source documentation for imunes.tcl

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diff --git a/imunes.tcl b/imunes.tcl
index 7aac88d6f065dfa10dcb84b74386b769463303e5..605b05b62bda1d1aacf6ee9f8d23f85abbfe6dc0 100755 (executable)
--- a/imunes.tcl
+++ b/imunes.tcl
@@ -33,6 +33,22 @@
 # and Technology through the research contract #IP-2003-143.
 #
 
+#****h* imunes/imunes.tcl
+# NAME
+#    imunes.tcl
+# FUNCTION
+#    Starts imunes in batch or interactive mode. Include procedures from
+#    external files and initializes global variables.
+#
+#        imunes [-b|--batch] [filename]
+#    
+#    When starting the program in batch mode the option -b or --batch must 
+#    be specified. 
+#    
+#    When starting the program with defined filename, configuration for 
+#    file "filename" is loaded to imunes.
+#****
+
 if {[lindex $argv 0] == "-b" || [lindex $argv 0] == "--batch"} {
     set argv [lrange $argv 1 end]
     set execMode batch
@@ -49,6 +65,22 @@ if {[lindex $argv 0] == "-b" || [lindex $argv 0] == "--batch"} {
 # value by the installation script.
 #
 
+#****v* imunes.tcl/ROOTDIR
+# NAME
+#    ROOTDIR
+# FUNCTION
+#    The location of imunes library files. The ROOTDIR and LIBDIR variables 
+#    will be automatically set to the proper value by the installation script.
+#*****
+
+#****v* imunes.tcl/LIBDIR
+# NAME
+#    LIBDIR
+# FUNCTION
+#    The location of imunes library files. The ROOTDIR and LIBDIR variables 
+#    will be automatically set to the proper value by the installation script.
+#*****
+
 set LIBDIR ""
 set ROOTDIR "."
 
@@ -77,6 +109,47 @@ source "$ROOTDIR/$LIBDIR/filemgmt.tcl"
 #
 # Global variables are initialized here
 #
+
+#****v* imunes.tcl/node_list
+# NAME
+#    node_list
+# FUNCTION
+#    Represents the list of all the nodes in the simulation. When starting 
+#    the program this list is empty.
+#*****
+
+#****v* imunes.tcl/link_list
+# NAME
+#    link_list
+# FUNCTION
+#    Represents the list of all the links in the simulation. When starting 
+#    the program this list is empty.
+#*****
+
+#****v* imunes.tcl/canvas_list
+# NAME
+#    canvas_list
+# FUNCTION
+#    Contains the list of all the canvases in the simulation. When starting 
+#    the program this list is empty.
+#*****
+
+#****v* imunes.tcl/prefs
+# NAME
+#    prefs
+# FUNCTION
+#    Contains the list of preferences. When starting a program 
+#    this list is empty.
+#*****
+
+#****v* imunes.tcl/eid
+# NAME
+#    eid -- experiment id.
+# FUNCTION
+#    The id of the current experiment. When starting a program this variable 
+#    is set to e0.
+#*****
+
 set node_list {}
 set link_list {}
 set canvas_list {}