The user also may create pipelines.
To open an existent project, choose File->Open Project in the main menu. Then choose the project's folder.
To create a new project, use File->New Project in the main menu. In the "Create new Project" dialog, enter folder name for a new project. It will also be assigned as a name of a project itself. If you want to change the location of the project folder, press Browse button. If the project folder already exists in the current location or contains invalid symbols, the "OK" button in the "Create new Project" dialog will be inactive. The project name is shown on top of the Project Tab. You can change the name, it does not have to match the folder name or be unique. Press the "OK" button to confirm. A new project with the specified name has now been created.
Choose a program group in Toolbox Tab and double click to a program to append it to a list in Project Tab. Generally, the task is not yet ready and cannot be enabled unless its mandatory parameters (also called properties) are assigned values - for instance, FGENESH cannot run unless genefinding matrix (human, monocot plants etc.) is specified. Project tasks are also displayed in Pipeline Tab.
TThe properties (parameter values) of a task can be edited in Property Editor of Properties Tab. . Before a task can be executed, you must set values to all necessary parameters. If a mandatory parameter is not set or its value is wrong, MolQuest highlights it with red color and "!" mark, like this:
Only tasks that are in "Ready" status can be enabled (see Task Status).
When a project is run, its tasks are executed one by one in the same order as they appear in the list of project tasks, from top to bottom (Project Tab). A user can, at any time, change an order in which tasks are executed. To change an order, use Task->Move Up and Task->Move Down commands of the Main menuor and buttons.
If you want to execute only one task of a project, select the task at the Project Tab or the Pipeline Tab and click . If you run a single task rather than a project, that task can have not only status "Enabled" , but also "Ready".
When a task is being run, its status is "In Progress" ( ) status (Task Status).
Completed tasks have status "Completed" () status (Task Status).
If an error occurred during the execution of a task, the task gets either "Completed with Warnings!" (( or "Completed with ERROR!" (( status (Task Status).
If you interrupt a task, a project continues running, the next task in a queue being executed, unless you run a single task by pressing a button (see above).
An output of a task can be viewed in Project Tab (column "Results"), Results Tab or View/Console Tab.
A project may consist of a complex sequence of tasks, where an output of one task is used as an input for another. Such kind of project is called a pipeline.
There are two ways of making an output of one task an input of another task: You can use either Property Editor or Pipeline Tab.
In Property Editor , , choose "Pipe" type for required input source. The button appears which, when pressed, displays "Select Task Output" dialog listing outputs of all project's tasks that can potentially be used as inputs.
Alternatively, you can use Pipeline Tab , which displays MolQuest projects as block diagrams in user-editable form.
Here, to create a pipeline, connect output and input of corresponding tasks with a mouse: click on an output of a task, and a cursor takes this form: , now move a cursor to an input area of a "downstream" task. Yellow line will follow a cursor there. If two tasks cannot be linked in a pipeline, a cursor transforms into this icon: . If, however, link is possible, it will look like this: . Click on an input area, and two tasks are linked into pipeline relationship. Similarly, you can start with an input field of a downstream task and move to output field of an upstream task. In such case, cursor will assume this look: .
If output and input formats of tasks are compatible, a pipeline link between them looks as a solid gray line: . If formats are incompatible, but a correspondent converter is registered with MolQuest, a link looks like a dotted gray line: . Finally, if formats are incompatible and there is no converter available, it looks as a black line: .