com.compomics.util.experiment.identification.amino_acid_tags.matchers

Class TagMatcher

java.lang.Object

com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher

public class TagMatcher
extends Object

This class matches tags to peptides.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
TagMatcher(ArrayList<String> fixedModifications, ArrayList<String> variableModifications, SequenceMatchingPreferences sequenceMatchingPreferences) Constructor.

Method Summary

Modifier and Type	Method and Description
ArrayList<SequenceSegment>	addSequenceSegmentsToCache(HashMap<Integer,ArrayList<SequenceSegment>> indexCache, String sequence, AminoAcid aminoAcid, Integer currentIndex, Integer aaIndex, boolean nTerminus) Adds the possible new sequence segments generated when appending the given amino acid to the given cache and returns the list of possible segments.
ArrayList<SequenceSegment>	addSequenceSegmentsToCacheSynchronized(HashMap<Integer,ArrayList<SequenceSegment>> indexCache, String sequence, AminoAcid aminoAcid, Integer currentIndex, Integer aaIndex, boolean nTerminus) Adds the possible new sequence segments generated when appending the given amino acid to the given cache and returns the list of possible segments.
void	addVariableModifications(HashMap<String,Double> variableModifications, SequenceSegment noModSegment, ArrayList<SequenceSegment> possibleSegments) Adds the potential sequence segments obtained after adding the given variable modifications on a segment terminus to the given list of possible segments.
HashMap<Integer,ArrayList<Peptide>>	buildPeptides(String sequence, ArrayList<SequenceSegment> nTermPossibleSequences, String seedSequence, ArrayList<SequenceSegment> cTermPossibleSequences, HashMap<Integer,ArrayList<ModificationMatch>> modificationsAtIndex, int mutationsAtIndex) Builds the possible peptides based on the given terminal segments and the seed sequence.
void	clearCache() Clears the cache.
ArrayList<SequenceSegment>	getCombinationsForAminoAcid(String sequence, ArrayList<SequenceSegment> possibleSequences, AminoAcid aminoAcid, Integer currentIndex, Integer aaIndex, boolean nTerminus) Adds the possible new sequence segments generated when appending the given amino acid.
HashMap<Integer,ArrayList<SequenceSegment>>	getIndexCache(String accession, Integer currentIndex, boolean nTerminus) Returns the index cache for the given segment seed, accession and index.
HashMap<Integer,ArrayList<Peptide>>	getPeptideMatches(Tag tag, String accession, String sequence, Integer tagIndex, Integer componentIndex, double massTolerance) Returns the possible peptides which can be created on this sequence indexed by their start index.
void	setSynchronizedIndexing(boolean synchronizedIndexing) Sets whether the indexing of the sequence should be executed in a synchronized method.
void	setUseCache(boolean useCache) Sets whether a cache should be used.
boolean	validateSegments(ArrayList<SequenceSegment> possibleSequences, ArrayList<SequenceSegment> validSequences, double massGap, double massTolerance, String sequence, char sequenceAa, boolean nTerminus) Removes the segments which cannot match the mass gap from the possible sequences and transfers the valid segments to the valid sequences.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TagMatcher

public TagMatcher(ArrayList<String> fixedModifications,
                  ArrayList<String> variableModifications,
                  SequenceMatchingPreferences sequenceMatchingPreferences)

Constructor.

Parameters:

fixedModifications - list of fixed modifications

variableModifications - list of variable modifications

sequenceMatchingPreferences - the sequence matching preferences

Method Detail

getPeptideMatches

public HashMap<Integer,ArrayList<Peptide>> getPeptideMatches(Tag tag,
                                                             String accession,
                                                             String sequence,
                                                             Integer tagIndex,
                                                             Integer componentIndex,
                                                             double massTolerance)

Returns the possible peptides which can be created on this sequence indexed by their start index. Null if not found. Note: PTMs must be in the PTM factory. PTMs are considered at a target amino acid only, longer patterns are not taken into account.

Parameters:

tag - the tag to look for

accession - the accession of the protein

sequence - the sequence where to look for the tag

tagIndex - the index where the tag is located

componentIndex - the index of the component of the tag indexed by tagIndex in the content list

massTolerance - the ms2 tolerance

Returns:

the possible peptides which can be created on this sequence indexed by their start index

buildPeptides

public HashMap<Integer,ArrayList<Peptide>> buildPeptides(String sequence,
                                                         ArrayList<SequenceSegment> nTermPossibleSequences,
                                                         String seedSequence,
                                                         ArrayList<SequenceSegment> cTermPossibleSequences,
                                                         HashMap<Integer,ArrayList<ModificationMatch>> modificationsAtIndex,
                                                         int mutationsAtIndex)

Builds the possible peptides based on the given terminal segments and the seed sequence.

Parameters:

sequence - the protein sequence

nTermPossibleSequences - the N-terminal possible segments

seedSequence - the seed sequence

cTermPossibleSequences - the C-terminal possible segments

modificationsAtIndex - the seed modifications

mutationsAtIndex - the seeds mutations

Returns:

the possible peptides in a map: index on protein > list of peptides

getIndexCache

public HashMap<Integer,ArrayList<SequenceSegment>> getIndexCache(String accession,
                                                                 Integer currentIndex,
                                                                 boolean nTerminus)

Returns the index cache for the given segment seed, accession and index.

Parameters:

accession - the accession of the protein

currentIndex - the index on the protein

nTerminus - boolean indicating whether the N or C terminus cache should be used

Returns:

the index cache

addSequenceSegmentsToCacheSynchronized

public ArrayList<SequenceSegment> addSequenceSegmentsToCacheSynchronized(HashMap<Integer,ArrayList<SequenceSegment>> indexCache,
                                                                         String sequence,
                                                                         AminoAcid aminoAcid,
                                                                         Integer currentIndex,
                                                                         Integer aaIndex,
                                                                         boolean nTerminus)

Adds the possible new sequence segments generated when appending the given amino acid to the given cache and returns the list of possible segments.

Parameters:

indexCache - the cache for this index on the sequence

sequence - the protein sequence

aminoAcid - the amino acid object

currentIndex - the current indexing level on the protein sequence

aaIndex - the amino acid index

nTerminus - indicates whether the sequencing goes toward the N (true) or the C (false) terminus

Returns:

the new possible sequences

addSequenceSegmentsToCache

public ArrayList<SequenceSegment> addSequenceSegmentsToCache(HashMap<Integer,ArrayList<SequenceSegment>> indexCache,
                                                             String sequence,
                                                             AminoAcid aminoAcid,
                                                             Integer currentIndex,
                                                             Integer aaIndex,
                                                             boolean nTerminus)

Adds the possible new sequence segments generated when appending the given amino acid to the given cache and returns the list of possible segments.

Parameters:

indexCache - the cache for this index on the sequence

sequence - the protein sequence

aminoAcid - the amino acid object

currentIndex - the current indexing level on the protein sequence

aaIndex - the amino acid index

nTerminus - indicates whether the sequencing goes toward the N (true) or the C (false) terminus

Returns:

the new possible sequences

getCombinationsForAminoAcid

public ArrayList<SequenceSegment> getCombinationsForAminoAcid(String sequence,
                                                              ArrayList<SequenceSegment> possibleSequences,
                                                              AminoAcid aminoAcid,
                                                              Integer currentIndex,
                                                              Integer aaIndex,
                                                              boolean nTerminus)

Adds the possible new sequence segments generated when appending the given amino acid.

Parameters:

sequence - the protein sequence

possibleSequences - the possible previous sequences

aminoAcid - the amino acid object

currentIndex - the current indexing level on the protein sequence

aaIndex - the amino acid index

nTerminus - indicates whether the sequencing goes toward the N (true) or the C (false) terminus

Returns:

the new possible sequences

validateSegments

public boolean validateSegments(ArrayList<SequenceSegment> possibleSequences,
                                ArrayList<SequenceSegment> validSequences,
                                double massGap,
                                double massTolerance,
                                String sequence,
                                char sequenceAa,
                                boolean nTerminus)

Removes the segments which cannot match the mass gap from the possible sequences and transfers the valid segments to the valid sequences. Returns a boolean indicating whether the sequence iteration should be terminated.

Parameters:

possibleSequences - the possible sequences

validSequences - the valid sequences

massGap - the mass gap

massTolerance - the mass tolerance to use

sequence - the protein sequence

sequenceAa - the amino acid at terminus on the protein sequence

nTerminus - indicates whether the sequencing goes toward the N (true) or the C (false) terminus

Returns:

if true no more sequence segment can be mapped

addVariableModifications

public void addVariableModifications(HashMap<String,Double> variableModifications,
                                     SequenceSegment noModSegment,
                                     ArrayList<SequenceSegment> possibleSegments)

Adds the potential sequence segments obtained after adding the given variable modifications on a segment terminus to the given list of possible segments.

Parameters:

variableModifications - the variable modifications to add

noModSegment - the sequence segment without modification

possibleSegments - the possible segment where to add the modified segments

clearCache

public void clearCache()

Clears the cache.

setUseCache

public void setUseCache(boolean useCache)

Sets whether a cache should be used.

Parameters:

useCache - if true a cache will be used

setSynchronizedIndexing

public void setSynchronizedIndexing(boolean synchronizedIndexing)

Sets whether the indexing of the sequence should be executed in a synchronized method. Use this in case different threads might attempt to sequence the same sequence at the same index at the same time.

Parameters:

synchronizedIndexing - true if the indexing of the sequence should be executed in a synchronized method