Definitions

Definitions

Overview

Definitions are list of items that can be attached to Ranges, allowing the automatic resolution of a specific name for each range index.
Definitions can only be attached to Ranges, regular Areas (Sample and controls) do not support this functionality. A Range can be linked to only one definition at a time.
Definitions can be managed by clicking the Definitions button available in the Areas group of the [Menu Panel]. This opens a form listing the available ranges (1), a summary of their definition status (2), a preview of the name resolved (3), if any, and controls to attach/replace files (4), edit the mapping for the current file (5), or remove the attached definition (6).

Ranges available
The available Ranges defined in the layout will be summarized in this table. Select a Range to display a preview of the definition file. Note that the preview is limited to the 50 first lines from the files.
The properties of the range are also displayed here, in particular the number of counts, or indices, available in the Range.

Definition status
For a Range that has a definition attached, this field summarizes information related to the definition file.
- Source: file or manual, see Import section below.
- # items: how many items in total are available in this definition file. Each item can be used to match a range index.
- # plates: if the number of items available in the definition file exceeds the current number of counts, or indices, available in the Range, the extra items are used to define additional plates. If the definition file includes a column for mapping plate names, then the count of unique plate names found for this column will be indicated here.

Definition preview
A preview of the file content is indicated here. For definition files without well or plate mapping (direct mapping), the item number is indicated, followed by the name to use for the corresponding range index.
If a well and/or a plate mapping are setup, the preview will list the elements as they appear in the file, displaying the plate name, the well name and the item name on a same line, separated with dots.

Select File
Click here to select or change the definition file for the selected Range. See the Import section below.

Edit Mapping
Click here to edit the column mapping for the definition file attached to the selected Range. See also the Mapping section below.

Reset
Click here to remove the definition for the selected result file.

Import, parsing and Mapping

When attaching a definition file to a Range, a new form will open to let the user select a file from the hard-disk drive (or type a manual input), adjust the parsing options and map the desired columns.
All this is done using the import form that is described in details in the [Data Import] page of this Wiki. Specific features linked with the import of Definition are detailed here.

Import
Only one file can be selected when attaching a definition file to a Range. If multiple files need to be used, consider merging them into one or copy/pasting their content in the manual import form.

Parsing
Parsing can be completed as described in the [Data Import] page.

Mapping
Mapping for definition files requires the selection of a Definition column, that will be used to read the name of the item. The column can contain text, numbers or a combination of both.
Optionally, a Well ID and Plate ID columns can be mapped, individually or together, depending on your file structure. Based on which columns were mapped, resolution of the name for a given range index will be conducted differently, and the different scenarios are explained below.

Strategies for the resolution of name
Name resolution will differ depending on the mapping configuration for the definition file:

Columns mapped	Rule
-	Names are fetched row-by-row, as they appear in the file. For a range with n indices, fetch the name at row i + (n × j), where i is the desired range index and j the desired plate index.
Well ID	Fetch the name that match the j-th occurrence of the well ID, where j is the desired plate index.
Plate ID	Fetch the name that match the i-th occurrence of the plate ID, where i is the desired range index.
Well ID & Plate ID	Fetch the name that match the desired well ID and plate ID.

Additional note for the Well ID & Plate ID mapping scenario:
In this case, the range index is not used. If several rows in the file share identical Well ID and Plate ID information, the last occurence will be displayed in the Plate view, while the first occurence will be displayed in the well information popup.
This discrepancy is due to the fact that the items are fetched in a different way depending on the situation. The well information popup has a "lazy" behavior and will stop as soon as a matching entry is found, while the Plate view will gather data for the whole file prior to display.