Uses of Class
com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent

Packages that use MatrixContent

Package	Description
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.

Uses of MatrixContent in com.compomics.util.experiment.identification.protein_inference.fm_index

Fields in com.compomics.util.experiment.identification.protein_inference.fm_index declared as MatrixContent

Modifier and Type	Field	Description
MatrixContent	MatrixContent.previousContent	Index of the originating entry of a particular cell with the pattern searching matrix.

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type MatrixContent

Modifier and Type	Method	Description
void	FMIndex.mapTagToProteinTermini(MatrixContent cell, double combinationMass, boolean CTermDirection, LinkedList<MatrixContent>[] matrix, int k, int leftIndex, int rightIndex)

Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type MatrixContent

Modifier	Constructor	Description
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int[] numSpecificVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int numVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int ambiguousChar, int tagComponent)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int[] numSpecificVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int numVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch, int length, int numX, int tagComponent, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int ambiguousChar)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX)	Constructor for simple sequence mapping.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, double mass, int length)	Constructor for simple tag mapping.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, double mass, int length, String peptideSequence)	Constructor for simple tag mapping with peptide sequence.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, int length, int[] numSpecificVariants, char variant)	Constructor for sequence with variants.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, int modificationPos, int length, int numVariants, char variant)	Constructor for sequence with variants.
	MatrixContent(MatrixContent foreign)	Copy constructor.

Constructor parameters in com.compomics.util.experiment.identification.protein_inference.fm_index with type arguments of type MatrixContent

Modifier	Constructor	Description
	CacheElement(Double massFirst, String sequence, Double massSecond, ArrayList<MatrixContent> cachedPrimary)	Constructor.