Uses of Class
com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment

Packages that use SequenceSegment

Package	Description
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.amino_acid_tags.matchers	Tag matching classes.

Uses of SequenceSegment in com.compomics.util.experiment.identification.amino_acid_tags

Methods in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type SequenceSegment

Modifier and Type	Method and Description
void	SequenceSegment.appendTerminus(SequenceSegment sequenceSegment) Appends a sequence segment to the terminus of sequencing.

Constructors in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type SequenceSegment

Constructor and Description
SequenceSegment(SequenceSegment sequenceSegment) Constructor.

Uses of SequenceSegment in com.compomics.util.experiment.identification.amino_acid_tags.matchers

Methods in com.compomics.util.experiment.identification.amino_acid_tags.matchers that return types with arguments of type SequenceSegment

Modifier and Type	Method and Description
ArrayList<SequenceSegment>	TagMatcher.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>	TagMatcher.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.
ArrayList<SequenceSegment>	TagMatcher.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>>	TagMatcher.getIndexCache(String accession, Integer currentIndex, boolean nTerminus) Returns the index cache for the given segment seed, accession and index.

Methods in com.compomics.util.experiment.identification.amino_acid_tags.matchers with parameters of type SequenceSegment

Modifier and Type	Method and Description
void	TagMatcher.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.

Method parameters in com.compomics.util.experiment.identification.amino_acid_tags.matchers with type arguments of type SequenceSegment

Modifier and Type	Method and Description
ArrayList<SequenceSegment>	TagMatcher.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>	TagMatcher.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	TagMatcher.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>>	TagMatcher.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.
HashMap<Integer,ArrayList<Peptide>>	TagMatcher.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.
ArrayList<SequenceSegment>	TagMatcher.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.
boolean	TagMatcher.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.
boolean	TagMatcher.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.