Class DbTool

DbTool - retrieves information from database - used (mainly) by search

Nette\Object

Extended by

BaseModule\Services\BaseService

Extended by

DispatchModule\Tools\BaseTool

Extended by

DispatchModule\Tools\DbTool implements DispatchModule\Tools\ToolInterface

Direct known subclasses

DispatchModule\Tools\AnnotationDbTool, DispatchModule\Tools\TaxonomyDbTool

Namespace: DispatchModule\Tools
Located at DispatchModule/DbTool.php

Methods summary
`public`	# `__construct( Nette\DI\Container $container, ...Object $initialization )` Constructor used to save container Constructor used to save container Parameters `$container` `$initialization` triplet label, description, wanted parameters; or an array with database tools to union Overrides `BaseModule\Services\BaseService::__construct()`
`public boolean`	# `addCriteria( string $name, mixed $value )` Adds search criteria Adds search criteria Parameters `$name` `$value` Returns boolean Implementation of `DispatchModule\Tools\ToolInterface::addCriteria()`
`public ResultSet`	# `execute( )` Executes query Executes query Returns ResultSet Implementation of `DispatchModule\Tools\ToolInterface::execute()`
`public integer`	# `getCount( string $accession = null, integer $start = null, integer $stop = null )` Executes count query, returns resultset size Executes count query, returns resultset size Parameters `$accession` `$start` `$stop` Returns integer size of the result
`protected boolean`	# `checkReservedWord( string $name, string $value )` Checks whether incoming key is a reserved word Checks whether incoming key is a reserved word Parameters `$name` parameter name `$value` parameter value Returns boolean true, if key is reserved word
`protected string\|false`	# `containsAttribute( string $name )` Check whether the db_attribute exists in the completeData and returns its prefix. Check whether the db_attribute exists in the completeData and returns its prefix. Parameters `$name` name of the input Returns string\|false prefix with that the attribut exists
`protected array\|false`	# `getCriteriaParam( string $name, string $value )` Returns array with information for db criteria (table attribute name and rule) Returns array with information for db criteria (table attribute name and rule) Parameters `$name` name of the input `$value` user input value Returns array\|false contains three elements, criteria ('eq', 'gt'), attribute key and its value; returns false if parameter does not add criteria
`protected Nette\Database\Table\Selection`	# `prepareCriteria( string $select, string $base = 'vw_acc_ann_tax' )` Prepares criteria for query Prepares criteria for query Parameters `$select` select part of the query `$base` base view to select from - vw_acc_ann_tax, vw_acc_ann_tax_grouped_acc, vw_acc_ann_tax_grouped_name Returns Nette\Database\Table\Selection query with all criteria
`protected string`	# `prepareKey( string $key, string $base )` Replaces key for use in SQL query (replaces %BASE_VIEW% for actual view name) Replaces key for use in SQL query (replaces %BASE_VIEW% for actual view name) Parameters `$key` desired key `$base` base table Returns string database key
`protected string`	# `chooseBaseTable( )` Chooses proper base table - vw_acc_ann_tax_grouped_acc, vw_acc_ann_tax_grouped_name or vw_acc_ann_tax Chooses proper base table - vw_acc_ann_tax_grouped_acc, vw_acc_ann_tax_grouped_name or vw_acc_ann_tax Returns string base table name
`public string`	# `getLabel( )` Gets human-readable short description (name) of the tool Gets human-readable short description (name) of the tool Returns string human-readable short description of the tools Implementation of `DispatchModule\Tools\ToolInterface::getLabel()`
`protected array`	# `getPredictionFeatures( integer $predictionId, string $type )` Gets specified characteristic for prediction (with its positions) Gets specified characteristic for prediction (with its positions) Parameters `$predictionId` id of prediction `$type` name of the characteristic - bulges, foverhangs, hairpins, helices, junctions, loops or toverhangs Returns array arary containing information about predicted characteristics
`protected`	# `defineMultipliedRules( string $key, array $allValues, array $allDirections )` Sets possible second length criteria Sets possible second length criteria Parameters `$key` attribute key `$allValues` all length values `$allDirections` all length directions (lesser than, greater than)
`protected string`	# `getTaxonomyPath( integer $value )` Gets taxonomy path for specified taxonomy record (category) Gets taxonomy path for specified taxonomy record (category) Parameters `$value` taxonomy.id Returns string taxonomy path
`protected integer`	# `lastTaxonomySelected( array $value )` Selects id of the last taxonomic category in the tree (from array of category inputs) Selects id of the last taxonomic category in the tree (from array of category inputs) Parameters `$value` taxonomy category inputs Returns integer id of last category
`public Array`	# `getNameValues( String $organismName )` Returns organism names containing $organismName Returns organism names containing $organismName Parameters `$organismName` Organism name Returns Array organism names
`public`	# `setSimpleSearch( boolean $val )` Set simple search flag - defines, whether only basic sequence info should be loaded Set simple search flag - defines, whether only basic sequence info should be loaded Parameters `$val` new simpleSearch value

Methods inherited from DispatchModule\Tools\BaseTool
`getName(), getWantedParameters(), requireParameter(), used()`

Constants summary
`string`	`RULE_EQ` Equals rule (can be also used as IN rule, if value is an array) Equals rule (can be also used as IN rule, if value is an array)	# `'eq'`
`string`	`RULE_GT` Greater than rule Greater than rule	# `'gt'`
`string`	`RULE_LT` Less than than rule Less than than rule	# `'lt'`
`string`	`RULE_LIKE` Like rule Like rule	# `'like'`
`string`	`RULE_PREFIX` Prefix like rule Prefix like rule	# `'prefix'`

Properties summary
`protected BaseModule\Repository\TestRepository`	`$repository` Test repository Test repository Inject	#
`protected array`	`$wantedParameters` array of wanted parameters array of wanted parameters	#
`protected integer`	`$offset` offset of results offset of results	# `0`
`protected integer`	`$limit` limitation of result count limitation of result count	# `0`
`public string`	`$label` short name of the tool short name of the tool	#
`protected boolean`	`$aggregateByAccession` if true, only record with longest sequence each accession number is returned if true, only record with longest sequence each accession number is returned	# `false`
`protected boolean`	`$simpleSearch` indicates whether simple search loading only basic sequence info should be performed indicates whether simple search loading only basic sequence info should be performed	# `false`
`protected array`	`$criteria` list of criterias for query list of criterias for query	# `array( self::RULE_EQ => array(), self::RULE_GT => array(), self::RULE_LT => array(), self::RULE_LIKE => array(), self::RULE_PREFIX => array() )`

Properties inherited from DispatchModule\Tools\BaseTool
`$completeData, $description, $fileName`

Properties inherited from BaseModule\Services\BaseService
`$container`