Tripal
Public Member Functions | Static Public Attributes | List of all members
FASTAImporter Class Reference
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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: