data
Class Configuration

java.lang.Object
  extended by data.Configuration
All Implemented Interfaces:
java.io.Serializable

public class Configuration
extends java.lang.Object
implements java.io.Serializable

Class to mantain the core configuration.

Version:
1.0
Author:
Oscar Flores
See Also:
Serialized Form

Field Summary
private  int bestScoredCount
          This number indicates the number of taxa that has to be considered on the best scored taxa list and unexpected list
private  float foundValue
          Minimum value to fire the Identified panel
private  float minUnexpectedScore
          Minimum score to show the taxon at the unexpected results list
(package private) static long serialVersionUID
           
private  float SignalScoreLimitLow
          When determining if a test positive, negative or variable, there are two cut points.
private  float SignalScoreLimitUpp
          When determining if a test is positive, negative or variable, there are two cut points.
private  float ZeroSkipValue
          To avoid lose information, change 0.00f prob. for this value
 
Constructor Summary
Configuration()
          Default constructor wich loads Bayesian id. default values
 
Method Summary
 int getBestScoredCount()
           
 float getFoundValue()
           
 float getMinAliveScore()
           
 float getSignalScoreLimitLow()
           
 float getSignalScoreLimitUpp()
           
 float getZeroSkipValue()
           
 void setBestScoredCount(int bestScoredCount)
           
 void setFoundValue(float foundValue)
           
 void setMinUnexpectedScore(float minAliveScore)
           
 void setSignalScoreLimitLow(float signalScoreLimitLow)
           
 void setSignalScoreLimitUpp(float signalScoreLimitUpp)
           
 void setUpBayesDefaults()
          Set the current Configuration to use Bayesian Id. defaults
 void setUpTreeDefaults()
          Set the current Configuration to use Tree Id. defaults
 void setZeroSkipValue(float zeroSkipValue)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

serialVersionUID

static final long serialVersionUID
See Also:
Constant Field Values

ZeroSkipValue

private float ZeroSkipValue
To avoid lose information, change 0.00f prob. for this value


minUnexpectedScore

private float minUnexpectedScore
Minimum score to show the taxon at the unexpected results list


SignalScoreLimitUpp

private float SignalScoreLimitUpp
When determining if a test is positive, negative or variable, there are two cut points. That point is the limit beetween Positive and Variable results.


SignalScoreLimitLow

private float SignalScoreLimitLow
When determining if a test positive, negative or variable, there are two cut points. That point is the limit beetween Variable and Negative results.


foundValue

private float foundValue
Minimum value to fire the Identified panel


bestScoredCount

private int bestScoredCount
This number indicates the number of taxa that has to be considered on the best scored taxa list and unexpected list

Constructor Detail

Configuration

public Configuration()
Default constructor wich loads Bayesian id. default values

Method Detail

setUpBayesDefaults

public void setUpBayesDefaults()
Set the current Configuration to use Bayesian Id. defaults


setUpTreeDefaults

public void setUpTreeDefaults()
Set the current Configuration to use Tree Id. defaults


getMinAliveScore

public float getMinAliveScore()
Returns:
Minimum taxon absolute probability before discard it

getSignalScoreLimitLow

public float getSignalScoreLimitLow()
Returns:
Lower limit of variable results

getSignalScoreLimitUpp

public float getSignalScoreLimitUpp()
Returns:
Upper limit of variable results

getZeroSkipValue

public float getZeroSkipValue()
Returns:
Value of a zero if skipped

setMinUnexpectedScore

public void setMinUnexpectedScore(float minAliveScore)
Parameters:
minAliveScore - Minimum taxon absolute probability before discard it

setSignalScoreLimitLow

public void setSignalScoreLimitLow(float signalScoreLimitLow)
Parameters:
signalScoreLimitLow - Lower limit of variable results

setSignalScoreLimitUpp

public void setSignalScoreLimitUpp(float signalScoreLimitUpp)
Parameters:
signalScoreLimitUpp - Upper limit of variable results

setZeroSkipValue

public void setZeroSkipValue(float zeroSkipValue)
Parameters:
zeroSkipValue - Value of a zero if skipped

getFoundValue

public float getFoundValue()
Returns:
Minimum relative probability before achieve a identification

setFoundValue

public void setFoundValue(float foundValue)
Parameters:
foundValue - Minimum relative probability before achieve a identification

getBestScoredCount

public int getBestScoredCount()
Returns:
Number of taxa to analyze looking for unexpected values

setBestScoredCount

public void setBestScoredCount(int bestScoredCount)
Parameters:
bestScoredCount - Number of taxa to analyze looking for unexpected values