Running GUI client

Starting

The GUI client can be started from the command line using the PFMFind.pyw script:

$ PFMFind.pyw [--console] [config_file]

The client will contain a Python console (useful for debugging) if the option --console is set. The config_file optional argument is the path to an XML file containing the information about the database and the index to be connected. This file can also be specified directly from the GUI.

GUI workflow

PFMFind GUI allows users to perform searches of protein sequence databases using queries consisting of short fragments with ungapped similarity measures. The fragment length can vary between 6 and 20. The user interface consists of a Menu Bar (with only two options File and View), a Query Navigation Bar, and the main functional area accessed through six tabs: Settings, Experiment, Index, Search, Hits, and Keyword. If the –console is specified on the command line, an additional Console tab containing a Python console appears.

The PFMFind GUI workflow consists of the following steps:

When the GUI is started the first time, only the Settings tab is enabled. Once the connection to the PostgreSQL database is established, the Experiment tab is also enabled. The Index tab is enabled when the client connects to a master search index. The final three tabs require the user to set a particular experiment, in addition to acquiring a database connection. The Search tab also requires a connection to an index. In this way, it is possible to examine previous search results without establishing a connection to an index.

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