Java Configuration

The configuration of the program is specified in the Command line and in a configuration file. Command line has priority over the configuration file. If none of them are specified, default values are taken.

Configuration file

Program execution

Command line argument	Variable	Default value	Type	Description
-a, --allProteome	allProteome	false	Boolean	If set to true, the set of vertices for the result graph will be the set of proteins in SwissProt. If set to false, an input list is requested.
-i, --inputListFile	inputListFile	./input.txt	String	Path to the input file.
-m, --maxNumVertices	maxNumVertices	21000	Integer	The graph will contain at most this number of vertices. If the input list has more proteins than this number, only the first maxNumVertices are used.
--ignoreMisformattedRows	ignoreMisformattedRows	true	Boolean	If set to true, the misformatted rows of the input are ignored and continues to the other rows. If set to false, the execution of the program stops completely when a misformatted row appears.
-v, --verboseConsole	verboseConsole	true	Boolean	If set to true, the console shows more messages along the process.
-c, --configFile	configFile	./Config.txt	String	Path to, and name of, the configuration file. This is not a variable that you can change in the configuration file itself. It looks for the file in that path, unless another path is specified using command line arguments.
-o, --outputGraphFile	outputGraphFile	./output.sif	String	Output file name with path.

Neo4j database access

Variable	Default value	Type	Description
-h, --host	host	bolt://localhost	String
-u, --username	username	neo4j	String
-p, --password	password	neo4j	String

Graph

Command line argument	Variable	Default value	Type	Description
--onlyNeighborsInList	onlyNeighborsInList	true	Boolean	Output graph will only contain proteins(vertices) in the input list.
--onlyOrderedEdges	onlyOrderedEdges	true	Boolean	For the edges indicating a set or complex neighbour, output each pair of proteins only once.
--showMissingProteins	showMissingProteins	true	Boolean	If set to true, the output graph will include the proteins contained in the input file but not are not present in Reactome.
--showIsolatedVertices	showIsolatedVertices	true	Boolean	If set to true, the output graph will include the proteins contained in the input file but do not have connections.
-cn	cn	true	Boolean	Show edges indicating complex neighbours.
-ds	ds	true	Boolean	Show edges indicating defined set neighbours.
-os	os	true	Boolean	Show edges indicating open set neighbours.
-cs	cs	true	Boolean	Show edges indicating candidate set neighbours.
-io	io	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as input and the other as output.
-oi	oi	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as output and the other as input.
-ci	ci	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as catalyst and the other as input.
-co	co	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as catalyst and the other as output.
-oc	oc	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as output and the other as catalyst.
-ri	ri	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as regulator and the other as input.
-ro	ro	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as regulator and the other as output.
-or	or	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as output and the other as regulator.