Sequence Options
The Sequence Options dialog serves for defining the sequence parameters. It can be opened using the 
icon or the Sequence - Sequence Options command of the Sequence window.
Sequence Options
The description of the displayed sequence.
Defines the operation mode of the sequence — whether it is fully controlled by Clarity (Active) or triggered externally without further checks (Passive). For more details on how to connect autosamplers, see the Connecting Autosamplers topic in the Getting Started manual.
In Passive mode, the autosampler (or other source of a start signal) initiates the start of each analysis. Clarity waits for the external start signal and begins the sequence and data acquisition once the signal is received.
In this mode, the behavior of the External Start/Stop setting in the Method Setup - Measurement tab of the method is respected as configured (Start Only, Start-Restart, or Start-Stop). The Autostop setting is not required.
If Autostop is defined in the method, Clarity will wait for the next start signal after it has elapsed. The analysis can also be manually ended using the Stop button twice, or via the external input if the External Start/Stop setting is set to Start - Restart or Start - Stop.
In Active mode, Clarity controls the start of the sequence. When all devices are ready, it sends a signal to the autosampler to initiate an injection process. The autosampler performs the defined operations and then signals Clarity that the injection is complete. Data acquisition begins only after this signal is received. No further injections are allowed until the current one is completed and all devices are ready again.
Autostop and External Start/Stop must be enabled in the Method Setup - Measurement tab of the selected method. In this mode, the External Start/Stop setting is always interpreted as Start Only, regardless of the selected option.
Input/output assignments can be modified in the System Configuration dialog, under the corresponding Instrument tab (Ext. Start Dig. Input and Ready Dig. Output fields). Active sequence mode can be used even without an autosampler controlled by Clarity. Proper synchronization using the Start In and Ready Out synchronization cables is sufficient.
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 Idle time has elapsed. Possible values are within 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.
Sets the line numbers of the Sequence Table to be run in the measurement. Particular line numbers should be separated by a comma (e.g. 1,3,5), ranges should be entered using a dash (e.g. 1-8).
A list of lines to be run can be defined interactively using the checkboxes in the Run column of the Sequence Table (the selected lines will be automatically filled in the Run lines field).
Sets the value and properties of the %n variable (analysis counter) used in the Sequence Table.
Value of the counter increases every time an analysis (injection) is performed and a chromatogram is created.
When taking Snapshots, the value of the Counter is incremented only once, even if more than one snapshot is taken. Old snapshots are thus overwritten by new snapshots and eventually by the resulting chromatogram.
Defines if the %n variable will be reset to 0 or 1 at the moment defined in the following Reset when field.
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
Never - The counter is never reset.
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.
Caution:
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.
Sets the method for resolving the conflict of chromatogram names when multiple chromatograms with the same File Name would be created on a single row. This only influences the pattern for the File Name. If a conflict in chromatogram name is left unsolved by user, the set name is appended by counter to prevent file overwriting.
The pattern will be automatically modified by addition of %v and/or %i if multiple vials and/or multiple injections are to be used from a single row.
The pattern will not be modified.
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 the 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.
Sets the sequence to Standard Addition mode (it is necessary to set the Display and Calculation mode to STDADD in the calibration and method), where a calibration clone is created from the original calibration on the first row of the sequence, and then again on every Unknown/Blank that follows a Standard.
When multiple consecutive Unknowns follow the same Standard, they are treated as recalibration points for the same Unknown level in the current calibration. Whether the responses are averaged or replaced is determined by the Recalibration setting in the Calibration Options of the template calibration.
This mode is not available on EA Instruments.
Bracketing is a simplified direct calibration method used to compensate for variations in the instrument response with time.
This option sets the sequence and calibration to the calibration bracketing mode. In this mode, every unknown sample series is enclosed between calibration standards and uses a single calibration file. The calibration is cloned from the previous calibration clone whenever an unknown sample or blank follows a calibration standard in a sequence. The newly cloned calibration file has all the previous responses cleared except for the last series of calibration standards (standards that immediately precede the current unknown sample).
Calibration bracketing will work correctly only if the used calibration has the Recalibration option selected and set to Average (at least 2 points) in the Calibration Options.
In the EA mode, the name of the cloned calibration file is hard-set as the original name incremented by the sequence line number (%L parameter).
Note:
At each calibration cloning, the original calibration and thus the results of the chromatograms measured earlier are preserved, under the name as set in the Method Setup - Calculation dialog, Calibration Cloning In Sequence option (conflicting names will be complemented by a three-digit counter to avoid overwriting).
Allows to set actions to be performed when the sequence is finished
Specifies a method to be sent to the instrument when the sequence is finished. The method can be selected using the 
button. The 
button allows to edit the currently selected method.
If no other options are checked, Clarity will send the parameters of the specified method to the instrument and no acquisition will be performed.
An analysis according to the specified method will be performed. The resulting chromatogram will be saved to the current project as <SequenceName> - Shutdown - <MethodName> - %R.prm
Sets the type of the sample being measured by the shutdown method. The possible options are:
- Unknown - a controlled autosampler will perform an injection
- Bypass - no injection will be performed
The vial number / injection number of the given vial. If the configured autosampler supports graphical interface for inserting vial number, the 
button is present - clicking this button invokes the Select Vial dialog for selecting a vial.
Defines the volume of injection. The present units are as set in the Instrument Units dialog available in System Configuration.
Note:
Several autosamplers require specific values for the Vial no. or Inj. vol. although no injection is performed. If these values are missing, the user is informed during the validity check.
When the sequence is finished, all connected controlled devices will be shut down. The shutdown command is sent after sending (and possibly completing) the 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 for the controlled instruments to become ready.
Caution:
The parameters of the After sequence is finished section are also executed when the user stops the sequence by the 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.