$em
$em : \Doctrine\ORM\EntityManager
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.
fetch(string $sSeqId) : \Amelaye\BioPHP\Domain\Database\Service\ParseSwissprotManager|\Amelaye\BioPHP\Domain\Database\Service\ParseGenbankManager|\Amelaye\BioPHP\Domain\Database\Service\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.
| string | $sSeqId | The id of the seq obj. |
recording(string $sDbName, string $sDbFormat = "GENBANK", mixed ...$sDataFile) : 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
| string | $sDbName | Name of the database |
| string | $sDbFormat | Format of the database |
| mixed | $sDataFile variadic | Files to parse |