Returns:

ordered set of Range

setRanges

public void setRanges(java.util.TreeSet<Range> ranges)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

write

public static void write(java.util.TreeSet<Score> scores,
                         java.io.Writer writer)
                  throws java.io.IOException

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

 
 #MethodName [comma separated list of ranges] <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
 #COILS 22-33, 44-56 0.121 3.212
 
 

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

Parameters:

scores - the list of scores to output

writer -

Throws:

java.io.IOException - if the OutputStream cannot be written into

java.lang.NullPointerException - if the output stream is null

compareTo

public int compareTo(Score o)

Specified by:

compareTo in interface java.lang.Comparable<Score>