FASTAImporter Class Reference

Inheritance diagram for FASTAImporter:

Collaboration diagram for FASTAImporter:

Public Member Functions
	form ($form, &$form_state)
	formValidate ($form, &$form_state)
	run ()
Public Member Functions inherited from TripalImporter
	__construct (TripalJob $job=NULL)
	setJob (TripalJob $job)
	create ($run_args, $file_details=[])
	load ($import_id)
	submitJob ()
	prepareFiles ()
	cleanFile ()
	logMessage ($message, $variables=[], $severity=TRIPAL_INFO)
	formSubmit ($form, &$form_state)
	postRun ()
	getArguments ()

Static Public Attributes
static	$name = 'Chado FASTA Loader'
static	$machine_name = 'chado_fasta_loader'
static	$description = 'Load sequences from a multi-FASTA file into Chado'
static	$file_types
static	$upload_description = 'Please provide the FASTA file. The file must have a .fasta extension.'
static	$upload_title = 'FASTA Upload'
static	$button_text = 'Import FASTA file'
static	$methods
Static Public Attributes inherited from TripalImporter
static	$name = 'Tripal Loader'
static	$machine_name = 'tripal_loader'
static	$description = 'A base loader for all Tripal loaders'
static	$file_types = []
static	$upload_description = ''
static	$upload_title = 'File Upload'
static	$use_analysis = TRUE
static	$require_analysis = TRUE
static	$button_text = 'Import File'
static	$use_button = TRUE
static	$methods
static	$file_required = TRUE
static	$argument_list = []
static	$cardinality = 1
static	$menu_path = ''
static	$callback = ''
static	$callback_module = ''
static	$callback_path = ''

Additional Inherited Members
Static Public Member Functions inherited from TripalImporter
static	byID ($import_id)
Protected Member Functions inherited from TripalImporter
	setTotalItems ($total_items)
	addItemsHandled ($num_handled)
	setItemsHandled ($total_handled)
	setInterval ($interval)
Protected Attributes inherited from TripalImporter
	$job
	$arguments
	$import_id
	$is_prepared
	$reported = 0

Member Function Documentation

form()

FASTAImporter::form	(		$form,
		&	$form_state
	)

See also

TripalImporter::form()

Reimplemented from TripalImporter.

formValidate()

FASTAImporter::formValidate	(		$form,
		&	$form_state
	)

See also

TripalImporter::formValidate()

Reimplemented from TripalImporter.

run()

FASTAImporter::run

(

)

See also

TripalImporter::run()

Reimplemented from TripalImporter.

Member Data Documentation

$button_text

FASTAImporter::$button_text = 'Import FASTA file'

static

Text that should appear on the button at the bottom of the importer form.

$description

FASTAImporter::$description = 'Load sequences from a multi-FASTA file into Chado'

static

A brief description for this loader. This description will be presented to the site user.

$file_types

FASTAImporter::$file_types

static

Initial value:

= [
    'fasta',
    'txt',
    'fa',
    'aa',
    'pep',
    'nuc',
    'faa',
    'fna',
  ]

An array containing the extensions of allowed file types.

$machine_name

FASTAImporter::$machine_name = 'chado_fasta_loader'

static

The machine name for this loader. This name will be used to construct the URL for the loader.

$methods

FASTAImporter::$methods

static

Initial value:

= [
    
    'file_upload' => TRUE,
    
    'file_local' => TRUE,
    
    'file_remote' => TRUE,
  ]

Indicates the methods that the file uploader will support.

$name

FASTAImporter::$name = 'Chado FASTA Loader'

static

The name of this loader. This name will be presented to the site user.

$upload_description

FASTAImporter::$upload_description = 'Please provide the FASTA file. The file must have a .fasta extension.'

static

Provides information to the user about the file upload. Typically this may include a description of the file types allowed.

$upload_title

FASTAImporter::$upload_title = 'FASTA Upload'

static

The title that should appear above the file upload section.

---

The documentation for this class was generated from the following file:

• tripal_chado/includes/TripalImporter/FASTAImporter.inc