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  • PredictModule
  • SearchModule

Classes

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  • BaseParser
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  • ResultSet
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Class SearchParser

SearchParser is responsible for parsing form query (from user) and running services for needed tools - it also contains support functions for connecting search form with tools

Nette\Object
Extended by BaseModule\Services\BaseService
Extended by DispatchModule\BaseParser
Extended by DispatchModule\SearchParser
Namespace: DispatchModule
Located at DispatchModule/SearchParser.php
Methods summary
public
# __construct( Nette\DI\Container $container )

Constructor used to save container

Constructor used to save container

Parameters

$container

Overrides

DispatchModule\BaseParser::__construct()
public string
# getFileName( string $fileId = null )

Generate a file name to save results

Generate a file name to save results

Parameters

$fileId
identifier of the search

Returns

string
file name
public string
# getFilePath( string $fileName = null )

Generate a file path to save results

Generate a file path to save results

Parameters

$fileName
file name

Returns

string
file path
public DispatchModule\ResultSet
# parseForm( BaseModule\Form $form )

Main method parses form and initializes tool classes

Main method parses form and initializes tool classes

Parameters

$form

Returns

DispatchModule\ResultSet
result of the search
public integer
# saveLog( DispatchModule\ResultSet $result, string $name )

Saves result set

Saves result set

Parameters

$result
Saves the result set into the temporary file
$name
File name

Returns

integer
number of saved results
protected DispatchModule\ResultSet
# performSimplesearch( DispatchModule\SearchTools\DbTool $dbTool, array $formValues )

Performs simple search - firtst sequence is loaded completely, but for the rest only basic information is loaded

Performs simple search - firtst sequence is loaded completely, but for the rest only basic information is loaded

Parameters

$dbTool
DBTool instance
$formValues
serach criterias (from the form)

Returns

DispatchModule\ResultSet
resulting sequences (only first complete)
protected array
# getActiveTools( array $formValues )

Get active tools based on the params of the search

Get active tools based on the params of the search

Parameters

$formValues
search criteria (from the form)

Returns

array
currently active tools (prefixes)
protected boolean
# isActiveDb( array $activeTools )

Check whether there is any active database tool based on the params of the search

Check whether there is any active database tool based on the params of the search

Parameters

$activeTools
active tools (prefixes)

Returns

boolean
TRUE if any database tool is active
protected boolean
# isActiveDbOnly( array $activeTools )

Check whether database tools are the only active based on the params of the search

Check whether database tools are the only active based on the params of the search

Parameters

$activeTools
active tools (prefixes)

Returns

boolean
TRUE if no non-database tool is active
public
# getNameValues( type $organismName )

Returns organism names containing $organismName

Returns organism names containing $organismName

Parameters

$organismName
public integer
# getResultCount( array $data )

Gets resultset size for specific DbTool query

Gets resultset size for specific DbTool query

Parameters

$data
data for DbTool

Returns

integer
number of results
protected array
# getAttributeProperties( string $inputName )

Extract name and prefix from input name

Extract name and prefix from input name

Parameters

$inputName
input name (with prefix)

Returns

array
array with two elements - name and prefix
public integer
# save( DispatchModule\ResultSet $result, string $fileName = null )

Saves result set

Saves result set

Parameters

$result
Saves the result set into the temporary file
$fileName
name of the temporary file

Returns

integer
number of saved results
public DispatchModule\ResultSet
# load( string $fileName = null )

Load sequences from the temporary file

Load sequences from the temporary file

Parameters

$fileName
name of the temporary file

Returns

DispatchModule\ResultSet
Result set
public DispatchModule\Sequence
# convertLineIntoSeq( string $line )

Converts line (separated by ";") into sequence

Converts line (separated by ";") into sequence

Parameters

$line
Line that will be converted

Returns

DispatchModule\Sequence
converted sequence
public DispatchModule\ResultSet
# getResultSet( integer $totalSeq, string $fileName = null )

Gets result set of sequences

Gets result set of sequences

Parameters

$totalSeq
maximal number of sequences
$fileName
name of the file with results

Returns

DispatchModule\ResultSet
Result set
Methods inherited from DispatchModule\BaseParser
addFormParameters(), getName(), getParameterList(), getTools(), getVisualizers()
Properties summary
public string $dbTempDirectory

DB Temporary directory - is used when the DB searching is off. - stores resultSet generated from other tools

DB Temporary directory - is used when the DB searching is off. - stores resultSet generated from other tools
#
public string $dbTempFile

DB Temporary file - is used when the DB searching is off. - stores resultSet generated from other tools

DB Temporary file - is used when the DB searching is off. - stores resultSet generated from other tools
#
Properties inherited from DispatchModule\BaseParser
$container, $parameterList
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