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java.lang.Object org.strbio.mol.lib.AlignmentParameters org.strbio.mol.lib.AlignmentParametersEA
public class AlignmentParametersEA
Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition.
Field Summary | |
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DVector |
asns1
asns1 values for each match (there is no such thing for non-matches |
DVector |
avgScoreMatch
scores for each match (gapped alignment score) |
DVector |
avgScoreNonMatch
scores for each non-match |
DVector |
totalZMatch
z score of total score for each match. |
DVector |
totalZNonMatch
z score of total score for each non-match. |
Fields inherited from class org.strbio.mol.lib.AlignmentParameters |
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gapModel, scoreList |
Constructor Summary | |
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AlignmentParametersEA()
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AlignmentParametersEA(GapModel gm,
ScoreList sl)
|
Method Summary | |
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boolean |
canEstimateAA()
will this return valid results for estAsns1, etc? |
boolean |
canEstimateFR()
will this return valid results for estFR*? |
void |
clearEstAAStats()
remove stats for estimating alignment accuracy |
void |
clearEstFRStats()
remove stats for estimating fold recognition accuracy. |
java.lang.String |
defaultEAFileAA()
get the default file name (in the classpath) for alignment accuracy parameters. |
java.lang.String |
defaultEAFileFR()
get the default file name (in the classpath) for fold recognition parameters. |
double |
estASns1(double score)
estimate the asns1, given an average score (with gap penalties counted). |
double |
estASns1SD(double score)
get the SD for the asns1 estimation, given an average score (with gap penalties counted). |
double |
estFRAccy(double avgScore,
double zScore)
Estimate the accuracy of a given prediction, given the average score and the z score of the total score. |
void |
loadEstAAStats()
Load the default accuracy stats from a file in the classpath. |
void |
loadEstAAStats(java.io.BufferedReader infile)
Get the accuracy stats out of a file. |
void |
loadEstAAStats(java.lang.String filename)
Get the accuracy stats out of a file. |
void |
loadEstAAStatsRaw(java.io.BufferedReader infile)
Get raw accuracy stats out of a file. |
void |
loadEstAAStatsRaw(java.lang.String filename)
Get the raw accuracy stats out of a file. |
void |
loadEstFRStats()
Load the default accuracy stats from a file in the classpath. |
void |
loadEstFRStats(java.io.BufferedReader infile)
Get the FR accuracy stats out of a file. |
void |
loadEstFRStats(java.lang.String filename)
Get the FR accuracy stats out of a file. |
void |
loadEstFRStatsRaw(java.io.BufferedReader infile)
Get the raw FR accuracy stats out of a file. |
void |
loadEstFRStatsRaw(java.lang.String filename)
Get the raw FR accuracy stats out of a file. |
void |
processAA()
process the AA stats, for speed in estimation. |
void |
processFR()
process the FR stats, for speed in estimation. |
void |
saveEstAAStats(Printf outfile)
Save accuracy stats to a file. |
void |
saveEstAAStats(java.lang.String filename)
Save alignment accuracy stats to a file. |
void |
saveEstFRStats(Printf outfile)
Save accuracy stats to a file. |
void |
saveEstFRStats(java.lang.String filename)
Save alignment accuracy stats to a file. |
Methods inherited from class org.strbio.mol.lib.AlignmentParameters |
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addScoreFunction, addScoreFunction, describe, finished, normalizeWeights, setAlignment, setup |
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 DVector avgScoreMatch
public DVector avgScoreNonMatch
public DVector totalZMatch
public DVector totalZNonMatch
public DVector asns1
Constructor Detail |
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public AlignmentParametersEA()
public AlignmentParametersEA(GapModel gm, ScoreList sl)
Method Detail |
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public java.lang.String defaultEAFileAA()
public java.lang.String defaultEAFileFR()
public double estASns1(double score)
public double estASns1SD(double score)
public void processAA()
public double estFRAccy(double avgScore, double zScore)
public void processFR()
public boolean canEstimateAA()
public boolean canEstimateFR()
public void clearEstAAStats()
public void clearEstFRStats()
public void saveEstAAStats(java.lang.String filename) throws java.io.IOException
java.io.IOException
public void saveEstAAStats(Printf outfile) throws java.io.IOException
java.io.IOException
public void loadEstAAStatsRaw(java.io.BufferedReader infile) throws java.io.IOException
java.io.IOException
public void loadEstAAStats(java.io.BufferedReader infile) throws java.io.IOException
java.io.IOException
public void loadEstAAStats(java.lang.String filename) throws java.io.IOException
java.io.IOException
public void loadEstAAStatsRaw(java.lang.String filename) throws java.io.IOException
java.io.IOException
public void loadEstAAStats() throws java.io.IOException
java.io.IOException
public void saveEstFRStats(java.lang.String filename) throws java.io.IOException
java.io.IOException
public void saveEstFRStats(Printf outfile) throws java.io.IOException
java.io.IOException
public void loadEstFRStats(java.io.BufferedReader infile) throws java.io.IOException
java.io.IOException
public void loadEstFRStatsRaw(java.io.BufferedReader infile) throws java.io.IOException
java.io.IOException
public void loadEstFRStats(java.lang.String filename) throws java.io.IOException
java.io.IOException
public void loadEstFRStatsRaw(java.lang.String filename) throws java.io.IOException
java.io.IOException
public void loadEstFRStats() throws java.io.IOException
java.io.IOException
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