#GEL Reference
Some commands require parenthesis and some commands do not. This is because some of the commands are statement commands while others are functions.
abs
Returns the absolute value of numeric data.
print abs(-2.34); // returns 2.34
print abs(3); // returns 3
acos
Converts cosine value to angle value in radians.
print acos(0.5); // returns 1.047198
asin
Converts sine value to angle value in radians.
print sin(1); // returns 0.841471
atan
Converts tangent value to angle value in radians.
print tan(0.3); // returns 0.309336
ceil
Rounds a given value up to its ceiling integer.
print ceil(3.1); // returns 4
print ceil(2); // returns 2
print ceil(1.5); // returns 2
center
Centers a given graph on the xyz coordinates (0,0,0). If a node name is also given, the entire graph will be shifed so that the given node's xyz coordinates is at (0,0,0).
center(graph);
center(graph,"jack"); // we focus on "jack" node
clear
Clears/removes all data and graph objects from Mango.
clear;
clearconsole
Clears any text from the console panel.
clearconsole();
clearmessage
Clears any text from the message panel.
clearmessage();
cos
Converts the angle in radians to the cosine value.
print cos(3.14/4); // returns 0.707388
delete
Deletes variables, graphs, node or link types. See clear to delete all variables.
delete var1;
delete var1, graph2, node3, link4;
desc
Describes the named data objects by printing out data type as well as data value in the messages pane. If no data objects are given, describes all data objects in memory.
desc var1;
desc var1, graph2, node3, link4;
desc; // describes all data objects
exec
Executes a given Gel script. No returning to the code.
exec "command.txt";
exp
Exponential function. Raise natural e to the given value power.
double v = exp(3); // e^3
export
export(string filename, string format, graph one, graph two, …) filename: name of file to save the exported graph(s)
format: either “csv” or “tsv” for Excel or “dot” for Graphviz one, two, …: name of selected graphs to export; all graphs will be exported if none is specified.
Note: do not use the import/export functions to save your data. Instead, use the save and run/exec commands to save your data in the native Gel language format.
node(string name) nt;
link[] lt;
graph(nt,lt) ran=random(10);
export(“ran.csv”, “csv”, ran);
floor
Rounds a number down to the nearest integer.
print floor(3.9); // returns 3
print floor(2); // returns 2
print floor(1.1); // returns 1
foreach
foreach scans through all nodes and all links in a graph and allow certain attributes to be set accordingly. The where clause is optional but if it is specified, only nodes or links satisfying the condition will be modified.
foreach node in graph_abc where count>2 set count=2;
foreach link in graph_abc set weight=(in.count+out.count)/2.0;
graph
Compound data type declaration. All declarations can take on initialization values or (in the case of node or link types) default attribute values.
graph(node_type, directed) g1;
// declared a graph with node_type and directed link type
graph(node_type, undirected) g2 = { ("node1", 1)[12.0f,2.0]("node2",2) };
getwd
returns a string of the current working directory
string s = getwd();
print getwd();
help
display all help topics by default. look up a particular function
help; // display all help topics
help verbose; // display verb description
help rand; // display rand function description
import
graph = import(string filename, string delimiter)
filename: name of graph data file to be imported delimiter: character(s) that separate fields in a line
Note: do not use the import/export functions to save your data. Instead, use the save and run/exec commands to save your data in the native Gel language format.
import a graph from a delimited file into Mango.
node(string name) nt;
link[]lt;
graph(nt,lt) net = import("net.csv",",");
graph(nt,lt) net = import("net.tsv", "\t");
int
integers, one of the four primitive data types
int i = 0;
i=40;
layout
preset graph layouts, applied to the given graph g.
layout(type) type: either "random", "cube", or "circle"
layout(g,"circle");
layout(g,"random");
layout(g,"cube");
len
Returns the number of characters in a string, length of the string.
print len("Hello World!"); // returns 12
link
compound data type declaration, necessary for defining the graph type
link [float weight, double value, ...] undirected; // defined an undirected link type
link <float weight, double value, ...> directed; // defined a directed link type
link[] lt;
link[weight] lt;
link<float transferspeed> lt;
list
list the named data objects. If no data objects are given, list all data objects in memory.
list var1, graph2, node3, link4;
log
natural log of a value
double d = 315.3;
double logd = log(d);
map
Renames node ids based on a digraph. Multiple nodes can be mapped to the same id, combiing nodes.
help map;
graph = map(graph g, map_info, int keep, int loop)
g: graph whose nodes are to be mapped, or renamed
map_info: mapping information. Can be a graph or an attribute name
If a graph, it should be directed, and its links define the map
If an attribute name, it should be defined in nodes on graph a
keep: 0 will discard unmappped nodes or nodes whose map attribute
contains a null string; 1 will collect them unchanged to output
loop: 0 will discard self-pointing loops in output; 1 otherwise
match
Compares sequence (dna/protein/other letter) data in two graphs. Creates a new graph depending on the minimal sequence match length. Can also determine DNA reverse complement matches.
help match;
graph = match(graph a, graph b, string a_attr, string b_attr, int min_match, int revcomp, int in_graph)
a, b: graphs whose nodes are compared; in-graph comparision if a==b
a_attr: the node attribe name in a that contains sequence data
b_attr: the node attribe name in b that contains sequence data
min_match: minimal match length to produce a match link in output
revcomp: for DNA, 1 finds revese-complement matches; 0 otherwise
in_graph: 1 or when a==b allows in-graph matches; 0 otherwise
node
compound data type declaration, necessary for defining the graph type.
node(string name, int count, ...) nodetype;
node(string name) nt;
node(string id) nt;
node(string id, int age) nt;
pause
Pauses a few miliseconds.Useful when used inside animation loops. If delay has value of 0, pause for user input.
pause(1000); // 1000 milisecond pause
pause(0); // pause for user
pow
Raises a number to a power.
print pow(4,2); // returns 16, or 4^2
only scalar expressions can be given to the print command
print "The number of nodes in graph A is ", nodes(A);
print "Sum of nodes in graph A and B is ", nodes(A)+nodes(B);
r_mat
help r_mat;
graph = r_mat(int nodes, int degree, int loop, int seed, float a, float b, float c, float d)
nodes: number of nodes in the random graph
degree: average connectivity degree of nodes
loop: 0 no loop back to the same node; 1 otherwise
seed: seed to random number generator; 0 automatic
a, b, c, d: probabilities of falling into each quadrant
rand
generates a random number between a min and max value. By default, min value equals 0.0 and max value is 1.0.
double min = -5;
double max = 7;
double v = rand(min,max);
random
graph = random(int nodes, double percent, int loop, int seed)
nodes: number of nodes in the random graph percent: percent of connected links among nodes loop: 0 no loop back to the same node; 1 otherwise seed: seed to random number generator; 0 automatic
node(string name) nt;
link[] lt;
graph(nt,lt) ran = random(10); // 10 nodes with 50% connectivity
ran = random(10,0.25); // 10 nodes with 25% connectivity
run
run the gel script file and then the next command (if any)
run "command.txt";
save
save the named data objects to be loaded back into Mango later. If no data objects are given, all data objects in memory are saved to the given filename. Saved file is a Gel script that can be loaded back using the run or exec commands.
save "data.txt", var1, graph2,node3, link4;
select
Either nodes or links can be the selection target. In the where clause a boolean condition can be specified for the selection. Special in and out value are defined: in node selection, in and out denote the in-degree and out-degree of each node being considered for selection. In link selection in and out denote the nodes connected by each link under consideration, whose attributes can be accessed as in.count or out.name
subgraph = select node from graph_abc where count>10 && in>2;
subgraph = select link from graph_abc where weight>5.0 && in.count>2;
setwd
pops a window to set the working directory, can also return the string of the working directory
setwd();
string wk = setwd();
print setwd();
string
string and characters, one of the four primitive data types
string s = "hello world";
string c = "c";
sin
trigonometric sin function given the angle in radians
double s = sin(3.14);
substr
for substring function
string s = "hello world";
s = substr(s,0,5); /* s="hello"*/
tan
trigonometric tan function given the angle in radians
double v = tan(315.5);
time
The time out value when waiting for a loop to finish.
time; /* check what the current time out value is */
time 2000; /* set to 2000 ms */
tocamel
Converts strings to camel case.
string s = tocamel("hello world"); /* s="Hello World" */
tolower
Converts strings to lower case.
string s = tolower("Hello World"); /* s = "hello world" */
toupper
Converts strings to upper case.
string s = tolower("Hello World"); /* s = "HELLO WORLD" */
trim
Drops spaces at the beginning and end of the string.
string s = trim(" hello world "); /* s ="hello world" */
verb
set Gel verbose level
- n=0 Gel reports critical errors that stops it
- n=1 Gel reports data redefinitions or deletions
- n=2 Gel echo typed commands (default level)
- n=3 Gel echos scalar computation results
- n=4 Gel echos resulted graph node and link types
- n=5 Gel echos resulted graph complete information
verb 3; // set verbose level to 3
verb; //check current verbose level
while
Gel has looping constructs
int i=10;
while(i<10) i++;