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

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter

public class GenePredicter
extends java.lang.Object

class is representing a geneprediction program (its prediction).

For example:

 GenePredicter gp = new GenePredicter(seqOrg, seqComp, predFileName);
 

Version:
1.0
Author:
Sebastian R. Spiegler

Field Summary
private  double acp
          average conditional probability of geneprediction program
private  java.lang.String name
          name of geneprediction program
 
Constructor Summary
GenePredicter(org.biojava.bio.seq.Sequence seqOrg, org.biojava.bio.seq.Sequence seqComp, java.lang.String predFileName)
          constructor of GenePredicter objects
 
Method Summary
private  double calcAcp(org.biojava.bio.seq.Sequence seqOrg, org.biojava.bio.seq.Sequence seqComp)
          method which retrieves average conditional probability from PredAccuracy object.
 double getAcp()
          accessor method which returns average conditional probability of genepredicter program.
 java.lang.String getName()
          accessor method which returns name of genepredicter.
private  java.lang.String retrieveName(org.biojava.bio.seq.Sequence seq, java.lang.String fname)
          method which retrieves name of genepredicter program from gene prediction file.
private  void setAcp(double _acp)
          accessor method which sets average conditional probability of genepredicter program.
private  void setName(java.lang.String _name)
          accessor method which sets name of genepredicter.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

name

private java.lang.String name
name of geneprediction program


acp

private double acp
average conditional probability of geneprediction program

Constructor Detail

GenePredicter

public GenePredicter(org.biojava.bio.seq.Sequence seqOrg,
                     org.biojava.bio.seq.Sequence seqComp,
                     java.lang.String predFileName)
constructor of GenePredicter objects

Parameters:
seqOrg - annotation
seqComp - gene predictions
predFileName - filename of prediction file
Method Detail

getName

public java.lang.String getName()
accessor method which returns name of genepredicter. genepredicter name is retrieved from method-tag in prediction file.

Returns:
name of genepredicter

setName

private void setName(java.lang.String _name)
accessor method which sets name of genepredicter.

Parameters:
_name - name of genepredicter

getAcp

public double getAcp()
accessor method which returns average conditional probability of genepredicter program.

Returns:
acp value
See Also:
PredAccuracy

setAcp

private void setAcp(double _acp)
accessor method which sets average conditional probability of genepredicter program.

Parameters:
_acp - average conditional probability of genepredicter program
See Also:
PredAccuracy

retrieveName

private java.lang.String retrieveName(org.biojava.bio.seq.Sequence seq,
                                      java.lang.String fname)
method which retrieves name of genepredicter program from gene prediction file.

Parameters:
seq - sequence which contains BioJava feature with method-tag each
fname - filename of geneprediction file
Returns:
genepredicter name

calcAcp

private double calcAcp(org.biojava.bio.seq.Sequence seqOrg,
                       org.biojava.bio.seq.Sequence seqComp)
method which retrieves average conditional probability from PredAccuracy object.

Parameters:
seqOrg - annotation
seqComp - gene predictions
Returns:
acp value