$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, mixed $sDataPath) : \Amelaye\BioPHP\Domain\Database\Service\ParseSwissprotManager
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. |
mixed | $sDataPath | The path to the data file. |
| ParseGenbankManager | bool
getEntryid(array $flines, string $linestr, string $dbformat) : string
Gets the primary accession number of the sequence entry which we are currently processing. This uniquely identifies a sequence entry.
array | $flines | Buffed file as array |
string | $linestr | Current line |
string | $dbformat | Original DB format (Swissprot, Genbank) |