uk.ac.sanger.psu.gfmerge.datacomp
Class Prediction

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.datacomp.Prediction
All Implemented Interfaces:
PredictionAble

public class Prediction
extends java.lang.Object
implements PredictionAble

class Prediction is wrapping a BioJava sequence object.

Apart from the sequence it contains an association to the GenePredicter and references to the genemodels on the sequence. For example:

 Prediction prediction = new Prediction(sequence, filename, genePredicter);
 

Version:
1.0
See Also:
GenePredicter, GeneModel

Field Summary
private  java.util.ArrayList geneModels
          ArrayList of predicted genemodels on sequence
private  GenePredicter genePredicter
          reference to gene prediction program
private  java.lang.String genePredicterName
          name of gene prediction program (method tag in prediction file)
private  org.biojava.bio.seq.Sequence sequence
          BioJava sequence object
 
Constructor Summary
Prediction(org.biojava.bio.seq.Sequence _sequence, java.lang.String _fname, java.util.ArrayList _genePredicters)
          constructor of Prediction objects
 
Method Summary
 java.util.ArrayList getGeneModels()
          accessor method which returns ArrayList of genemodels on sequence
 GenePredicter getGenePredicter()
          accessor method which returns genepredicter object
 java.lang.String getGenePredicterName()
          accessor method which returns the genepredicter name in the method tag of the prediction file
 org.biojava.bio.seq.Sequence getSequence()
          accessor method which return BioJava sequence object
private  void setGeneModels(org.biojava.bio.seq.Sequence _sequence)
          accessor method which sets ArrayList of genemodels on sequence
private  void setGenePredicter(java.lang.String _fname, java.util.ArrayList _genePredicters)
          accessor method which sets reference to genepredicter object
private  void setGenePredicterName(org.biojava.bio.seq.Sequence _sequence, java.lang.String _fname)
          accessor method which sets genepredicter name
private  void setSequence(org.biojava.bio.seq.Sequence _sequence)
          accessor method which sets reference to BioJava sequence object
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

sequence

private org.biojava.bio.seq.Sequence sequence
BioJava sequence object


genePredicter

private GenePredicter genePredicter
reference to gene prediction program


genePredicterName

private java.lang.String genePredicterName
name of gene prediction program (method tag in prediction file)


geneModels

private java.util.ArrayList geneModels
ArrayList of predicted genemodels on sequence

Constructor Detail

Prediction

public Prediction(org.biojava.bio.seq.Sequence _sequence,
                  java.lang.String _fname,
                  java.util.ArrayList _genePredicters)
constructor of Prediction objects

Parameters:
_sequence - BioJava sequence object
_fname - filename of prediction file
_genePredicters - ArrayList of genepredicters, reference to particular genepredicter is obtained by using the genePredicterName of prediction and training data files
Method Detail

getSequence

public org.biojava.bio.seq.Sequence getSequence()
accessor method which return BioJava sequence object

Specified by:
getSequence in interface PredictionAble
Returns:
BioJava sequence object

getGenePredicter

public GenePredicter getGenePredicter()
accessor method which returns genepredicter object

Specified by:
getGenePredicter in interface PredictionAble
Returns:
genepredicter object

getGeneModels

public java.util.ArrayList getGeneModels()
accessor method which returns ArrayList of genemodels on sequence

Specified by:
getGeneModels in interface PredictionAble
Returns:
ArrayList of genemodels on sequence

getGenePredicterName

public java.lang.String getGenePredicterName()
accessor method which returns the genepredicter name in the method tag of the prediction file

Specified by:
getGenePredicterName in interface PredictionAble
Returns:
genepredicter name

setSequence

private void setSequence(org.biojava.bio.seq.Sequence _sequence)
accessor method which sets reference to BioJava sequence object

Parameters:
_sequence - BioJava sequence object

setGenePredicter

private void setGenePredicter(java.lang.String _fname,
                              java.util.ArrayList _genePredicters)
accessor method which sets reference to genepredicter object

Parameters:
_fname - filename
_genePredicters - reference to genepredicter

setGeneModels

private void setGeneModels(org.biojava.bio.seq.Sequence _sequence)
accessor method which sets ArrayList of genemodels on sequence

Parameters:
_sequence - ArrayList of genemodels

setGenePredicterName

private void setGenePredicterName(org.biojava.bio.seq.Sequence _sequence,
                                  java.lang.String _fname)
accessor method which sets genepredicter name

Parameters:
_sequence - BioJava sequence object obtained from prediction file
_fname - filename