public class PSMModeller extends Object
Constructor and Description |
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PSMModeller(Integer nrFiles,
boolean oboLookup) |
Modifier and Type | Method and Description |
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boolean |
addPSMforFile(Integer fileID,
IntermediatePeptideSpectrumMatch psm)
Adds the given PSM to the end of the list of PSMs for the file specified
by fileID.
|
void |
calculateAllFDR()
Calculates the FDR of the PSMs for all files
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void |
calculateFDR(Integer fileID)
Calculates the FDR of the PSMs for the file selected by its ID
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String |
getFdrScoreAccession(Integer fileID)
Getter for the score set for FDR estimation of the file given by fileID
|
String |
getFilesMainScoreAccession(Integer fileID)
Returns the main score of the file given by its ID.
|
List<IntermediatePeptideSpectrumMatch> |
getFilesPSMs(Integer fileID)
Returns the List of PSMs for the given file
|
int |
getNrPSMs(Integer fileID)
Returns the number of PSMs for the given file.
|
void |
setDecoyFilter(ProteinAccessionFilter decoyFilter)
Sets the filter for decoy identification.
|
void |
setFdrScoreAccession(Integer fileID,
String accession)
Sets the given accession as the accession used for FDR calculation of the
file given by fileID.
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public PSMModeller(Integer nrFiles, boolean oboLookup)
public boolean addPSMforFile(Integer fileID, IntermediatePeptideSpectrumMatch psm)
fileID
- psm
- public int getNrPSMs(Integer fileID)
fileID
- public void setFdrScoreAccession(Integer fileID, String accession)
fileID
- accession
- public String getFdrScoreAccession(Integer fileID)
fileID
- public String getFilesMainScoreAccession(Integer fileID)
fileID
- public List<IntermediatePeptideSpectrumMatch> getFilesPSMs(Integer fileID)
fileID
- public void setDecoyFilter(ProteinAccessionFilter decoyFilter)
public void calculateFDR(Integer fileID)
public void calculateAllFDR()
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