public interface IdfileReader
Modifier and Type | Method and Description |
---|---|
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)
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) 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 mapsIOException
IllegalArgumentException
SQLException
ClassNotFoundException
InterruptedException
JAXBException
HashMap<String,LinkedList<Peptide>> getPeptidesMap()
HashMap<String,LinkedList<SpectrumMatch>> getTagsMap()
Copyright © 2014. All rights reserved.