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java.lang.Objectcom.compomics.util.preferences.ProcessingPreferences
public class ProcessingPreferences
This class groups the user preferences for the initial PeptideShaker processing.
Constructor Summary | |
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ProcessingPreferences()
Constructor with default settings. |
Method Summary | |
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void |
estimateAScore(boolean shouldEstimateAScore)
Deprecated. use the PTM scoring preferences instead |
double |
getPeptideFDR()
Returns the initial peptide FDR. |
Double |
getProteinConfidenceMwPlots()
Returns the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab. |
double |
getProteinFDR()
Returns the initial protein FDR. |
double |
getPsmFDR()
Returns the initial PSM FDR. |
boolean |
isAScoreCalculated()
Deprecated. use the PTM scoring preferences instead |
void |
setPeptideFDR(double peptideFDR)
Sets the initial peptide FDR. |
void |
setProteinConfidenceMwPlots(Double proteinConfidenceMwPlots)
Sets the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab. |
void |
setProteinFDR(double proteinFDR)
Sets the initial protein FDR. |
void |
setPsmFDR(double psmFDR)
Sets the initial PSM FDR. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProcessingPreferences()
Method Detail |
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public boolean isAScoreCalculated()
public void estimateAScore(boolean shouldEstimateAScore)
shouldEstimateAScore
- whether the A-score should be calculatedpublic double getPeptideFDR()
public void setPeptideFDR(double peptideFDR)
peptideFDR
- the initial peptide FDRpublic double getProteinFDR()
public void setProteinFDR(double proteinFDR)
proteinFDR
- the initial protein FDRpublic double getPsmFDR()
public void setPsmFDR(double psmFDR)
psmFDR
- the initial PSM FDRpublic Double getProteinConfidenceMwPlots()
public void setProteinConfidenceMwPlots(Double proteinConfidenceMwPlots)
proteinConfidenceMwPlots
- minimum confidence
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