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3.2 How to run qodgui

The qodgui program can be either launch on command line or by setting a link.

If no arguments is provided to the binary, then a window appears (see fig:qod:select), proposing to select the central genome and the pairwise comparison available for it, according to your preference settings (see Configuring qodgui).

qodgui-select.png

Figure 3.1: Screenshot of the selection window of qodgui .

If you have wide files or/and you don't wan't to change all your settings, you also can use an open dialog (see Figure 3.1), enabling you to manually choose the central genome sequence file (fasta –eventually gzipped– formatted), optionnaly the annotation file (sequin –eventually gzipped– formatted) and as much pairwise similarities as you want (mat or axt –eventually gzipped– formatted). You just be ensure that all your pairwise similarity files use the same format (i.e., mat or axt).

qodgui-open.png

Figure 3.2: Screenshot of the Open dialog of qodgui .

3.2.1 Setting a shortcut on your desktop

The following can't be exhaustive, since it depends on your operating system. Although, the description should be almost the same on most platforms.

On Windows, right click an open area on your desktop, then point to New, and select Shortcut. Now, you need to click on Browse, then to select the qodgui program (the file qodgui.exe directly under the directory where you unzip your qod distribution). You need to click Open, and then click Next. You can name the shortcut as you want, say qodgui. If a Finish button or a Next appears at the bottom of the dialog box, click it. Now, you just need to click the icon you want to use for the shortcut (if you dislike the default icon), and then click Finish. You can launch qodgui by just clicking on this shortcut.

On Linux with Gnome as desktop manager, the procedure is about the same as the one previously described: right click an open area on your desktop, then select Create Launcher. Now, fill the three first fields at your convenience. For the fourth field, you need to click on Browse, then to select the qodgui program (the file qodgui should be located under the directory /usr/local/bin). Now, you just need to click the No Icon button and select the image you want to use for the shortcut (you should find qod icons under /usr/local/share/qod/), and then click Ok. You can launch qodgui by just clicking on this shortcut.

On Linux with KDE as desktop manager, the procedure is similar too: right click an open area on your desktop, then point Create New and select Link. On the General tab of the window that pops up, you can set the icon for the launcher (click the button with the icon on), and set the name of the launcher (the text label that will be shown under its icon). Some icons in various sizes can be found in /usr/local/share/qod/. Now, in the Application tab you set the command for the launcher (the file qodgui should be located under the directory /usr/local/bin) and optionally the comment and description. The comment will be displayed in the tooltip for the launcher when you hover it with the mouse, and the description may be used by KDE in the applications menu.

On Macos, after mounting the dmg file, click on the mounted drive, then copy the Qod App bundle to your Application directory. Now, select the Qod App bundle under the Application directory, then hold down the Command/Apple key and the Alt key, drag it onto your desktop. You can also drag it onto your Dock if you want it on your Dock.

On Linux with other desktop manager or on other operating system, we don't currently provide any documentation. Feel free to send the procedure you follow to qod-project@lirmm.fr.

3.2.2 Command line invokation

The format for running the qodgui program is: 

     qodgui [Options...] [files...]
     
     qodgui --help|-h
     qodgui --version|-v
     qodgui --full-version|-V
   supports the following options:

--help|-h Display the help message, then exit.
--version|-v Display version information, then exit.
--full-version|-V Display full version information, then exit.
--cardinality=|-n <num> Cardinality of each set of intervals (for random generation).
--number=|-k <num> Number of collection of set of interval (for random generation).
--fsa=|-f <file> Set the central genome sequence from file <file> (fasta –eventually gzipped– formatted).
--annotations=|-a <file> Read annotation of the central genome sequence in file <file> (sequin –eventually gzipped– formatted).
[files...] The [files...] should contain the description of pairwise local similarities.
If no argument is passed to the program, then a selection window is first shown. Furthermore, providing the -n and/or -k options prohibit the use of -f, -a and [files...] and reciproquely.

If provided, each file from [files...] should contain the pairwise local similarities between the central genome and a given related genome. The files can be gzipped and must either follow the axt format (autodection according to file extension) or formatted as follow: 

       #Header
       #W_1
       [a_1,b_1] [c_1,d_1]
       ⋮
     
       #W_n
       [a_n,b_n] [c_n,d_n]

where W_i is the weight of the i^th interval, beginning at position a_i and ending at position b_i on the central genome sequence, and matching segment beginning at position \min(c_i, d_i) and ending at position \max(c_i,d_i) on the compared genome sequence. If c_i is greater than d_i, then the match occurs on the reverse complement of the compared sequence.