startup.features
Class FeatureRecognition

java.lang.Object
  extended by startup.features.FeatureRecognition
All Implemented Interfaces:
java.lang.Runnable

public class FeatureRecognition
extends java.lang.Object
implements java.lang.Runnable

Class designed to take care of selected features by a feature selection algorithm. WARNING: class is still definitely in alpha stage, so some functionality is still missing, known (I have better things to do) and unknown bugs are present, ...

Author:
Michiel Van Bel

Nested Class Summary
static class FeatureRecognition.TARGET
          What action to do: a) WRITE_SVG : simply make an SVG picture of the features.
 
Field Summary
static int BLOCKSIZE
          Size of the blocks of a single feature in an SVG picture.
 
Constructor Summary
FeatureRecognition(org.apache.log4j.Logger logger, java.lang.String feature_filename, java.lang.String outputDir, int splicesite_increase)
          Constructor.
FeatureRecognition(org.apache.log4j.Logger logger, java.lang.String feature_filename, java.lang.String positive_data_filename, java.lang.String negative_data_filename, java.lang.String outputDir, int funsite)
          constructor.
 
Method Summary
 FeatureRecognition.TARGET getTarget()
           
 void printFeatures(java.util.List<java.lang.Double> features)
           
 void printScores(java.util.List<java.lang.Double> scores)
           
 void run()
           
 void setTarget(FeatureRecognition.TARGET target)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

BLOCKSIZE

public static final int BLOCKSIZE
Size of the blocks of a single feature in an SVG picture. Size is in pixels.

See Also:
Constant Field Values
Constructor Detail

FeatureRecognition

public FeatureRecognition(org.apache.log4j.Logger logger,
                          java.lang.String feature_filename,
                          java.lang.String positive_data_filename,
                          java.lang.String negative_data_filename,
                          java.lang.String outputDir,
                          int funsite)
constructor. Initialization of some basic variables.

Parameters:
logger - The logging facility (cannot be null).
feature_filename - The name of the file containing the feature filter.
positive_data_filename - The name of the file containing positive training data (can be null in certain cases).
negative_data_filename - The name of the file containing negative training data (can be null in certain cases).
outputDir - The directory to which the results should be written.
funsite - The location of the functional site in the training data.

FeatureRecognition

public FeatureRecognition(org.apache.log4j.Logger logger,
                          java.lang.String feature_filename,
                          java.lang.String outputDir,
                          int splicesite_increase)
Constructor. Initialization of some basic variables.

Parameters:
logger - The logging facility.
feature_filename - The name of the file containing the feature filter.
outputDir - The location of the directory to which results should be written.
splicesite_increase - The increase
Method Detail

run

public void run()
Specified by:
run in interface java.lang.Runnable

printScores

public void printScores(java.util.List<java.lang.Double> scores)

printFeatures

public void printFeatures(java.util.List<java.lang.Double> features)

getTarget

public FeatureRecognition.TARGET getTarget()

setTarget

public void setTarget(FeatureRecognition.TARGET target)