public class MsAmandaIdfileReader extends ExperimentObject implements IdfileReader
Constructor and Description |
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MsAmandaIdfileReader()
Default constructor for the purpose of instantiation.
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MsAmandaIdfileReader(File msAmandaCsvFile)
Constructor for an MS Amanda csv result file reader.
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MsAmandaIdfileReader(File msAmandaCsvFile,
WaitingHandler waitingHandler)
Constructor for an MS Amanda csv 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)
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,
SequenceMatchingPreferences sequenceMatchingPreferences)
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,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.
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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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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.
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addUrParam, getParameterKey, getUrParam
public MsAmandaIdfileReader()
public MsAmandaIdfileReader(File msAmandaCsvFile) throws FileNotFoundException, IOException
msAmandaCsvFile
- FileNotFoundException
IOException
public MsAmandaIdfileReader(File msAmandaCsvFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException
msAmandaCsvFile
- waitingHandler
- FileNotFoundException
IOException
public String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler) 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.IOException
IllegalArgumentException
SQLException
ClassNotFoundException
InterruptedException
JAXBException
public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SequenceMatchingPreferences sequenceMatchingPreferences) 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.sequenceMatchingPreferences
- the sequence matching preferences to
use for the creation of the secondary mapsIOException
IllegalArgumentException
SQLException
ClassNotFoundException
InterruptedException
JAXBException
public void close() throws IOException
IdfileReader
close
in interface IdfileReader
IOException
public 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
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