public class MatrixContent extends Object
Modifier and Type | Field and 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[] |
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 and Description |
---|
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 length,
int numVariants,
char variant)
Constructor for sequence with variants.
|
MatrixContent(MatrixContent foreign)
Copy constructor.
|
public int left
public int right
public int character
public MatrixContent previousContent
public double mass
public String peptideSequence
public String peptideSequenceSearch
public int length
public int numX
public ModificationMatch modification
public ArrayList<ModificationMatch> modifications
public int modificationPos
public int numVariants
public int[] numSpecificVariants
public char variant
public String allVariants
public int ambiguousChar
public int tagComponent
public ArrayList<int[]> allXcomponents
public double XMassDiff
public MatrixContent(int right)
right
- right index boundarypublic MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX)
left
- left index boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidspublic MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, double mass, int length)
left
- left index boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidsmass
- current masslength
- current peptide lengthpublic MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, double mass, int length, String peptideSequence)
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 sequencepublic MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, int length, int numVariants, char variant)
left
- left index boundaryright
- right index boundarycharacter
- current character storedpreviousContent
- previous matrix contentnumX
- number of current X amino acidslength
- length of the current peptidenumVariants
- number of edit operationsvariant
- type of edit operationpublic MatrixContent(int left, int right, int character, MatrixContent previousContent, int numX, int length, int[] numSpecificVariants, char variant)
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 operationpublic MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int ambiguousChar, int tagComponent)
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 indexpublic 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)
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 characterpublic 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)
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 PTMpublic MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int numVariants, char variant, String allVariants)
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 variantspublic MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, int length, int numX, int modifictationPos, int[] numSpecificVariants, char variant, String allVariants)
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 variantspublic 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)
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 variantspublic 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)
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 variantspublic MatrixContent(MatrixContent foreign)
foreign
- foreign matrix content instanceCopyright © 2019. All rights reserved.