$sequenceManager
$sequenceManager : \Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager
Dependency injection for the Sequences Services
Represents the result of an alignment performed by various third-party software such as ClustalW. The alignment is usually found in a file that uses a particular format. Right now, my code supports only FASTA and CLUSTAL formats.
Properties and methods allow users to perform post-alignment operations, manipulations, etc.
$sequenceManager : \Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager
Dependency injection for the Sequences Services
$aAlphabet : array
Letters of the alphabet
$iLength : int
The length of the longest sequence in the alignment set.
$iGapCount : int
The total number of gaps ("-") in all sequences in the alignment set.
$bFlush : bool
A boolean or logical value: TRUE if all the sequences in the alignment have the same length, FALSE otherwise.
$sFilename : string
Filename of the original parsed file.
$sFormat : string
Format of the original parsed file.
sortAlpha(string $sOption = "ASC") : mixed
Rearranges the sequences in an alignment set alphabetically by their sequence id.
In addition, you can specify if you wish it be in ascending or descending order via $sOption. The sOption accepts either "ASC" or "DESC" in whatever case (uppercase, lowercase, mixed case). This determines the sort order of the alignment set.
| string | $sOption | ASCendant or DESCendant |
charAtRes(int $iSeqIdx, int $iRes) : bool
Returns the character found at a given residue number in a given sequence.
| int | $iSeqIdx | Index of the sequence in the array |
| int | $iRes | The residue number of the character we wish to get or extract |
| string A single character representing an amino acid residue or a "gap".
substrBwRes(int $iSeqIdx, int $iResStart, int $iResEnd) : string
Gets the substring between two residues in a sequence that is part of an alignment set.
| int | $iSeqIdx | Index of the sequence in the array |
| int | $iResStart | Start of the subsequence |
| int | $iResEnd | End of the subsequence |
| boolean A substring within the specified sequence.
colToRes(int $iSeqIdx, int $iCol) : bool|string
Converts a column number to a residue number in a sequence that is part of an alignment set.
| int | $iSeqIdx | Index number of the desired sequence within the alignment set. |
| int | $iCol | The column number which we want to convert to a residue number. |
An integer representing the residue number corresponding to the given column number.
resToCol(int $iSeqIdx, int $iRes) : bool|int
Converts a residue number to a column number in a sequence in an alignment set.
| int | $iSeqIdx | The index number of the desired sequence in the alignment set. |
| int | $iRes | The residue number we wish to convert into a column number. |
An integer representing the column number corresponding to the given residue number.
subalign(int $iStart, int $iEnd) : mixed
Creates a new alignment set from a series of contiguous/consecutive sequences.
| int | $iStart | The index number of the first sequence to include in the new SeqAlign object. |
| int | $iEnd | The index number of the last sequence to include in the new SeqAlign object. |
resVar(int $iThreshold = 100) : array
Determines the index position of both variant and invariant residues according to a given "percentage threshold" similar to that in the consensus() method.
| int | $iThreshold | a number between 0 to 100, indicating the percentage threshold below which the current index position is considered variant, and on or above which the current index position is considered invariant. If omitted, this is set to 100 by default. |
consensus(int $iThreshold = 100) : string
Returns the consensus string for an alignment set. See technical reference for details.
| int | $iThreshold | A number between 0 to 100, indicating the percentage threshold before (or below which) the unknown character "?" is used in a particular position or column in the consensus string. If omitted, this is set to 100 by default. |
The consensus string formed according to the given threshold.
addSequence(\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence $oSequence) : int
Adds a sequence to an alignment set. It does not perform any sequence alignment.
| \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence | $oSequence | The object to be added to the alignment set. |
The number of sequences in the alignment set after the call.
validationRes(int $iSeqIdx, int $iRes, int $iNonGapCount, int $iLength, string $sContext) : bool|int|string
Fetches something found at a given residue number in a given sequence
| int | $iSeqIdx | The index number of the desired sequence in the alignment set. |
| int | $iRes | The residue number we wish to convert. |
| int | $iNonGapCount | Number of non-gap characters |
| int | $iLength | Length of a sequence |
| string | $sContext | The original function calling |