External Control of Gitools
-------------------------------------------------


As of version 1.7.0 Gitools can be addressed from outside of the application. At the moment there is one command availabe.

Gitools is listening to the port **50151** by default. So it is possible to send the commands to this port. Alternatively it is possible to change the port by editing the **ui.xml** file in the Gitools configuration folder. (For Linux and Mac OS X users this should be at **/.gitools**).


Overview of commands
-------------------------------------------------

================================================  ============================================  ===================================================================================== ======================  
 Command                                           Description                                   Options                                                                               as of Version
================================================  ============================================  ===================================================================================== ======================  
**add-header-colored-labels**                      Adds a new colored labels header                                                                                                    2.0.0
                                                                                                 - -c (--color) <color>     : A Hex color as '#FF0000' - depends on --value
                                                                                                 - -h (--heatmap) <heatmap> : Heatmap name or ``last`` for the last added 
                                                                                                 - -n (--no-auto-generate)  : Specify if auto color generation is not desired.
                                                                                                 - -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}
                                                                                                 - -s (--side) <side>       : Indicate where to add the header: 'rows' or 'columns'.
                                                                                                 - -t (--text-visible)      : Set for visible text labels
                                                                                                 - -v (--value) <value>     : A value corresponding to a color
**add-header-text-labels**                         Adds a new text header to the heatmap
                                                                                                 -  -h (--heatmap) <heatmap> : Heatmap 
                                                                                                 -  -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}     2.0.0
                                                                                                 -  -s (--side) <side>       : Indicate where to add the header: 'rows' or 'columns'.
**load **\ matrix-file                             Tells Gitools to load a file.                 - **--rows** ( **-r**)     : File rows annotations                                    1.7.0
                                                                                                 - **--cols** ( **-c**)     : File cols annotations
**version**                                        Prints Gitools version.                                                                                                             1.7.1
================================================  ============================================  ===================================================================================== ======================  



How to send a command to Gitols
-------------------------------------------------

There is several ways to send the commands listed above to Gitools. We will make three examples here:

Command line
.................................................

With a terminal application that lets you execute command line you can create a new Gitools instance with command to execute upon startup.

 ::
 $ gitools load /home/user/matrix-file.tdm --cols /home/user/col-annotations.tsv --rows /home/user/row-annotations.tsv 
 ::

HTTP
.................................................

By HTTP it is possible to send the command like this:

 ::
 $ http://localhost:50151/load?file =/home/user/matrix-file.tdm&cols =/home/user/col-annotations.tsv&rows =/home/user/row-annotations.tsv 
 ::

Python
.................................................

Python or any other programming environment can make use of the  `Telnet <http://en.wikipedia.org/wiki/Telnet>`__  internet protocol. See below to understand how python can connect to Gitools and send it a command.

 ::
 import socket
 gitools = socket .socket(socket .AF\_INET, socket .SOCK\_STREAM)
 gitools .connect(( ’localhost’, 50151))
 command = ”load /home/user/matrix-file.tdm --cols /home/user/col-annotations.tsv --rows /home/user/row-annotations.tsv”
 gitools .send( command )
 gitools .close()
 ::
