public interface IdfileReader
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)
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,
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.
|
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.
|
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.
|
HashMap<String,ArrayList<String>> getSoftwareVersions()
String getExtension()
void close() throws IOException
IOException
LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.IOException
IllegalArgumentException
SQLException
ClassNotFoundException
InterruptedException
JAXBException
LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
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 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
HashMap<String,LinkedList<Peptide>> getPeptidesMap()
HashMap<String,LinkedList<SpectrumMatch>> getTagsMap()
void clearTagsMap()
void clearPeptidesMap()
Copyright © 2014. All rights reserved.