Documentation

DatabaseManager
in package
implements DatabaseInterface uses FormatsTrait

This class does many things like create and/or read a collection of database's index files, initialize certain SeqDB properties, etc.

Syntax: $seqdb = new seqdb($dbname, $dbformat, $file1, $file2, ...); Behavior: if $dbname exists and user gave no specific values for $file1, $file2, ... then seqdb() object USES/OPENS existing database (index files). if $dbname exists and user gave specific values for $file1, $file2, ... then seqdb() object OVERWRITES existing database (index files). if $dbname does not exist, then seqdb() object CREATES new database. even if $file1, $file2, ... are not specified. We provide the create() method to explicitly create a new database. We provide the use() or open() method to explicitly use an existing database.

Tags
author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

DatabaseInterface
Interface RecordingOnLocalDb

Properties

$em  : EntityManager
$sPath  : string

Methods

__construct()  : mixed
DatabaseManager constructor.
fetch()  : ParseSwissprotManager|ParseGenbankManager|ParseEmblManager|bool
Retrieves all data from the specified sequence record and returns them in the form of a Seq object. This method invokes one of several parser methods.
getmin()  : int
Gets the minimum of three (usually numeric) values $x, $y, and $z.
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.
recording()  : mixed
Records the new elements of a collection, reads a collection db exists fileX args ACTION Y Y create Y N use N Y create N N create
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.
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.
line2r()  : array<string|int, mixed>|bool
Copies the lines belonging to a single sequence entry into an array.

Properties

Methods

__construct()

DatabaseManager constructor.

public __construct(EntityManagerInterface $em, string $sPath) : mixed
Parameters
$em : EntityManagerInterface

Entity Manager, for Doctrine

$sPath : string

Path to the data

fetch()

Retrieves all data from the specified sequence record and returns them in the form of a Seq object. This method invokes one of several parser methods.

public fetch(string $sSeqId) : ParseSwissprotManager|ParseGenbankManager|ParseEmblManager|bool
Parameters
$sSeqId : string

The id of the seq obj.

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throws
Exception
Return values
ParseSwissprotManager|ParseGenbankManager|ParseEmblManager|bool

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

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

recording()

Records the new elements of a collection, reads a collection db exists fileX args ACTION Y Y create Y N use N Y create N N create

public recording(string $sDbName[, string $sDbFormat = "GENBANK" ], mixed ...$sDataFile) : mixed
Parameters
$sDbName : string

Name of the database

$sDbFormat : string = "GENBANK"

Format of the database

$sDataFile : mixed

Files to parse

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throws
Exception

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

line2r()

Copies the lines belonging to a single sequence entry into an array.

private line2r(mixed $fpseq, mixed $sDbFormat[, mixed $iLineNo = 0 ]) : array<string|int, mixed>|bool
Parameters
$fpseq : mixed
$sDbFormat : mixed
$iLineNo : mixed = 0
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throws
Exception
Return values
array<string|int, mixed>|bool
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