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 variables

Program execution

Command line argument	Variable	Default value	Type	Description
-a	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	./input.txt	String	Path to, and name of, the input file.
-m	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.
-imr	ignoreMisformattedRows	false	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	false	Boolean	If set to true, the console shows more messages along the process.
-c	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	./output.sif	String	Path to, and name of, the output file.

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
-nil	onlyNeighborsInList	false	Boolean	Output graph will only contain proteins(vertices) in the input list.
-oe	onlyOrderedEdges	false	Boolean	For the edges indicating a set or complex neighbour, output each pair of proteins only once.
-mp	showMissingProteins	false	Boolean	If set to true, the output graph will include the proteins contained in the input file but not are not present in Reactome.
-ip	showIsolatedProteins	false	Boolean	If set to true, the output graph will include the proteins contained in the input file but do not have connections.

Types of edges

Command line argument	Variable	Default value	Type	Description
-cn	cn	true	Boolean	Show edges indicating complex neighbours.
-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.

• If none of the variables for edge types are specified in the command line, nor in the configuration file, then it is assumed that the output graph must contain all types of edges. If at least one of the edge type variables is specified then only the specified types will be included in the output graph.

• The Boolean variables are flags in the command line. The value is set to true by writing the variable as argument.