\App\Domain\Sequence\ServiceSequenceMatchManager

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

Summary

Methods

Properties

Constants

left()
right()
intrim()
getmin()
rem_right()
trim_element()
setSubMatrix()
compareLetter()
hamdist()
levdist()
xlevdist()
match()
partialMatch()

No public properties found

No constants found

No protected methods found

No protected properties found

N/A

No private methods found

$subMatrix

N/A

File: Domain/Sequence/Service/SequenceMatchManager.php
Package: Sequence\Service
Class hierarchy: \App\Domain\Sequence\Service\SequenceMatchManager
Implements: \App\Domain\Sequence\Interfaces\SequenceMatchInterface
Uses traits: \App\Domain\Sequence\Traits\FormatsTrait

Properties

$subMatrix

$subMatrix : \App\Domain\Sequence\Entity\SubMatrix

Type

\App\Domain\Sequence\Entity\SubMatrix

Methods

left()

left(string  $str, integer  $numchars) : boolean|string

Returns the first $numchars characters of a string.

Parameters

string	$str
integer	$numchars

Returns

boolean|string

right()

right(string  $str, integer  $numchars) : boolean|string

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

Parameters

string	$str
integer	$numchars

Returns

boolean|string

intrim()

intrim(string  $string) : mixed

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

Parameters

string

$string

Returns

mixed

getmin()

getmin(integer  $x, integer  $y, integer  $z) : integer

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

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

Parameters

integer	$x
integer	$y
integer	$z

Returns

integer

rem_right()

rem_right(string  $str, integer  $charcount = 1) : boolean|string

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

Parameters

string	$str
integer	$charcount

Returns

boolean|string

trim_element()

trim_element(  $value,   $key)

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.

Parameters

	$value
	$key

setSubMatrix()

setSubMatrix(\App\Domain\Sequence\Entity\SubMatrix  $subMatrix)

Parameters

\App\Domain\Sequence\Entity\SubMatrix

$subMatrix

compareLetter()

compareLetter(string  $sLetter1, string  $sLetter2, array  $aMatrix = null, string  $sEqual = null, string  $sPartial = "+", string  $sNomatch = ".") : string

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

Parameters

string	$sLetter1	The first amino acid residue symbol to match.
string	$sLetter2	The second amino acid residue symbol to match.
array	$aMatrix	The substitution matrix to use in matching.
string	$sEqual	The character symbol to return if $let1 and $let2 are exact matches.
string	$sPartial	The character symbol to return if $let1 and $let2 are partial matches.
string	$sNomatch	The character symbol to return if $let1 and $let2 are totally mismatched.

Throws

\Exception

Returns

string —

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

hamdist()

hamdist(string  $sSequence1, string  $sSequence2) : integer

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

Parameters

string	$sSequence1	The first sequence
string	$sSequence2	The second sequence

Throws

\Exception

Returns

integer —

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.

levdist()

levdist(string  $sSequence1, string  $sSequence2, integer  $iCostInser = 1, integer  $iCostRepl = 1, integer  $iCostDel = 1) : integer

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.

For more information, see technical reference.

Parameters

string	$sSequence1	The first sequence, with a length not exceeding 255 symbols.
string	$sSequence2	The second string or sequence, with a length not exceeding 255 symbols.
integer	$iCostInser	The cost or weight of an insertion operation.
integer	$iCostRepl	The cost or weight of a replacement operation.
integer	$iCostDel	The cost or weight of a deletion operation.

Throws

\Exception

Returns

integer —

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.

xlevdist()

xlevdist(string  $sSequence1, string  $sSequence2) : integer

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

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

string	$sSequence1	The first sequence, with a length not exceeding 1024 symbols.
string	$sSequence2	The second string or sequence, with a length not exceeding 1024 symbols.

Throws

\Exception

Returns

integer —

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

match()

match(string  $sSequence1, string  $sSequence2, array  $aMatrix = null, string  $sEqual = null, string  $sPartial = "+", string  $sNonmatch = ".") : 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.

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

Parameters

string	$sSequence1	The first of two sequences being compared.
string	$sSequence2	The second of two sequences being compared.
array	$aMatrix	An array specifying valid symbol substitution and equivalence rules.
string	$sEqual	The symbol to output if the symbol in the first sequence is exactly the same as the corresponding symbol in the second sequence.
string	$sPartial	The symbol to output if the symbol in the first sequence is equivalent but not identical to the corresponding symbol in the second sequence.
string	$sNonmatch	The symbol to output if the symbol in the first sequence is neither identical nor equivalent to the corresponding symbol in the second sequence.

Throws

\Exception

Returns

string —

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

partialMatch()

partialMatch(string  $sLet1, string  $sLet2, array  $aMatrix) : boolean

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

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

string	$sLet1	The first amino acid residue.
string	$sLet2	The second amino acid residue.
array	$aMatrix	The substitution matrix to use for determining partial matches.

Returns

boolean —

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