org.strbio.mol
Class AlignmentStats

java.lang.Object
  extended by org.strbio.mol.AlignmentStats

public class AlignmentStats
extends java.lang.Object

A class holding alignment statistics for a given alignment.

  Version 1.01, 9/1/99 - fixed to account for MinareaResults changes
  Version 1.0, 4/21/99 - original version
  

Version:
1.01, 9/1/99
Author:
JMC

Field Summary
 double asns
          alignment sensitivity, tolerance 0
 double asns1
          alignment sensitivity, tolerance 1
 double asns4
          alignment sensitivity, tolerance 4
 double aspc
          alignment specificity, tolerance 0
 double aspc1
          alignment specificity, tolerance 1
 double aspc4
          alignment specificity, tolerance 4
 double avgScoreWithGaps
          average score of the calculated alignment, including gaps, or NaN if not available.
 double avgScoreWithoutGaps
          average score of the calculated alignment, not including gaps, or NaN if not available.
 double calcPctAligned
          pct aligned, calculated.
 double calcPctAlignedLong
          pct aligned, calculated, vs longest seq
 double calcPctID
          pct ID, calculated
 double calcRMS
          RMS, calculated alignment.
 double estASns1
          estimated asns1
 double estASns1SD
          estimated SD in asns1
 double estPMatch
          estimated probability of match
 double pctAligned
          pct aligned, correct.
 double pctAlignedLong
          pct aligned, correct, vs longest seq
 double pctID
          pct ID, correct.
 double pctRight1
          percent correct, tolerance 1.
 double RMS
          RMS, correct alignment.
 double shift
          average alignment shift
 
Constructor Summary
AlignmentStats()
          The default object has all stats undefined (Double.NaN), or -1 for integers.
 
Method Summary
 void calculate(Alignment correct, Alignment calculated, MinareaResults ma)
          Calculate all results (that can be), given correct and calculated alignments, and minarea results (for RMS only; can be null to ignore).
 void calculateCorrect(Alignment correct)
          Only calculate the stats that depend on correct alignment
 void calculateEstimated(Alignment calculated)
          Only calculate the estimated stats.
 void calculateScores(Alignment al, ScoreList sc)
          Calculate scores, given a score list.
 void load(java.lang.String buffer)
          load results from a line in a saved file.
 void save(Printf outfile)
          Write these results to an output file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

pctRight1

public double pctRight1
percent correct, tolerance 1.


aspc

public double aspc
alignment specificity, tolerance 0


asns

public double asns
alignment sensitivity, tolerance 0


aspc1

public double aspc1
alignment specificity, tolerance 1


asns1

public double asns1
alignment sensitivity, tolerance 1


aspc4

public double aspc4
alignment specificity, tolerance 4


asns4

public double asns4
alignment sensitivity, tolerance 4


shift

public double shift
average alignment shift


avgScoreWithGaps

public double avgScoreWithGaps
average score of the calculated alignment, including gaps, or NaN if not available.


avgScoreWithoutGaps

public double avgScoreWithoutGaps
average score of the calculated alignment, not including gaps, or NaN if not available.


calcRMS

public double calcRMS
RMS, calculated alignment.


RMS

public double RMS
RMS, correct alignment.


calcPctAligned

public double calcPctAligned
pct aligned, calculated.


pctAligned

public double pctAligned
pct aligned, correct.


calcPctAlignedLong

public double calcPctAlignedLong
pct aligned, calculated, vs longest seq


pctAlignedLong

public double pctAlignedLong
pct aligned, correct, vs longest seq


calcPctID

public double calcPctID
pct ID, calculated


pctID

public double pctID
pct ID, correct.


estASns1

public double estASns1
estimated asns1


estASns1SD

public double estASns1SD
estimated SD in asns1


estPMatch

public double estPMatch
estimated probability of match

Constructor Detail

AlignmentStats

public AlignmentStats()
The default object has all stats undefined (Double.NaN), or -1 for integers.

Method Detail

calculate

public void calculate(Alignment correct,
                      Alignment calculated,
                      MinareaResults ma)
Calculate all results (that can be), given correct and calculated alignments, and minarea results (for RMS only; can be null to ignore).


calculateEstimated

public void calculateEstimated(Alignment calculated)
Only calculate the estimated stats.


calculateCorrect

public void calculateCorrect(Alignment correct)
Only calculate the stats that depend on correct alignment


calculateScores

public void calculateScores(Alignment al,
                            ScoreList sc)
Calculate scores, given a score list.


save

public void save(Printf outfile)
          throws java.io.IOException
Write these results to an output file. Only some get saved for now, due to inefficiency.

Throws:
java.io.IOException

load

public void load(java.lang.String buffer)
load results from a line in a saved file. Usually, there is only one result per line, so this function gets called multiple times.