java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
All Implemented Interfaces:
Serializable

public class MatrixContent
extends ExperimentObject
Element for the matrix necessary in pattern search of the FMIndex.
Author:
Dominik Kopczynski
See Also:
Serialized Form
  • Field Details

    • left

      public int left
      Left index.
    • right

      public int right
      Right index.
    • character

      public int character
      Character which was chosen.
    • previousContent

      public MatrixContent previousContent
      Index of the originating entry of a particular cell with the pattern searching matrix.
    • mass

      public double mass
      Current mass.
    • peptideSequence

      public String peptideSequence
      Current peptide sequence.
    • peptideSequenceSearch

      public String peptideSequenceSearch
      Current peptide sequence needed for search.
    • length

      public int length
      Current peptide sequence length.
    • numX

      public int numX
      Current number of contained X's.
    • modification

      public ModificationMatch modification
      Index to the modifications list.
    • modifications

      public ArrayList<ModificationMatch> modifications
      List of all modifications.
    • modificationPos

      public int modificationPos
      List of all modifications.
    • numVariants

      public int numVariants
      List of all modifications.
    • numSpecificVariants

      public int[] numSpecificVariants
      The specific variants. (0) deletion, (1) insertion, (2) substitution.
    • variant

      public char variant
      Type of edit operation, either deletion 'd', substitution 's' or insertion 'i'.
    • allVariants

      public String allVariants
      Current storing of all variant operations.
    • ambiguousChar

      public int ambiguousChar
      If original character was B, J, X, Z.
    • tagComponent

      public int tagComponent
      Information about the component where the X belongs to.
    • allXcomponents

      public ArrayList<int[]> allXcomponents
      Information about all component where the Xs belong to.
    • XMassDiff

      public double XMassDiff
      The X mass difference,
    • allXMassDiffs

      public HashMap<Integer,​Double> allXMassDiffs
      The all X mass differences.
    • numPTMs

      public int numPTMs
      The number of PTMs.
  • Constructor Details

    • MatrixContent

      public MatrixContent()
      Empty default constructor.
    • MatrixContent

      public MatrixContent​(int right)
      Constructor almost empty.
      Parameters:
      right - right index boundary
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, int numX)
      Constructor for simple sequence mapping.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      numX - number of current X amino acids
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, int numX, double mass, int length)
      Constructor for simple tag mapping.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      numX - number of current X amino acids
      mass - current mass
      length - current peptide length
    • MatrixContent

      public 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.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      numX - number of current X amino acids
      mass - current mass
      length - current peptide length
      peptideSequence - peptide sequence
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, int numX, int modificationPos, int length, int numVariants, char variant)
      Constructor for sequence with variants.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      numX - number of current X amino acids
      modificationPos - modification positions
      length - length of the current peptide
      numVariants - number of edit operations
      variant - type of edit operation
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, int numX, int length, int[] numSpecificVariants, char variant)
      Constructor for sequence with variants.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      numX - number of current X amino acids
      length - length of the current peptide
      numSpecificVariants - number of the specific edit operations
      variant - type of edit operation
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int ambiguousChar, int tagComponent)
      Constructor.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      length - current peptide length
      numX - number of current X amino acids
      modifictationPos - index to modification list for ptm
      ambiguousChar - ambiguous character
      tagComponent - the tag component index
    • MatrixContent

      public 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.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      peptideSequence - intermediate peptide sequence
      peptideSequenceSearch - intermediate peptide sequence for search
      length - current peptide length
      numX - number of current X amino acids
      modification - index to modification list
      modifications - intermediate list of modifications
      modifictationPos - index to modification list for ptm
      ambiguousChar - ambiguous character
    • MatrixContent

      public 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.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      peptideSequence - intermediate peptide sequence
      peptideSequenceSearch - intermediate peptide sequence for search
      length - current peptide length
      numX - number of current X amino acids
      tagComponent - the tag component index
      modification - index to modification list
      modifications - intermediate list of modifications
      modifictationPos - index to modification list for PTM
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int numVariants, char variant, String allVariants)
      Constructor.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      length - current peptide length
      numX - number of current X amino acids
      modifictationPos - index to modification list for PTM
      numVariants - number of edit operations
      variant - type of variant
      allVariants - all variants
    • MatrixContent

      public MatrixContent​(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int[] numSpecificVariants, char variant, String allVariants)
      Constructor.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      length - current peptide length
      numX - number of current X amino acids
      modifictationPos - index to modification list for PTM
      numSpecificVariants - number of the specific edit operations
      variant - type of variant
      allVariants - all variants
    • MatrixContent

      public 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.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      peptideSequence - intermediate peptide sequence
      length - current peptide length
      numX - number of current X amino acids
      modification - index to modification list
      modifications - intermediate list of modifications
      modifictationPos - index to modification list for PTM
      numVariants - number of edit operations
      variant - type of variant
      allVariants - all variants
    • MatrixContent

      public 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.
      Parameters:
      left - left index boundary
      right - right index boundary
      character - current character stored
      previousContent - previous matrix content
      mass - current mass
      peptideSequence - intermediate peptide sequence
      length - current peptide length
      numX - number of current X amino acids
      modification - index to modification list
      modifications - intermediate list of modifications
      modifictationPos - index to modification list for PTM
      numSpecificVariants - number of the specific edit operations
      variant - type of variant
      allVariants - all variants
    • MatrixContent

      public MatrixContent​(MatrixContent foreign)
      Copy constructor.
      Parameters:
      foreign - foreign matrix content instance