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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.datacomp.Prediction
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);
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 |
private org.biojava.bio.seq.Sequence sequence
private GenePredicter genePredicter
private java.lang.String genePredicterName
private java.util.ArrayList geneModels
Constructor Detail |
public Prediction(org.biojava.bio.seq.Sequence _sequence, java.lang.String _fname, java.util.ArrayList _genePredicters)
_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 filesMethod Detail |
public org.biojava.bio.seq.Sequence getSequence()
getSequence
in interface PredictionAble
public GenePredicter getGenePredicter()
getGenePredicter
in interface PredictionAble
public java.util.ArrayList getGeneModels()
getGeneModels
in interface PredictionAble
public java.lang.String getGenePredicterName()
getGenePredicterName
in interface PredictionAble
private void setSequence(org.biojava.bio.seq.Sequence _sequence)
_sequence
- BioJava sequence objectprivate void setGenePredicter(java.lang.String _fname, java.util.ArrayList _genePredicters)
_fname
- filename_genePredicters
- reference to genepredicterprivate void setGeneModels(org.biojava.bio.seq.Sequence _sequence)
_sequence
- ArrayList of genemodelsprivate void setGenePredicterName(org.biojava.bio.seq.Sequence _sequence, java.lang.String _fname)
_sequence
- BioJava sequence object obtained from prediction file_fname
- filename
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