public class PepNovoIdfileReader extends ExperimentObject implements IdfileReader
Modifier and Type | Field and Description |
---|---|
double |
cTermCorrection
The mass to add to the C-terminal gap so that is corresponds to a peptide
fragment.
|
double |
nTermCorrection
The mass to add to the N-terminal gap so that is corresponds to a peptide
fragment.
|
static String |
tableHeader
The standard format.
|
Constructor and Description |
---|
PepNovoIdfileReader()
Default constructor for the purpose of instantiation.
|
PepNovoIdfileReader(File identificationFile)
Constructor, initiate the parser.
|
PepNovoIdfileReader(File identificationFile,
WaitingHandler waitingHandler)
Constructor, initiate the parser.
|
Modifier and Type | Method and Description |
---|---|
void |
close()
Closes the file reader.
|
HashSet<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler)
This methods retrieves all the identifications from an identification
file as a list of spectrum matches It is very important to close the file
reader after creation.
|
String |
getExtension()
This method should return the extension of the file for which this
IdfileReader can be used.
|
String |
getMgfFileName()
Returns the spectrum file name.
|
static String |
getPTM(PepnovoParameters pepnovoParameters,
String pepNovoModification)
Get a PTM.
|
String |
getSoftwareVersion()
Returns the name and version of the software used to generate the
identification file, e.g., Mascot 2.3.0 or X! Tandem Sledgehammer
(2013.09.01.1).
|
addUrParam, getParameterKey, getUrParam
public static final String tableHeader
public final double cTermCorrection
public final double nTermCorrection
public PepNovoIdfileReader()
public PepNovoIdfileReader(File identificationFile) throws FileNotFoundException, IOException
identificationFile
- the identification file to parseFileNotFoundException
- exception thrown whenever the provided file
was not foundIOException
- exception thrown whenever an error occurred while
reading the filepublic PepNovoIdfileReader(File identificationFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException
identificationFile
- the identification file to parsewaitingHandler
- a waiting handler providing progress feedback to
the userFileNotFoundException
- exception thrown whenever the provided file
was not foundIOException
- exception thrown whenever an error occurred while
reading the filepublic HashSet<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, Exception
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.IOException
- exception thrown whenever an error occurred while
reading the fileIllegalArgumentException
- exception thrown whenever an error
occurred while parsing the fileException
- exception thrown whenever an error occurred while
working with the filepublic String getMgfFileName()
public String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public void close() throws IOException
IdfileReader
close
in interface IdfileReader
IOException
public static String getPTM(PepnovoParameters pepnovoParameters, String pepNovoModification)
pepnovoParameters
- the PepNovo parameterspepNovoModification
- the PepNovo modificationpublic String getSoftwareVersion()
IdfileReader
getSoftwareVersion
in interface IdfileReader
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