Class MatrixContent
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
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Field Summary
Fields Modifier and Type Field Description String
allVariants
Current storing of all variant operations.ArrayList<int[]>
allXcomponents
Information about all component where the Xs belong to.HashMap<Integer,Double>
allXMassDiffs
The all X mass differences.int
ambiguousChar
If original character was B, J, X, Z.int
character
Character which was chosen.int
left
Left index.int
length
Current peptide sequence length.double
mass
Current mass.ModificationMatch
modification
Index to the modifications list.int
modificationPos
List of all modifications.ArrayList<ModificationMatch>
modifications
List of all modifications.int
numPTMs
The number of PTMs.int[]
numSpecificVariants
The specific variants.int
numVariants
List of all modifications.int
numX
Current number of contained X's.String
peptideSequence
Current peptide sequence.String
peptideSequenceSearch
Current peptide sequence needed for search.MatrixContent
previousContent
Index of the originating entry of a particular cell with the pattern searching matrix.int
right
Right index.int
tagComponent
Information about the component where the X belongs to.char
variant
Type of edit operation, either deletion 'd', substitution 's' or insertion 'i'.double
XMassDiff
The X mass difference, -
Constructor Summary
Constructors Constructor Description MatrixContent()
Empty default constructor.MatrixContent(int right)
Constructor almost empty.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. -
Method Summary
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Field Details
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left
public int leftLeft index. -
right
public int rightRight index. -
character
public int characterCharacter which was chosen. -
previousContent
Index of the originating entry of a particular cell with the pattern searching matrix. -
mass
public double massCurrent mass. -
peptideSequence
Current peptide sequence. -
peptideSequenceSearch
Current peptide sequence needed for search. -
length
public int lengthCurrent peptide sequence length. -
numX
public int numXCurrent number of contained X's. -
modification
Index to the modifications list. -
modifications
List of all modifications. -
modificationPos
public int modificationPosList of all modifications. -
numVariants
public int numVariantsList of all modifications. -
numSpecificVariants
public int[] numSpecificVariantsThe specific variants. (0) deletion, (1) insertion, (2) substitution. -
variant
public char variantType of edit operation, either deletion 'd', substitution 's' or insertion 'i'. -
allVariants
Current storing of all variant operations. -
ambiguousChar
public int ambiguousCharIf original character was B, J, X, Z. -
tagComponent
public int tagComponentInformation about the component where the X belongs to. -
allXcomponents
Information about all component where the Xs belong to. -
XMassDiff
public double XMassDiffThe X mass difference, -
allXMassDiffs
The all X mass differences. -
numPTMs
public int numPTMsThe number of PTMs.
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Constructor Details
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MatrixContent
public MatrixContent()Empty default constructor. -
MatrixContent
public MatrixContent(int right)Constructor almost empty.- Parameters:
right
- right index boundary
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MatrixContent
Constructor for simple sequence mapping.- Parameters:
left
- left index boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acids
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidsmass
- current masslength
- current peptide length
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidsmass
- current masslength
- current peptide lengthpeptideSequence
- peptide sequence
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidsmodificationPos
- modification positionslength
- length of the current peptidenumVariants
- number of edit operationsvariant
- type of edit operation
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidslength
- length of the current peptidenumSpecificVariants
- number of the specific edit operationsvariant
- type of edit operation
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masslength
- current peptide lengthnumX
- number of current X amino acidsmodifictationPos
- index to modification list for ptmambiguousChar
- ambiguous charactertagComponent
- the tag component index
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masspeptideSequence
- intermediate peptide sequencepeptideSequenceSearch
- intermediate peptide sequence for searchlength
- current peptide lengthnumX
- number of current X amino acidsmodification
- index to modification listmodifications
- intermediate list of modificationsmodifictationPos
- index to modification list for ptmambiguousChar
- ambiguous character
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masspeptideSequence
- intermediate peptide sequencepeptideSequenceSearch
- intermediate peptide sequence for searchlength
- current peptide lengthnumX
- number of current X amino acidstagComponent
- the tag component indexmodification
- index to modification listmodifications
- intermediate list of modificationsmodifictationPos
- index to modification list for PTM
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masslength
- current peptide lengthnumX
- number of current X amino acidsmodifictationPos
- index to modification list for PTMnumVariants
- number of edit operationsvariant
- type of variantallVariants
- all variants
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masslength
- current peptide lengthnumX
- number of current X amino acidsmodifictationPos
- index to modification list for PTMnumSpecificVariants
- number of the specific edit operationsvariant
- type of variantallVariants
- all variants
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masspeptideSequence
- intermediate peptide sequencelength
- current peptide lengthnumX
- number of current X amino acidsmodification
- index to modification listmodifications
- intermediate list of modificationsmodifictationPos
- index to modification list for PTMnumVariants
- number of edit operationsvariant
- type of variantallVariants
- all variants
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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 boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentmass
- current masspeptideSequence
- intermediate peptide sequencelength
- current peptide lengthnumX
- number of current X amino acidsmodification
- index to modification listmodifications
- intermediate list of modificationsmodifictationPos
- index to modification list for PTMnumSpecificVariants
- number of the specific edit operationsvariant
- type of variantallVariants
- all variants
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MatrixContent
Copy constructor.- Parameters:
foreign
- foreign matrix content instance
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