GS Amplicon Variant Analyzer

4.	GS Amplicon Variant Analyzer – Special Topics

4.1	Addressing Simultaneous Multiple Users’ Access to an Amplicon Project

Only one instance of the GS Amplicon Variant Analyzer can be “in control” of a given Amplicon Project at any given time, i.e. be able to save changes or carry out / stop computations in the Project. This is important because if multiple users or instances of the software had the same project open simultaneously and each were used to edit the project, saving from either instance would overwrite the changes of the other. To help minimize this risk, the AVA software presents a message window at the time a project is opened, if it appears to be in use by another user or another instance of the software (Figure 4‑1).

Figure 4‑1: Message window alerting you that the Amplicon Project you are trying to open is already open in another instance of the AVA software. This message gives you the choice of opening the Project as Read-Only or to preempt control of the Project from the other instance.

This message provides you with:

•	the logon name of the other user

•	the approximate time at which that user last interacted with the Project (such as by saving an update or running a computation)

•	the choice to load the Project

◦	but to operate in a “read-only” mode, or

◦	to preempt control of the Project from the other user.

The goal of this message is to inform users of a potential conflict, not to enforce any policy with respect to these conflicts. Thus, although it is possible to preempt control from the other AVA instance, it would likely be better to first contact the indicated user to see if they are still working with the Project, or if they might have simply neglected to shutdown the application. Another possibility is that the other instance may have been terminated with a control-C or was otherwise unable to carry out a clean shutdown. In such a case it would merely appear that another instance is actively using the Project, when none actually is. If the other user cannot readily be contacted, the last activity indicator of the message may help you determine if it is safe to preempt control of the Project without unduly affecting the other user.

If you open the Project in Read-Only mode, you will be able to make changes internally to the application (define new Reference Sequences, etc.) and use all the features of the Variants, Global Align, Consensus Align, and Flowgrams Tabs, including the export of pre-existing results (PNG, FASTA, Clustal, Ace, SAM, BAM, or Table files). However, you will not be able to save any changes to disk, or to use them in new calculations (which also involves writing the results to disk): the Save button will be grayed-out, which constitutes the only visual clue to the Read-Only status of the Project. Features like defining new Variants from selections on the Global and Consensus Align Tabs, though available, would be of little use since you would not be able to save the newly defined Variants to the disk or obtain frequency calculations for them in the Variants Tab. On the other hand, you would be able to observe (but not stop) a new computation of the Project if carried out by the currently controlling instance. If you have made changes to the Project and another user preempts control, the Save button may temporarily remain active (not grayed-out). If you then click on the Save button, you will be alerted to the transition to Read-Only mode, but you will not be able to save your changes. Clicking on either the Save, the Start computation or the Stop computation button, when in Read-Only mode, produces the following warning messages (Figure 4‑2).

A
B	C

Figure 4‑2: Messages indicating that you do not have “control” of the Amplicon Project (i.e. you are operating in Read-Only mode) and that you cannot (A) Save the changes to a Project, or (B) Start or (C) Stop computations in the Project.

If you preempt control of the Project from another user, either at this point or when you first opened the Project (see Figure 4‑1), the other user will be automatically and transparently transitioned to Read-Only mode. Not only will any of their unsaved changes become irremediably unsaveable (even trying to preempt control back from you would involve exiting the Project and thus the loss of unsaved changes), but no message will be sent to inform the other user that this transition to Read-Only occurred. The only visual clue to this state is that the Save button will remain grayed-out even after changes are made. More obvious functional clues are the reception of one of the messages of Figure 4‑2, if the other (“preempted”) user attempts to save Project changes or to start new computations (or stop your computation). Re-opening the Project would elicit the message of Figure 4‑1, which identifies the person who currently has control over the Project.

In a related feature, if you attempt to open an Amplicon Project in a file-system on which you do not have writing permissions, the message shown in Figure 4‑3 will be displayed, alerting you that the Project will open as Read-Only (assuming that you can actually read the files in that area of the file-system). Although the message specifies only the “Save” restriction, the computation restrictions apply as well.

Figure 4‑3: Alert message indication that the Amplicon Project you are trying to open will open in Read-Only mode