public class PepNovoIdfileReader extends ExperimentObject implements IdfileReader
Modifier and Type | Field and Description |
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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 |
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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 |
clearPeptidesMap()
Clears the peptides map.
|
void |
clearTagsMap()
Clears the tags map.
|
void |
close()
Closes the file reader.
|
LinkedList<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters)
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.
|
LinkedList<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations)
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()
Returns the extension of the file for which this IdfileReader can be
used.
|
String |
getMgfFileName()
Returns the spectrum file name.
|
HashMap<String,LinkedList<Peptide>> |
getPeptidesMap()
Returns a map of all the peptides found in this file in a map indexed by
the beginning of the peptide sequence.
|
static String |
getPTM(PepnovoParameters pepnovoParameters,
String pepNovoModification)
Get a PTM.
|
HashMap<String,ArrayList<String>> |
getSoftwareVersions()
Returns the names and versions of the software used to generate the
identification file in a map, e.g., Mascot > (2.2 and 2.3) and X!Tandem
> Sledgehammer (2013.09.01.1).
|
HashMap<String,LinkedList<SpectrumMatch>> |
getTagsMap()
Returns a map of all simple tags found in this file indexed by the
beginning of the amino acid sequence.
|
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 LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.searchParameters
- the search parametersIOException
IllegalArgumentException
SQLException
ClassNotFoundException
InterruptedException
JAXBException
public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.searchParameters
- the search parameterssequenceMatchingPreferences
- the sequence matching preferences to
use for the creation of the secondary mapsexpandAaCombinations
- if true, a peptide assumption (not
implemented for tag assumptions) will be created for all possible amino
acid combination for peptide sequences containing an ambiguity like an XIOException
IllegalArgumentException
SQLException
ClassNotFoundException
InterruptedException
JAXBException
public 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 HashMap<String,ArrayList<String>> getSoftwareVersions()
IdfileReader
getSoftwareVersions
in interface IdfileReader
public HashMap<String,LinkedList<Peptide>> getPeptidesMap()
IdfileReader
getPeptidesMap
in interface IdfileReader
public HashMap<String,LinkedList<SpectrumMatch>> getTagsMap()
IdfileReader
getTagsMap
in interface IdfileReader
public void clearTagsMap()
IdfileReader
clearTagsMap
in interface IdfileReader
public void clearPeptidesMap()
IdfileReader
clearPeptidesMap
in interface IdfileReader
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