XML Message Format
The FlowJo documentation for developers does not contain verbose examples of how FlowJo interprates the XML messages or how they are created. Due to this, it is extremely difficult to generate correct queries to FlowJo to retreive useful data. In the example of the contour points generated by getContourPolygons, the function does not execute correctly for other formats such as Psudocolor.
Query API Documentation
The query APIs necessary for handling the XML data lacked any documentation with the exception of a minor example code. The query API documentation would have been beneficial to properly query data from the fsc datasets for proper parsing and exporting as a CSV file.
FlowJo does not appear to have a way to debug the Plug-ins through the GUI. There are some windows that allow the XML messages being executed in FlowJo to be seen, but this does not provide information on what fields are required to be set .
There is also no method for viewing debug information such as Stack Traces. If the Plug-in fails to execute correctly during execution it simply fails out and does not generate subsequent data sets. Breakpointing is also not possible which would make it much easier to determine where data is located in the program flow as well as what the format of the data is. Many Treestar functions also do not contain java doc tips for how the implemented property or function will behave.
The developers guide shows the constructors and parameters of several functions that can be used by FlowJo such as PluginHelper and SElement. The only example however does not include code that executes and produces useful results that can be expanded upon.