Documentation

SequenceMatchManager
in package
implements SequenceMatchInterface uses FormatsTrait

Class SequenceMatchManager - This class represents the results of performing sequence analysis and matching on two or more sequences.

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author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

SequenceMatchInterface
Class SequenceMatchManager - This class represents the results of performing sequence analysis and matching on two or more sequences.

Properties

$subMatrix  : SubMatrix

Methods

compareLetter()  : string
Compares two letters $let1 and $let2 and returns another letter indicating if the two were exact matches, partial matches, or non-matches.
getmin()  : int
Gets the minimum of three (usually numeric) values $x, $y, and $z.
hamdist()  : int
Computes the Hamming Distance between two strings or Seq objects of equal length. For more information, consult the technical reference.
intrim()  : mixed
Removes "internal spaces" (as opposed to leading and trailing spaces) from a string.
left()  : bool|string
Returns the first $numchars characters of a string.
levdist()  : int
Computes the Levenshtein Distance between two sequences with equal/unequal lengths. You can pass custom values for cost of insertion, replacement, and deletion. If you don't pass any, they are assumed to be 1.
match()  : string
This method accepts two sequence strings (not objects) of equal length, and returns a sequence match result string, according to the following rules: If there is an exact match, return the amino acid symbol.
partialMatch()  : bool
We abbreviate substitution matrix to "submatrix". Each element in a submatrix is an array of symbols that are considered "partial matches" of each other.
rem_right()  : bool|string
Removes $charcount characters from the right (end) of a string.
right()  : bool|string
Returns the substring beginning at $numchars characters from the right end of a string.
setSubMatrix()  : mixed
trim_element()  : mixed
trim_element() removes leading and trailing spaces from a string. In conjunction with the array_walk() function, it removes spaces from each element of an array.
xlevdist()  : int
Extended version of levdist() which accepts strings with length greater than 255 but not to exceed 1024 .

Properties

Methods

compareLetter()

Compares two letters $let1 and $let2 and returns another letter indicating if the two were exact matches, partial matches, or non-matches.

public compareLetter(string $sLetter1, string $sLetter2[, array<string|int, mixed> $aMatrix = null ][, string $sEqual = null ][, string $sPartial = "+" ][, string $sNomatch = "." ]) : string
Parameters
$sLetter1 : string

The first amino acid residue symbol to match.

$sLetter2 : string

The second amino acid residue symbol to match.

$aMatrix : array<string|int, mixed> = null

The substitution matrix to use in matching.

$sEqual : string = null

The character symbol to return if $let1 and $let2 are exact matches.

$sPartial : string = "+"

The character symbol to return if $let1 and $let2 are partial matches.

$sNomatch : string = "."

The character symbol to return if $let1 and $let2 are totally mismatched.

Tags
throws
Exception
Return values
string —

A character symbol which indicates if the two residues are exact, partial, or negative matches.

getmin()

Gets the minimum of three (usually numeric) values $x, $y, and $z.

public getmin(int $x, int $y, int $z) : int

For now, this can't handle situations when one or more arguments is FALSE.

Parameters
$x : int
$y : int
$z : int
Return values
int

hamdist()

Computes the Hamming Distance between two strings or Seq objects of equal length. For more information, consult the technical reference.

public hamdist(string $sSequence1, string $sSequence2) : int
Parameters
$sSequence1 : string

The first sequence

$sSequence2 : string

The second sequence

Tags
throws
Exception
Return values
int —

The hamming distance between the two strings or sequences, defined to be the number of "mismatching" characters found in corresponding positions in the two strings.

intrim()

Removes "internal spaces" (as opposed to leading and trailing spaces) from a string.

public intrim(string $string) : mixed
Parameters
$string : string

left()

Returns the first $numchars characters of a string.

public left(string $str, int $numchars) : bool|string
Parameters
$str : string
$numchars : int
Return values
bool|string

levdist()

Computes the Levenshtein Distance between two sequences with equal/unequal lengths. You can pass custom values for cost of insertion, replacement, and deletion. If you don't pass any, they are assumed to be 1.

public levdist(string $sSequence1, string $sSequence2[, int $iCostInser = 1 ][, int $iCostRepl = 1 ][, int $iCostDel = 1 ]) : int

For more information, see technical reference.

Parameters
$sSequence1 : string

The first sequence, with a length not exceeding 255 symbols.

$sSequence2 : string

The second string or sequence, with a length not exceeding 255 symbols.

$iCostInser : int = 1

The cost or weight of an insertion operation.

$iCostRepl : int = 1

The cost or weight of a replacement operation.

$iCostDel : int = 1

The cost or weight of a deletion operation.

Tags
throws
Exception
Return values
int —

The Levenshtein Distance between two strings, defined to be the number of insertion, deletion, or replacement operations that must be performed on the strings before they can become identical.

match()

This method accepts two sequence strings (not objects) of equal length, and returns a sequence match result string, according to the following rules: If there is an exact match, return the amino acid symbol.

public match(string $sSequence1, string $sSequence2[, array<string|int, mixed> $aMatrix = null ][, string $sEqual = null ][, string $sPartial = "+" ][, string $sNonmatch = "." ]) : string

If there is a partial match, return a plus sign. If there is no match, return a whitespace character.

Parameters
$sSequence1 : string

The first of two sequences being compared.

$sSequence2 : string

The second of two sequences being compared.

$aMatrix : array<string|int, mixed> = null

An array specifying valid symbol substitution and equivalence rules.

$sEqual : string = null

The symbol to output if the symbol in the first sequence is exactly the same as the corresponding symbol in the second sequence.

$sPartial : string = "+"

The symbol to output if the symbol in the first sequence is equivalent but not identical to the corresponding symbol in the second sequence.

$sNonmatch : string = "."

The symbol to output if the symbol in the first sequence is neither identical nor equivalent to the corresponding symbol in the second sequence.

Tags
throws
Exception
Return values
string —

A string which indicates where exact, partial and no matches occur between the first and second sequences being compared.

partialMatch()

We abbreviate substitution matrix to "submatrix". Each element in a submatrix is an array of symbols that are considered "partial matches" of each other.

public partialMatch(string $sLet1, string $sLet2, array<string|int, mixed> $aMatrix) : bool

Default submatrix: ( ('G','A','V','L','I'), ('S','T'), ('N','Q'), ('F','Y','W'), ('C', 'M'), ('P'), ('D','E'), ('K','R','H'), ('*'), ('X') )

  1. Check if both $iLet1 and $let2 appear in the first element (G,A,V,L,I) of the substitution matrix.
  2. If they are, you've found a "hit", and $let1 and $let2 are partial matches. Return a TRUE value. If they are not, then go to the next element in the substitution matrix. Repeat steps 1 and 2 until you reach a submatrix element where both $let1 and $let2 appear, or until the last element in the submatrix has been checked.
  3. If you reach the last submatrix element without a "hit", return a FALSE value.
Parameters
$sLet1 : string

The first amino acid residue.

$sLet2 : string

The second amino acid residue.

$aMatrix : array<string|int, mixed>

The substitution matrix to use for determining partial matches.

Return values
bool —

TRUE if the two symbols belong to the same chemical group, FALSE otherwise.

rem_right()

Removes $charcount characters from the right (end) of a string.

public rem_right(string $str[, int $charcount = 1 ]) : bool|string
Parameters
$str : string
$charcount : int = 1
Return values
bool|string

right()

Returns the substring beginning at $numchars characters from the right end of a string.

public right(string $str, int $numchars) : bool|string
Parameters
$str : string
$numchars : int
Return values
bool|string

trim_element()

trim_element() removes leading and trailing spaces from a string. In conjunction with the array_walk() function, it removes spaces from each element of an array.

public trim_element(mixed &$value, mixed $key) : mixed
Parameters
$value : mixed
$key : mixed

xlevdist()

Extended version of levdist() which accepts strings with length greater than 255 but not to exceed 1024 .

public xlevdist(string $sSequence1, string $sSequence2) : int

The only drawback to xlevdist is that the cost of insertion, deletion, and replacement is fixed to 1. I have yet to find a way to allow custom values for these.

Parameters
$sSequence1 : string

The first sequence, with a length not exceeding 1024 symbols.

$sSequence2 : string

The second string or sequence, with a length not exceeding 1024 symbols.

Tags
throws
Exception
Return values
int —

The Levenshtein Distance between two strings, as defined in levdist().

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