## [bonds,status] = abg2cbg(system_name, system_type, full_name, port_bonds, infofile)

  ## ###############################################################
  ## ## Version control history
  ## ###############################################################
  ## ## $Id$
  ## ## $Log$
  ## ## Revision 1.53  2009/11/02 16:54:03  geraint
  ## ## Replaced deprecated functions from Octave 2.1 for Octave 3.0: is_struct -> isstruct, struct_contains -> isfield, struct_elements -> fieldnames, is_complex -> iscomplex, setstr -> char
  ## ##
  ## ## Revision 1.52  2004/09/07 18:22:53  geraint
  ## ## Issues a more helpful error message than the cryptic Octave stuff
  ## ## if there are unconnected ports.
  ## ##
  ## ## Revision 1.51  2004/02/20 20:42:40  geraint
  ## ## Initialize Flipped.cons with [] instead of "".
  ## ##

	mtt_error (sprintf ("abg2cbg: port_bond_direction(%d) does not exist.", i));
	exit(1);
      end
      if (sign(port.connections)!=port_bond_direction(i)) # Direction different?
      	eval(["ABG.ports.",name,".connections = - port.connections;"]); # Flip direction at port
	Flipped.ports=[Flipped.ports;name];	# Remember which port has been flipped
        bond_index=abs(port.connections); # Index of bond on port
      	mtt_info(sprintf("Flip port %s on %s"\
      	mtt_info(sprintf("Flip port %s on %s" ...
			 ,name,full_name),infofile); # And report
      	for [subsystem,name] = ABG.subsystems # and at the other end
	  for k=1:length(subsystem.connections)
	    if (abs(subsystem.connections(k))==bond_index) # Then flip the connection
	      eval(["ABG.subsystems.",name,".connections(k)   = -subsystem.connections(k);"]);
	      Flipped.subs=[Flipped.subs;name];	# Remember which subsystem has been flipped
	      Flipped.cons=[Flipped.cons;k];	# Remember which connection has been flipped
      	      mtt_info(sprintf("Flip subsystem %s on %s"\
      	      mtt_info(sprintf("Flip subsystem %s on %s" ...
			       ,name,full_name),infofile); # And report
	    endif
	  endfor
      	endfor			# subsystem = ABG.subsystems

      	ABG.bonds(bond_index,:) = -ABG.bonds(bond_index,:);	# Flip the bond causalities 
	##(these are arrow-orientated)

function args = alias_args(args,alias,delim,message,FileID,sys_name)

###############################################################
## Version control history
###############################################################
## $Id$
## $Log$
## Revision 1.10  2012/10/15 19:16:03  geraint
## split is obsolete in Octave, replaced with strsplit
##
## Revision 1.9  2009/11/02 16:54:03  geraint
## Replaced deprecated functions from Octave 2.1 for Octave 3.0: is_struct -> isstruct, struct_contains -> isfield, struct_elements -> fieldnames, is_complex -> iscomplex, setstr -> char
##
## Revision 1.8  2001/06/13 16:07:15  gawthrop
## Fixed bug with three separators in a row eg )/(
##
## Revision 1.7  2001/06/13 14:50:15  gawthrop

      Args = char(strsplit(args,delim)); args="";
      [N,M]= size(Args);
      for i=1:N
        arg = deblank(Args(i,:));
        arg_ = strrep(arg,",","__");
        if isfield(alias,arg_)
          eval(["new_arg = alias.", arg_,";"]);
  	  mtt_info(["Replacing ", arg, "\t by ",\
  	  mtt_info(["Replacing ", arg, "\t by ", ...
		    new_arg, message],FileID);
  	  mtt_save_alias(arg,sys_name);
##	  printf("%s --> %s\n",arg,new_arg);
          arg = new_arg;
## 	else
## 	  mtt_info(["NOT replacing ", arg, message],FileID);
        end

  ## Structure matrix [states,nonstates,inputs,outputs,zero_outputs]
  
  ## ###############################################################
  ## ## Version control history
  ## ###############################################################
  ## ## $Id$
  ## ## $Log$
  ## ## Revision 1.54  2009/11/02 16:54:03  geraint
  ## ## Replaced deprecated functions from Octave 2.1 for Octave 3.0: is_struct -> isstruct, struct_contains -> isfield, struct_elements -> fieldnames, is_complex -> iscomplex, setstr -> char
  ## ##
  ## ## Revision 1.53  2005/03/21 11:09:47  gawthrop
  ## ## Now handles bicausal SS component -
  ## ##   ie source-source or sensor-sensor
  ## ##
  ## ## Revision 1.52  2004/09/12 22:27:27  geraint
  ## ## Appended 't' to fopen mode string to open in text mode.
  ## ##

    full_name = system_name;
    full_name_repetition = system_name;
    system_type = system_name;
  else
    full_name = [full_name, sub_delim, system_name];

    if (repetition>1)
      full_name_repetition = [full_name_repetition, \
			      sub_delim, system_name, sub_delim, \
      full_name_repetition = [full_name_repetition, ...
			      sub_delim, system_name, sub_delim, ...
			      num2str(repetition)];
    else
      full_name_repetition = [full_name_repetition, \
      full_name_repetition = [full_name_repetition, ...
			      sub_delim, system_name];
    endif
    
  end;
  
  
  

  
  ## Set up the counters for the labelled SS. These are, by definition,
  ## encountered first and so the counters will not be messed up by subsystems.
  local_u_index = 0;
  local_y_index = 0;
  
  if (length(system_args)==0)
    mtt_info(sprintf("No arguments given so no argument aliasing done for system %s(%s)",\
    mtt_info(sprintf("No arguments given so no argument aliasing done for system %s(%s)", ...
		     system_name,system_type), infofilenum);
    AliasingArguments=0;
  else
    AliasingArguments=1;
  endif;
  
  if (length(system_cr)==0)
    mtt_info(sprintf("No cr given so no cr aliasing done for system %s(%s)",\
    mtt_info(sprintf("No cr given so no cr aliasing done for system %s(%s)", ...
		     system_name,system_type), infofilenum);
    AliasingCRs=0;
  else
    AliasingCRs=1;  endif;
  
  
  fields=["ports";"subsystems"]; # Do for both ports and subsystems -

    	direction = sign(comp)'*[1 1];
				# Convert from arrow orientated to component orientated causality
    	comp_bonds = CBG.bonds(bond_list,:).*direction;
	
    	## disp(["---- ", field, " ---"]);    
    	
	if AliasingArguments	# Alias the args list if appropriate
    	  message = sprintf("\tfor component  %s (%s) within %s",\
    	  message = sprintf("\tfor component  %s (%s) within %s", ...
			    comp_name,subsystem.type,full_name);    
    	  if isfield(CBG,"alias")
	    subsystem.arg = alias_args(subsystem.arg,CBG.alias,";",message,infofilenum,full_name);
    	  endif;
	endif;
	
	if AliasingCRs	# Alias the CR list if appropriate
    	  message = sprintf("\tfor component  %s (%s) within %s",\
    	  message = sprintf("\tfor component  %s (%s) within %s", ...
			    comp_name,subsystem.type,full_name);    
    	  if isfield(CBG,"alias")
	    subsystem.cr = alias_args(subsystem.cr,CBG.alias,";",message,infofilenum,full_name);
    	  endif;
	endif;

	## Substitute positional ($1 etc) arguments

	    ## Link up the bonds for this compound component
	    fprintf(ese_file, ...
		    "\n\t%s Equations linking up subsystem %s (%s)\n\n", ...
		    pc, comp_name, subsystem.type);
	    
	    if (k>1)
	      name_comp_name = sprintf("%s%s%s%s%d", ...
				       full_name_repetition, sub_delim, \
				       full_name_repetition, sub_delim, ...
				       comp_name, sub_delim, k);
	    else
	      name_comp_name = sprintf("%s%s%s", ...
				       full_name_repetition, sub_delim, \
				       full_name_repetition, sub_delim, ...
				       comp_name);
	    endif
	    
	    
	    printf("\n\t%s Equations linking up subsystem %s (%s)\n\n",\
	    printf("\n\t%s Equations linking up subsystem %s (%s)\n\n", ...
		   pc, comp_name, subsystem.type);
	    
	    u_index = 0; y_index = 0; ## Count the inputs and outputs
	    for port_number=1:length(bond_list)
	      repetition,port_number
              port_bond_number = bond_list(port_number)
# 	      this_bond_effort_unit = \
# 	      this_bond_effort_unit = ...
# 		  deblank(bond_effort_unit(port_bond_number,:))
# 	      this_bond_flow_unit = \
# 	      this_bond_flow_unit = ...
# 		  deblank(bond_flow_unit(port_bond_number,:));

# 	      ## Extract the unit/domain stuff
#               this_port_name = subABG.portlist(port_number,:);
              
#               eval(sprintf("this_port = subABG.ports.%s;", \
#               eval(sprintf("this_port = subABG.ports.%s;", ...
# 			   this_port_name));
# 	      if isfield(this_port,"units")
#                 eval(["effort_unit = \
#                 eval(["effort_unit = ...
# 		    subABG.ports.",this_port_name,".units.effort;"]);
#                 eval(["flow_unit = \
#                 eval(["flow_unit = ...
# 		    subABG.ports.",this_port_name,".units.flow;"]);
# 	      else
# 		effort_unit = "none";
# 		flow_unit = "none";
# 	      endif

# 	      ## and check consistency
#               ## Efforts
# 	      if strcmp(this_bond_effort_unit,"null") # set
# 		bond_effort_unit = \
# 		bond_effort_unit = ...
# 		    [bond_effort_unit(1:port_bond_number-1,:)
# 		     effort_unit
# 		     bond_effort_unit(port_bond_number+1:n_bonds,:)
# 		     ]
# 	      elseif (!strcmp(this_bond_effort_unit,"none") && !strcmp(effort_unit,"none")) # check
# 		mtt_info(sprintf(unit_info,full_name, effort_unit, \
# 		mtt_info(sprintf(unit_info,full_name, effort_unit, ...
# 				 this_bond_effort_unit), infofilenum);
# 		if !strcmp(this_bond_effort_unit,effort_unit)
# 		  error_string = sprintf(unit_error, full_name,\
# 					 effort_unit, \
# 		  error_string = sprintf(unit_error, full_name, ...
# 					 effort_unit, ...
# 					 this_bond_effort_unit);
# 		  mtt_error(error_string);
# 		endif
# 	      endif
# 	      ## Flows
# 	      if strcmp(this_bond_flow_unit,"null") # set
# 		bond_flow_unit = \
# 		bond_flow_unit = ...
# 		    [bond_flow_unit(1:port_bond_number-1,:)
# 		     flow_unit
# 		     bond_flow_unit(port_bond_number+1:n_bonds,:)
# 		     ]
# 	      elseif (!strcmp(this_bond_flow_unit,"none") && !strcmp(flow_unit,"none")) # check
# 		mtt_info(sprintf(unit_info,full_name, flow_unit, \
# 		mtt_info(sprintf(unit_info,full_name, flow_unit, ...
# 				 this_bond_flow_unit), infofilenum);
# 		if !strcmp(this_bond_flow_unit,flow_unit)
# 		  error_string = sprintf(unit_error, full_name,\
# 					 flow_unit, \
# 		  error_string = sprintf(unit_error, full_name, ...
# 					 flow_unit, ...
# 					 this_bond_flow_unit);
# 		  mtt_error(error_string);
# 		endif
# 	      endif
	      

	      ## Effort

		    cause_name = cause2name(-comp_bonds(1,k));
		  else		# Maybe multiport - but unicausal
		    cause_name = cause2name(-comp_bonds(k,1));
		  endif
 		  fprintf(structure_file, ...
 			  "%s\t%i\t%s\t%s%s%s\t%i\t%s\n", ...
 			  structure_name(which_index,:), value-k+1, ...
 			  comp_name, full_name_repetition, sub_delim, comp_name, \
 			  comp_name, full_name_repetition, sub_delim, comp_name, ...
 			  repetition, cause_name); 
 	    	endfor;
 	      endfor;
 	    endif;
	  endif
	endfor
	fflush (structure_file);

## -*-octave-*-

function [bonds,components,n_vector_bonds] = \
function [bonds,components,n_vector_bonds] = ...
      ibg2abg(name,bonds,infofile,errorfile)

  ## write useful quantity of data to log
  struct_levels_to_print(6);

  ################################
  ## create component structure ##

	    endif
	  endif
	  eval(sprintf("comp.%s = bond;", bond_name));
	endfor
	
	## attach labels to unlabelled ports
	if (n_named_ports == 0)
	  mtt_info(sprintf("Defaulting all ports on junction %s to 'in'", \
	  mtt_info(sprintf("Defaulting all ports on junction %s to 'in'", ...
			   comp_name), infofile);
	  for [bond, bond_name] = comp
	    if (index(bond_name, "bond") == 1)
	      bond.label = "in";
	    endif
	    eval(sprintf("comp.%s = bond;", bond_name));
	  endfor
	elseif (n_named_ports == 1)
	  mtt_info(sprintf("Defaulting all ports on junction %s to %s", \
	  mtt_info(sprintf("Defaulting all ports on junction %s to %s", ...
			   comp_name, port_label), infofile);
	  for [bond, bond_name] = comp
	    if (index(bond_name, "bond") == 1)
	      bond.label = port_label;
	    endif
	    eval(sprintf("comp.%s = bond;", bond_name));
	  endfor
	elseif (n_named_ports != comp.n_bonds)
	  mtt_error(sprintf("Junction must have 0,1 or %i port labels", \
	  mtt_error(sprintf("Junction must have 0,1 or %i port labels", ...
			    comp.n_bonds), errorfile);
	endif
	
      else
	## component is not a junction
	for [bond, bond_name] = comp
	  if (index(bond_name, "bond") == 1)

function [args] = mtt_alias (fullname,args,default);
  ## usage:  [cr,args] = mtt_alias (fullname,cr,args)
  ##
  ## Aliasing code for mtt.
  ## Abstracted from cbg2ese for use in cbg2sese_m2r

  ## Copyright (C) 2003 by Peter J. Gawthrop

  filenum = -1;			# No file number for messages

  [Name,name] = mtt_subname(fullname); # Split fullname

  if (length(args)==0)
    mtt_info(sprintf("No arguments given so no argument aliasing done for system %s",\
    mtt_info(sprintf("No arguments given so no argument aliasing done for system %s", ...
		     fullname));
    return
  endif
  
  ## Info for component and surrounding subsystem
  cbg = mtt_cbg(fullname);	# Structure for this component

function [known] = mtt_component_eqn (fullname, port, causality, \
function [known] = mtt_component_eqn (fullname, port, causality, ...
				      known, Cbg)

  ## function [known] = mtt_component_eqn (fullname, port, causality, known)
  ##
  ## Recursively finds the equations giving the signal of specified
  ## causality on the specified port of component named "name" within
  ## subsystem Name 

    if port>N_ports
      error(sprintf("port (%i) > N_ports (%i)", port, N_ports));
    else			# Get name and find equation
      name = deblank(cbg.portlist(port,:));
      if DEBUG
	disp("----> lower-level system")
      endif
      known = mtt_component_eqn (mtt_fullname(Name,name), 1, \
      known = mtt_component_eqn (mtt_fullname(Name,name), 1, ...
				 causality, known, cbg);
      return
    endif
  endif
  

  ## Other causality representations

  
  ## A useful composite name
  name_port_cause = sprintf("%s_%i_%s",name, port, cause);
  full_name_port_cause = mtt_fullname(Name,name_port_cause);

  ## If value is known, don't do anything.
  if findstr(sprintf(" %s ", full_name_port_cause), known)>0
    eqn = sprintf("%s The %s signal on port %i of %s is known already", \
    eqn = sprintf("%s The %s signal on port %i of %s is known already", ...
		  CD, causality, port, name);
    return
  else			# Add to list
    known = sprintf("%s %s", known, full_name_port_cause);
  endif
  
  

  bonds = cbg.bonds;

  ## List of component bond causality (component-orientated causality)
  comp_bonds = bonds(bond_list,:).*directions; # Component bonds

  ## What components are at the other ends of the in bonds?
  ## Effort
  [in_e_bonds,in_e_components,in_e_ports,N_e] = mtt_component_inputs \
  [in_e_bonds,in_e_components,in_e_ports,N_e] = mtt_component_inputs ...
      (name,comp_type,causality,"effort",comp_bonds,connections,cbg);
  ## Flow
  [in_f_bonds,in_f_components,in_f_ports,N_f] = mtt_component_inputs \
  [in_f_bonds,in_f_components,in_f_ports,N_f] = mtt_component_inputs ...
      (name,comp_type,causality,"flow",comp_bonds,connections,cbg);


  ##Composite values
  N_ef = N_e + N_f;
  in_ef_bonds = [in_e_bonds; in_f_bonds];
  in_ef_components = [in_e_components; in_f_components];

    ## Find its equation
    if DEBUG
      disp("----> higher level system")
    endif
    

    known = mtt_component_eqn (mtt_fullname(new_Name,in_name), \
    known = mtt_component_eqn (mtt_fullname(new_Name,in_name), ...
			       in_port, causality, known, cbg);

    LHS = Source_seqn ("external",Name);
    RHS = varname(NAME, abs(in_bond), i_cause);
    eqn = sprintf("%s%s%s := %s;", LHS, SD, name, RHS);

    if !DEBUG
      comment = sprintf("%s PORT", CD);
      disp(sprintf("%s\n%s",comment, eqn));
    endif

  endif
  

  ## Handle special components
  if strcmp(comp_type,"0")||strcmp(comp_type,"1") # Junctions
    [eqn,insigs,innames] = junction_seqn (comp_type,Name, outsig, \
    [eqn,insigs,innames] = junction_seqn (comp_type,Name, outsig, ...
					  insigs, innames);
  else				# Everything else
    if exist(sprintf("%s_cause", comp_type)) # Simple component
      ## Do the equations
      [eqn,insigs,innames] = eval(sprintf("%s_seqn (Name, name, cr, \
						    arg, outsig, \
						    insigs, \
						    innames, is_port_output);", \
      [eqn,insigs,innames] = eval(sprintf("%s_seqn (Name, name, cr, ...
						    arg, outsig, ...
						    insigs, ...
						    innames, is_port_output);", ...
					  comp_type));
      ## Resolve CR
      eqn = mtt_resolve_cr(eqn);

    else			# Compound component
      new_NAME = Name;
      new_Name = mtt_fullname(Name,name);

      RHS = Sensor_seqn ("external",new_Name);
      eqn = sprintf("%s := %s%s%s;", LHS, RHS, SD, port_name);

      if DEBUG
	disp("----> same-level subsystem")
      endif

      [known] = mtt_component_eqn \
      [known] = mtt_component_eqn ...
   	  (mtt_fullname(new_Name,new_name), port, causality, known, cbg);
      
    endif
  endif

  comment = \
      sprintf("%s Equation for %s signal on port %i of %s (%s), subsystem %s.", \
  comment = ...
      sprintf("%s Equation for %s signal on port %i of %s (%s), subsystem %s.", ...
     	      CD, causality, port, name, comp_type, Name);

  if DEBUG
    disp(sprintf("%s\n%s",comment, eqn));
  endif
  
  is_external = mtt_is_external(comp_type,outsig, insigs, is_port_output);

      other_port = insigs(i,3);
      other_name = deblank(innames(i,:));
      if DEBUG
	disp("----> same-level component")
      endif
      

      [known] = mtt_component_eqn \
    	  (mtt_fullname(Name,other_name), other_port, other_causality, \
      [known] = mtt_component_eqn ...
    	  (mtt_fullname(Name,other_name), other_port, other_causality, ...
	   known, cbg);
    endfor
  endif

  ## Write this signal
  ##comment_2 = sprintf("Connected to:%s", in_component_list);
  if !DEBUG
    disp(sprintf("%s\n%s",comment, eqn));
  endif

endfunction

function [in_bonds,in_components,in_ports,N] = mtt_component_inputs \
function [in_bonds,in_components,in_ports,N] = mtt_component_inputs ...
      (name,comp_type, out_causality, causality,comp_bonds,bond_list,cbg)

  ## usage:  [in_bonds,in_components,in_ports,N] = mtt_component_inputs 
  ##      (name,comp_type, out_causality, causality,comp_bonds,bond_list,cbg)
  ##
  ## 

    for j=1:length(theta)
      args = sprintf("%s %g",args, theta(j));
    endfor

    ## Run system and replace NaN by 1e30 -- easier to handle
    file_name = sprintf("%s_input.dat", system_name);
    if exist(file_name)==2	# Then use data from this file ...
      command = sprintf("./%s_ode2odes.out %s < %s | sed \'s/NAN/Inf/g\' >mtt_out_data.dat\n", \
      command = sprintf("./%s_ode2odes.out %s < %s | sed \'s/NAN/Inf/g\' >mtt_out_data.dat\n", ...
			system_name, args, file_name);
    else
      command = sprintf("./%s_ode2odes.out %s | sed \'s/NAN/Inf/g\' >mtt_out_data.dat\n", \
      command = sprintf("./%s_ode2odes.out %s | sed \'s/NAN/Inf/g\' >mtt_out_data.dat\n", ...
			system_name, args);
    endif
      
   system(command);

    ## Retrieve out_data
    load -force mtt_out_data.dat

## ###############################################################
## ## Version control history
## ###############################################################
## ## $Id$
## ## $Log$
## ## Revision 1.2  2003/01/07 09:11:53  gawthrop
## ## Octavised
## ##
## ## Revision 1.1  1998/07/25 09:47:43  peterg
## ## Initial revision
## ##
## ###############################################################



  if nargin<7
    eqnfile = "stdout";
  endif

  ## Find the number of ports
  ports = length(RHS_cause);

  ## Print the CR
  if length(cr) == 0 # No CR given - use unity CR
    fprintf(eqnfile, "%s;\n", varname(name,bond_number(outport), \
    fprintf(eqnfile, "%s;\n", varname(name,bond_number(outport), ...
				      RHS_cause(outport)));
  else # CR exists
    fprintf(eqnfile, "%s(%s", cr, name); # The CR name and component type
    if ports>1 # Multi ports - port no. is first arg of CR
      fprintf(eqnfile, "#1.0f,", outport);
    endif
    fprintf(eqnfile, "%s", args); # Print the arguments

function [bonds,components,n_vector_bonds] = rbg2abg(name,rbonds,rstrokes,rcomponents,\
				      port_coord,port_name,\
function [bonds,components,n_vector_bonds] = rbg2abg(name,rbonds,rstrokes,rcomponents, ...
				      port_coord,port_name, ...
				      infofile,errorfile)

  ## ###############################################################
  ## ## Version control history
  ## ###############################################################
  ## ## $Id$
  ## ## $Log$
  ## ## Revision 1.51  2012/10/15 19:22:44  geraint
  ## ## mtt_isunique replaces unique which masks a built-in function.
  ## ##
  ## ## Revision 1.50  2009/11/02 16:54:03  geraint
  ## ## Replaced deprecated functions from Octave 2.1 for Octave 3.0: is_struct -> isstruct, struct_contains -> isfield, struct_elements -> fieldnames, is_complex -> iscomplex, setstr -> char
  ## ##
  ## ## Revision 1.49  2004/07/22 13:18:02  geraint
  ## ## Minor typo in error message.
  ## ##
  ## ## Revision 1.48  2004/02/19 18:27:47  geraint

	      out_bonds++;
	      port_name_i = "out";
	    endif
	    
	  elseif (unlabelled_ports==2)
	    if port_direction>0
	      if (++in_bonds>1)
		mtt_error(["More than one unlabelled INport on component " \
		mtt_error(["More than one unlabelled INport on component " ...
			   comp_name " (" comp_type ")"],errorfile);
	      else
		port_name_i = "in";
	      end
	    else
	      if (++out_bonds>1)
		mtt_error(["More than one unlabelled OUTport on component " \
		mtt_error(["More than one unlabelled OUTport on component " ...
			   comp_name " (" comp_type ")"],errorfile);
	      else
		port_name_i = "out";
	      end
	    endif
	    
	  else
	    mtt_error(["More than two unlabelled ports on component " \
	    mtt_error(["More than two unlabelled ports on component " ...
		       comp_name " (" comp_type ")"],errorfile);
          endif
	  
	  mtt_info(["Defaulting port name [" port_name_i "]\t on component " \
	  mtt_info(["Defaulting port name [" port_name_i "]\t on component " ...
		    comp_name " (" comp_type ")" ],infofile);
	  port_name = [port_name; ["[" port_name_i "]"]];	# add to list
	  [port_name_index,junk] = size(port_name); # the corresponding
				# index
	  port_bond(port_name_index,:) = signed_bond; # add to port bond
	else  
	  port_name_i = mtt_strip_name(port_name(port_name_index,:))
	  ## port_name_i = deblank(port_name(port_name_index,:));
	  ## port_name_i = port_name_i(2:length(port_name_i)-1) # strip []
	endif
	
	
	## Replace by alias -- if any
    	eval( ["alias = ", comp_type, '_alias';]); # Get aliases
    	if isstruct(alias)		# are there any aliases
          if isfield(alias,port_name_i) # Is this an alias?
	    eval(["new_port_name_i = alias.",port_name_i]);
	    mtt_info(["Aliasing name [" port_name_i "]\t on component " \
	    mtt_info(["Aliasing name [" port_name_i "]\t on component " ...
		      comp_name " (" comp_type ")\t to [" new_port_name_i "]"],infofile);
	    port_name = replace_name(port_name, \
				     ["[",new_port_name_i,"]"], \
	    port_name = replace_name(port_name, ...
				     ["[",new_port_name_i,"]"], ...
				     port_name_index);
	  endif
	  
      	endif
	
      endfor
      
    endif
    
  endfor
  
  ## At this point, every port should be labeled (port_name) and \
  ## At this point, every port should be labeled (port_name) and ...
  ## associated with a bond (port_bond).
  disp("--- Completed portnames and the corresponding bonds ---")
  port_name, port_bond


  ## Deduce causality from the strokes (if any) and create the list of bonds
  causality = zeros(n_bonds,2);

    [n_comp_ports,m_comp_ports] = size(port_list);
    subport_list="";
    for p=1:n_comp_ports		# Expand any vector ports
      [subport,n_sub] = split_port(port_list(p,:), ','); # Find the components
				# of the vector port
      if n_sub>1
	mtt_info(sprintf("Expanding vector port %s of component type %s",\
	mtt_info(sprintf("Expanding vector port %s of component type %s", ...
			 port_list(p,:), comp_type, infofile));	
      endif
      
      subport_list = [subport_list; subport];
    endfor
    
    port_list = subport_list;	# Set the expanded port list.

	mtt_error(['Component ', comp_name, ' (', comp_type, ') has no labeled ports'], errorfile); 
      endif
      
      ##Write out the signed bond list in the correct order
      unsorted_port_list
      [n_list,m_list] = size(unsorted_port_list);
      if n_list!=n_comp_bonds
	error(sprintf("Component %s (%s) has %i bonds but %i port labels",\
	error(sprintf("Component %s (%s) has %i bonds but %i port labels", ...
		      comp_name, comp_type, n_comp_bonds, n_list))
      endif

      for j = 1:n_comp_bonds
	j
	name_k = unsorted_port_list(j,:)
	k = name_in_list(name_k, port_list);

## -*-octave-*-

function [bonds] = \
      rbg2ibg(name,rbonds,rstrokes,rcomponents,port_coord,port_name, \
function [bonds] = ...
      rbg2ibg(name,rbonds,rstrokes,rcomponents,port_coord,port_name, ...
	      infofile, errorfile)

  rbonds
  rstrokes
  rcomponents
  port_coord
  port_name

  arrow_end	= rbonds(:,3:4);
  other_end_2	= rbonds(:,5:6);

  distance_1	= length2d(other_end_1 - arrow_end);
  distance_2	= length2d(other_end_2 - arrow_end);
  which_end	= (distance_1 > distance_2) * [1, 1];
  one		= ones(size(which_end));
  other_end	= which_end .* other_end_1 + (one - which_end) .* \
  other_end	= which_end .* other_end_1 + (one - which_end) .* ...
      other_end_2;
  arrow_vector	= (which_end .* other_end_2 + (one - which_end) .* \
  arrow_vector	= (which_end .* other_end_2 + (one - which_end) .* ...
		   other_end_1) - arrow_end;
  
  ## Locate bond end nearest each port
  ## col 1 of port_near_bond contains a signed bond number (+ for arrow
  ## end)
  ## col 2 of port_near_bond contains the corresponding port index
  port_bond = [];
  for i = 1:n_ports
    near_bond = adjbond(port_coord(i,1:2), arrow_end, other_end);
    [rows,cols] = size(near_bond);
    if (rows > 1)
      error(sprintf ...
	    ("A port is near to more than one bond at coordinates \
	    ("A port is near to more than one bond at coordinates ...
	  %g,%g %s\n", ...
	     port_coord(i,1)/scale, port_coord(i,2)/scale, \
	     port_coord(i,1)/scale, port_coord(i,2)/scale, ...
	     deblank(port_name(i,:))));
    endif
    
    ## The (signed) bond corresponding to the ith port label
    port_bond(i,1) = near_bond(1) * sign(1.5 - near_bond(2));
  endfor
  port_bond

  ## Now have (signed) bond (port_bond(i)) corresponding to the ith port
  ## Create inverse mapping
  for i = 1:n_bonds
    eval(sprintf('bond_port_head%i = "[]"', i))
    eval(sprintf('bond_port_tail%i = "[]"', i))
  endfor  
  for i = 1:n_ports
    if (port_bond(i) > 0)
      eval(sprintf('bond_port_head%i = "%s"', port_bond(i), \
      eval(sprintf('bond_port_head%i = "%s"', port_bond(i), ...
		   deblank(port_name(i,:))))
    else
      eval(sprintf('bond_port_tail%i = "%s"', -port_bond(i), \
      eval(sprintf('bond_port_tail%i = "%s"', -port_bond(i), ...
		   deblank(port_name(i,:))))
    endif
  endfor
  
  ## Locate the components at the ends of each bond
  ## col 1 of comp_near_bond contains component nearest to the arrow end
  ## col 2 of comp_near_bond contains component nearest other end
  for i = 1:n_bonds
    comp_near_bond(i,:) = adjcomp(arrow_end(i,:), other_end(i,:), \
    comp_near_bond(i,:) = adjcomp(arrow_end(i,:), other_end(i,:), ...
				  rcomponents);
  endfor
  comp_near_bond

  ## Deduce causality from the strokes (if any)
  causality = zeros(n_bonds,2);
  if (n_strokes > 0)

		stroke_end_2(i,:)];


      ## Find the nearest bond end
      [index,distance] = adjbond(stroke(1,:),arrow_end,other_end);
      if (distance > (2 * stroke_length(i)))
	info = sprintf('Stroke at (%4.3f,%4.3f) is %4.3f away from the nearest bond\n', ...
		       stroke(1,1)/scale, stroke(1,2)/scale, \
		       stroke(1,1)/scale, stroke(1,2)/scale, ...
		       distance/scale);
      endif

      ## Bond end coordinates
      j = index(1,1);
      which_end = (index(1,2) == 1);
      bond_end = arrow_end(j,:) * which_end + other_end(j,:) * (1 - \
      bond_end = arrow_end(j,:) * which_end + other_end(j,:) * (1 - ...
								which_end);
      
      ## Now decide which bit of the stroke is nearest
      stroke_index = adjbond(bond_end, stroke, zeros(size(stroke)));

      if (stroke_index(1) == 1)	# uni-causal stroke
	causality(j,1:2) = (2 * which_end - 1) * [1, 1];

  causality

  ## Write data
  for i = 1:n_bonds
    [hc_type, hc_name] = eval([name, '_cmp(comp_near_bond(i,1))']);
    [tc_type, tc_name] = eval([name, '_cmp(comp_near_bond(i,2))']);
    ## components
    eval(sprintf("bonds.bond%i.head.component\t= '%s:%s'", i, hc_type, \
    eval(sprintf("bonds.bond%i.head.component\t= '%s:%s'", i, hc_type, ...
		 hc_name));
    eval(sprintf("bonds.bond%i.tail.component\t= '%s:%s'", i, tc_type, \
    eval(sprintf("bonds.bond%i.tail.component\t= '%s:%s'", i, tc_type, ...
		 tc_name));
    ## ports
    eval(sprintf("bonds.bond%i.head.ports\t= bond_port_head%i", i, i));
    eval(sprintf("bonds.bond%i.tail.ports\t= bond_port_tail%i", i, i));
    ## causality
    if (causality(i,1) == 1)
      effort_causality = "head"

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %% Version control history
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %% $Id$
% %% $Log$
% %% Revision 1.7  2001/07/03 22:59:10  gawthrop
% %% Fixed problems with argument passing for CRs
% %%
% %% Revision 1.6  1998/07/27 09:53:44  peterg
% %% No change
% %%
% %% Revision 1.5  1998/07/21 16:43:26  peterg
% %% Now writes to an explicit fileID - otherwise we may run out of IDs.
% %%
% %% Revision 1.4  1996/12/10 16:04:11  peterg

      % Test for empty argument -- replace by default and tell user
      message = 'Argument %1.0f of component %s(%s) of system %s is undefined - \n replacing by %s';
      if strcmp(arg_out,'')
	info = sprintf(message, ...
	    i, comp_name, comp_type, full_name, default);
	arg_out = default;
      else
	info = sprintf("Replacing $%i \t by %s for component %s (%s) \
	info = sprintf("Replacing $%i \t by %s for component %s (%s) ...
	within %s", i, arg_out, comp_name, comp_type, full_name);
      end;
      mtt_info(info,fileID);
      args_out = [args_out, arg_out];
    end;
  end;
end;

  format_hp = "  %s.bonds.bond%i.head.ports\t= \"%s\";\n";
  format_tp = "  %s.bonds.bond%i.tail.ports\t= \"%s\";\n";
  format_ce = "  %s.bonds.bond%i.causality.effort\t= \"%s\";\n";
  format_cf = "  %s.bonds.bond%i.causality.flow\t= \"%s\";\n";

  fprintf(fid, "## -*-octave-*-\n\n");
  fprintf(fid, "function [%s] = %s_ibg\n\n", system_name, system_name);
  fprintf(fid, "  ## Intermediate bond graph representation of %s\n", \
  fprintf(fid, "  ## Intermediate bond graph representation of %s\n", ...
	  system_name);

  fprintf(fid, "  ## Generated by MTT on %s\n", ctime(time));
  fprintf(fid, "  ## head refers to the harpoon end of a bond\n");
  fprintf(fid, "  ## tail refers to the other end of a bond\n");
  fprintf(fid, "  ## causality.? is the end at which ? is imposed\n\n");

  for i=1:nbonds
    fprintf(fid, "\n  ## bond %i\n", i);
    fprintf(fid, format_hc, system_name, i, \
    fprintf(fid, format_hc, system_name, i, ...
	    eval(sprintf("bonds.bond%i.head.component", i)));
    fprintf(fid, format_tc, system_name, i, \
    fprintf(fid, format_tc, system_name, i, ...
	    eval(sprintf("bonds.bond%i.tail.component", i)));
    fprintf(fid, format_hp, system_name, i, \
    fprintf(fid, format_hp, system_name, i, ...
	    eval(sprintf("bonds.bond%i.head.ports", i)));
    fprintf(fid, format_tp, system_name, i, \
    fprintf(fid, format_tp, system_name, i, ...
	    eval(sprintf("bonds.bond%i.tail.ports", i)));
    fprintf(fid, format_ce, system_name, i, \
    fprintf(fid, format_ce, system_name, i, ...
	    eval(sprintf("bonds.bond%i.causality.effort", i)));
    fprintf(fid, format_cf, system_name, i, \
    fprintf(fid, format_cf, system_name, i, ...
	    eval(sprintf("bonds.bond%i.causality.flow", i)));
  endfor;

  fprintf(fid, "\nendfunction\n");
  fclose(fid);

endfunction;