The Properties tab is purposed for setting up task parameters. The Properties tab contains:
• View List
• Property Editor
• Description page
• Constrains page

1. View List. 2. Property Editor. 3. Description console. 4. Constrains console.

View List.

View List contains a list of predefined task's Views (see View). The contextual menu of View List is as follows:

The contextual list menu contains the following commands:
• Add View Copy - create a copy of current view. Displays "Add View Copy" dialog, where user enters a name of a new View.


• Rename View - displays "Rename View" dialog, where user can change a name of a current View.


• Delete View - Delete View.
• Delete All Other Views - Deletes all Views except selected one.

Property Editor.

Before executing a task, user has to specify all task's properties (parameters), for instance type and location of an input, output options, and program options: for instance, organism-specific matrix or codon table for FGENESH. Some tasks have several dozens of properties with complex dependencies. Any single property can be mandatory or optional. Some properties have default values.

Property Editor handles all task properties in a convenient way. User can specify strings, numbers, files, lists of files, folders and other types of data as property values. Every property has a value, and some values are incompatible with each other. Property Editor checks properties for such incompatibilities or other errors, as well as for omissions. Properties can be nested (see example below).

Properties are grouped in sections, which vary depending on program. The most common sections are following:
• System - contains such informational properties as task name, program name and version etc. This section is mandatory, but filled automatically.
• Input - includes various input properties, such as a source of input data (pipe, file, list of files etc.), definitions for detailed input (lists of variables or cases in SelTag) etc.
• Output - includes various output properties, such as an output filename, its format, etc.
• Options - includes various task properties, such as processing modes, restrictions, coefficients etc.
• Preprocessing - includes settings for preliminary processing of input data.

Property Icons and Property Activity

Below is a window of Property Editor.

Left column contains name of each property, right column - its value. Some of properties can have the following information icons next to their names:

	This is a system property, not defined by user. One such property is program name.
	The value for this property is undefined or wrong.
	This node contains one or more nested properties, for which the values are undefined or wrong.
	This property is inactive and not used by the task, so its value can't be set.
	This property is active and its value must be set.
	This property is "Read only", and its value can't be changed. Unlike system property, value of read only property affects task results. A property can become "read only" either by user's choice (selection of "Property Permanently ReadOnly" command in contextual menu) or by such combination of values of other properties that allow only single value of this property.
	This property is disabled. If parent property is inactive or read only, nested properties are disabled.

Disabled and other inactive properties are shown in grey.

A program can have optional parameters, so some properties may be switched between active and inactive states by checking/unchecking the box: / . Other properties are permanently active. Active properties are used by a task, inactive are not.

Examples of disabled properties are below.

"Perform gapped alignment" property is optional and set active (box is checked), its nested properties are "Open Gap Cost" and "Extend Gap Cost". If "Perform gapped alignment" property is set inactive (box is unchecked), nested properties "Open Gap Cost" and "Extend Gap Cost" are disabled.

If a property is inactive, all nested properties are inactive as well, so Property Editor disables editing their values.

A property is also disabled if its parent property is read only, for example:

If "Multiply variants……" property is set to read only, all nested properties except selected become disabled, and selected properties become read only.

Contextual menu of Property Editor

Contextual menu of Property Editor contains the following commands:
• Collapse All - collapse all nodes.
• Expand All - expand all nodes.
• Top position - go to the top of a list.
• Copy Value - copy property value to clipboard.
• Paste Value - paste property value from clipboard.
• Copy Property String - copy property name and value to clipboard.
• Open folder - open folder where selected file is located.
• Open with text editor - îpen file using text editor.
• Open with viewer - file using special graphical viewer (must be installed).
• Property - Rename - rename a property. Displays "Rename Property" dialog.


• Property - Move Up - moves property up. Property can also be moved within nested group of parent property.
• Property - Move Down - moves property down.
• Property - Permanently Active - makes an optional property permanently active, i.e. mandatory. This action can't be undone in current View.
• Property - Permanently Hide - Hides property, locking its value and activity status at the same time. This action can't be undone in current View.
• Property - Permanently ReadOnly - makes property read only. All active nested properties also become read only, while inactive nested properties become disabled. This action can't be undone in current View.
List Item - Rename - Some properties have only a fixed set of acceptable values. For instance, genefinding parameters for FGENESH can only be human, mouse, Drosophila etc. This action renames one of such values chosen from a list, for instance user can change Drosophila to fruit fly. Displays "Rename Item" dialog.

• List Item - Permanently Active - make a list item permanently active, i.e. locks property value at this list item. This action can't be undone in current View.
• List Item - Permanently Hide - hides a list item permanently, i.e. deletes it from a list of acceptable values. This action can't be undone in current View.
• List Item - Permanently ReadOnly - set nested properties of this list item into read only mode, i.e. they become unavailable for editing. This action can't be undone in current View.
• SubNodes - Permanently Hide - hide children nodes. This command is available for radiogroups only. This action can't be undone in current View.

Warning! All commands with "Permanently …" in their names can't be undone in the current View. Therefore, before taking such actions, create a copy of current View so that you can restore original View. Otherwise, in order to undo such actions, you'll have to create a new View from scratch.

Values of properties

Depending on property type, values can be:
• selected from a list
• typed in manually
• files selected using standard Select File dialog, which appears when the corresponding button in property value column is pressed. Full path is required for input files, for output files - filename only. Path to a file can be typed in or selected in Select File dialog. You can also drag and drop files or paste them from a clipboard. In certain cases, files can be selected from a drop down menu.

For properties that define input data source, there are three possible value variants: File, Files list and Pipe:
• File - data are located in a file with user-specified path. Icon indicates that specified file exists, icon - that path or filename are incorrect, i.e. file cannot be located.
• Files list - a list consisting of one or more files created in File List dialog (evoked by pressing button) is used as an input. In such case MolQuest runs several passes, one file from a list at a time, in the same order they appear in a dialog window, until all files are processed. Results of each pass are shown in a list in Results Tab. Icon indicates that file list is empty, while means that it is not.

In File List dialog (see picture below), pressing button opens standard Add File window, which is used to add files to a list.

Order of files in a list can be changed by using and buttons.

To remove an individual file from a list, press button, and to remove all files, button.

• Pipe - input data are taken directly from output of another task in the same project. Correst link to pipe data source is indicated by icon The ,while undefined or wrong link - by icon the . Similarly, The icon means that destination for output data is correct, and the that link is not defined or incorrect.

To choose the link for input data, use button, which displays "Select Task Output" dialog with list of outputs of task within current project.

Some properties are mutually exclusive, i.e. if value of Property 1 is set, value of Property 2 cannot be set. Such properties are grouped into a radio node. In such cases, a separator "::" is placed after a name of a node (parent property), separating it from a name of selected nested property. User can change this default style with alternative ones in Rename Property dialog below.

For example, label "Multiply variants::Non-Overlapped variants::Number" means that parent property "Multiply variants" has nested property "Non-Overlapped variants" selected as its value, and this property "Non-Overlapped" has its own nested property, "Number" as its value:

Property Rename command in the contextual menu opens Rename Property dialog. If "Absolute Name" box is checked, name of selected nested property won't be added to node name after a separator.

Description page

Description page contains brief descriptions of some selected properties or their values.

Constrains page

Constrains page contains requirements to values of some properties (value type, minimum and maximum value etc.)