public class XTandemIdfileReader extends ExperimentObject implements IdfileReader
Constructor and Description |
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XTandemIdfileReader()
Default constructor for the purpose of instantiation.
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XTandemIdfileReader(File inputFile)
Constructor for an X!Tandem xml result file reader.
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XTandemIdfileReader(File inputFile,
WaitingHandler waitingHandler)
Constructor for an X!Tandem xml result file reader.
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Modifier and Type | Method and Description |
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void |
close()
Closes the file reader.
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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.
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LinkedList<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters 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.
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String |
getExtension()
Returns the extension of the file for which this IdfileReader can be
used.
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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).
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boolean |
hasDeNovoTags()
Returns a boolean indicating whether the file contains de novo results as tags.
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addUrParam, asLong, clearParametersMap, getUrParam, getUrParams, removeUrParam, setUrParams
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, toString, zooActivateRead, zooActivateWrite, zooActivateWrite
public XTandemIdfileReader()
public XTandemIdfileReader(File inputFile) throws FileNotFoundException, IOException
inputFile
- the Mascot dat fileFileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occurspublic XTandemIdfileReader(File inputFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException
inputFile
- the Mascot dat filewaitingHandler
- the waiting handlerFileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occurspublic String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, 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
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occurspublic LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters 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
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occursIllegalArgumentException
public void close() throws IOException
IdfileReader
close
in interface IdfileReader
IOException
- if an IOException occurspublic HashMap<String,ArrayList<String>> getSoftwareVersions()
IdfileReader
getSoftwareVersions
in interface IdfileReader
public boolean hasDeNovoTags()
IdfileReader
hasDeNovoTags
in interface IdfileReader
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