Sequence Options

Sequence Options dialog serves for defining the sequence parameters. It is opened by using the icon or the Sequence - Sequence command from the Sequence window.

Sequence Options


Describes a displayed sequence.

Sequence Mode

Serves for setting the operation mode of the sequence.

Active Sequence

In ACTIVE sequence the start is controlled by the station. Clarity sends the permission signal to the autosampler and waits until the sampler acknowledges the injection. Data acquisition will be started after the confirmation signal has been sent back to Clarity and the permission to another injection is disabled.

Passive Sequence

In PASSIVE sequence the start is controlled by the autosampler. Clarity only waits for external start signal from the autosampler and then starts the sequence and data acquisition.


When the ACTIVE sequence is used, Enable Autostop, External Start/Stop must be set in the Method Setup - Measurement dialog and the Start-Restart option of the External Start/Stop behave as Start Only.


When the PASSIVE sequence is used, External Start/Stop must be set in the Method Setup - Measurement dialog.

Once the analysis time of the method in question has elapsed (as set in the Run Time field of the Method Setup - Measurement dialog with Enable Autostop field enabled), the analysis will be completed and injection will be permitted once again.


Only the Start In and Ready Out synchronization cables are needed for the active sequence to function. The active sequence can thus be used even with an autosampler not governed by a specialized control module.


The confirmation signal is represented by a change against the initial value of the selected digital output. The default assignment of outputs is described in the corresponding hardware manual.

The assignment of digital inputs and outputs used for the synchronization can be changed on the tab of appropriate Instrument in the System Configuration dialog, where Ext. Start Dig. Input and Ready Dig. Output fields are placed. For more detailed information see chapter 6 in Getting Started.

Idle Time

Delays the sending of the permission to inject. The next injection after the end of an analysis will always be permitted only after the defined time has elapsed. Possible values are in the 0.01-100 min range. This field can only be edited when the sequence is set to Active.

Idle Time also before First Injection

Determines whether the Idle Time parameter will be used even before the first injection in the active sequence. This field can only be edited when the sequence is set to Active.

Run Lines

Sets the line numbers of the Sequence Table to be used in the measurement. Particular line numbers should be separated with a comma (e.g. 1,3,5), ranges should be entered using a dash (e.g. 1-8).

A list of lines that should be run defined interactively by the checkboxes in the Run column of the Sequence Table will be automatically filled to this field.

Counter (%n)

Sets the value and properties of the %n variable (analysis counter) used in a Sequence Table.

Value of the counter increases every time analysis (injection) is measured and chromatogram is created, even after Abort (when set in GLP Options), a Snapshot is taken. Even though one or more Snapshots are used (and the resulting chromatogram is either created or not), value of the Counter is incremented only once.

Start at:

Defines if the %n variable will be reset to 0 or 1 at the moment defined in the following Reset when field.

Reset when:

Sets the condition when the counter (%n variable) is reset. Available options are:

Run Sequence - The counter is reset every time the sequence is run.

Open Instrument - The counter is reset every time the Instrument window is opened.

Never - The counter is never reset.

Current Value

This field shows (and allows to modify) the current value of the sequence counter (%n variable). Each time a chromatogram is measured the value of counter increases by 1.


The station keeps two separate counters: one for the sequence and another one for the single analysis. This means that two %n variables with possibly different values exist simultaneously.

Solve conflict of filename

Sets the verification of the chromatogram names pattern (set in the File Name field) when measuring more than one chromatogram from particular line.


The pattern will be automatically modified to correspond to the number of measured chromatograms and to avoid possible loss (overwriting) of chromatograms.


When using the automatic format, variables will be complemented with zeros from the left in order to correspond with the defined number of samples (e.g. in a sequence where SV = 1 and EV = 100, filenames will automatically be numbered from 001 to 100).


The pattern will not be modified. Once the sequence has been run, you will be notified of a possible overwrite of chromatograms within one line.

Calibration and Sequence Usage

Selects the mode of the calibration and sequence usage.

Calibration used as specified by user

Sets the sequence and calibration to the standard Clarity use (the only way available since version 3.0). The calibration set in the Method Setup - Calculation dialog is used for calibration and recalibration, no calibration cloning is performed.

Clone on first recalibration (safe calibration usage)

Sets the sequence and calibration to the Safe Calibration Usage mode. This option will create a clone (copy) of calibration defined in the method upon completing the first row of the sequence. Cloned calibration is attached to each new chromatogram produced by the given sequence. The option is not available on EA Instruments.


This option will preserve the original calibration and thus preserve the results of chromatograms measured earlier.

Standard Addition Measurement

Sets the sequence and calibration to the Standard Addition mode use. As each unknown sample will use one calibration file, calibration will be cloned from the original calibration file whenever an unknown sample or blank follows the calibration standard. All responses are cleared from a newly cloned calibration. The option is not available on EA Instruments.

Calibration Bracketing

Bracketing is a simplified direct calibration method used to compensate for the variation on instrument response with time.

This option sets the sequence and calibration to the Calibration Bracketing mode use. As every unknown sample series is demarcated by calibration standards and as such uses a single calibration file, calibration will be cloned from the previous calibration clone whenever an unknown sample or blank follows the calibration standard. Newly cloned calibration file has all responses cleared - apart from the responses from the last series of calibration standards (standards that immediately precede the current unknown samples).

In the EA mode, the name of the cloned calibration file is hard-set to the original name incremented by the sequence line number (%L parameter).

After sequence is finished

Allows to set parameters when the sequence is finished

Send shutdown method

Specifies which method will be sent to the instrument when the sequence is finished. Method can be selected by using button, button allows to edit currently selected method.

If no other options are checked, Clarity will send the parameters of specified method to the instrument and no acquisition will be performed.

Run shutdown method

An analysis according to the specified method will be performed. Resulting chromatogram will be saved to the current project as <SequenceName> - Shutdown - <MethodName> - %R.prm

Sample Type

Sets the type of the sample being measured. The possible options are:

  • Unknown - controlled autosampler will perform an injection
  • Bypass - no injection will be performed

Vial No.:

The vial number / injection number from a given vial. For configured autosampler, which supports graphical interface for inserting vial number, is visible - clicking this button invokes Select Vial dialog for selecting a vial.

Inj. Vol.:

Defines the volume of injection. The units are set in the Instrument Units dialog available in System Configuration.


Several autosamplers requires specific values for Vial No. or Inj. Vol. although no injection is performed. If these values are missing, user is informed during validation check.

Perform shutdown

When the sequence is finished, all connected devices (controlled only) will be shut down. Shutdown command is sent after sending (and possibly completing) run of the shutdown method. When the shutdown method is just sent and no shutdown method run is performed, invoking the shutdown does not wait to controlled instruments becoming ready.


The parameters of the After sequence is finished section are also executed when the user stops the sequence by Stop command or the sequence is stopped by an error. If it is necessary to stop the running sequence without sending (and running) the shutdown method, use the Abort command.