Cancelling Batch Operations
Many, but not all, of the operations that you request FlowJo to perform can be canceled while they are happening. In general, when you cancel an operation, all further calculations cease. In the case of creating tables or layouts, this will stop any output from being generated. If you select many subpopulations and accidentally double click on one of them (this directs FlowJo to open them all), it may take some time for all of the graphs to be generated. If you cancel the operation, then FlowJo will stop opening graphs (but leave the windows up for the ones it has already opened).
To cancel an operation, you can either click on the Stop button in the progress bar window, or press command-period (i.e., press the command (or "Apple") key and period key simultaneously). If FlowJo can cancel the operation, it will do so, although it may take a few seconds before this happens. (For instance, if FlowJo is in the middle of reading a file, you will have to wait until the file is fully loaded before the cancel can occur). In any case, FlowJo will change the message in the progress bar as soon as you attempt to cancel to let you know that it will cease its functions as soon as it can.
There are operations which cannot be canceled, in which case FlowJo will simply continue computing. Clicking on the "Stop" button or pressing cmd-period again will not help! If you wish to cancel an operation, you only need to press "Stop" or cmd-period once; if FlowJo can cancel, it will.