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java.lang.Object org.strbio.mol.AlignmentStats
public class AlignmentStats
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
Field Summary | |
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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 | |
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AlignmentStats()
The default object has all stats undefined (Double.NaN), or -1 for integers. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public double pctRight1
public double aspc
public double asns
public double aspc1
public double asns1
public double aspc4
public double asns4
public double shift
public double avgScoreWithGaps
public double avgScoreWithoutGaps
public double calcRMS
public double RMS
public double calcPctAligned
public double pctAligned
public double calcPctAlignedLong
public double pctAlignedLong
public double calcPctID
public double pctID
public double estASns1
public double estASns1SD
public double estPMatch
Constructor Detail |
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public AlignmentStats()
Method Detail |
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public void calculate(Alignment correct, Alignment calculated, MinareaResults ma)
public void calculateEstimated(Alignment calculated)
public void calculateCorrect(Alignment correct)
public void calculateScores(Alignment al, ScoreList sc)
public void save(Printf outfile) throws java.io.IOException
java.io.IOException
public void load(java.lang.String buffer)
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