Index: /issm/trunk-jpl/src/m/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/m/Makefile.am	(revision 11863)
+++ /issm/trunk-jpl/src/m/Makefile.am	(revision 11864)
@@ -46,6 +46,4 @@
 
 #Special treatment of old classes
-pairoptionsdir=$(bindir)/@pairoptions
-pairoptions_DATA=./classes/@pairoptions/*.m
 modellistdir=$(bindir)/@modellist
 modellist_DATA=./classes/@modellist/*.m
Index: /issm/trunk-jpl/src/m/classes/pairoptions.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/pairoptions.m	(revision 11864)
+++ /issm/trunk-jpl/src/m/classes/pairoptions.m	(revision 11864)
@@ -0,0 +1,223 @@
+%PAIROPTIONS class definition
+%
+%   Available verbosity levels:
+%      mprocessor  : model processing 
+%      module      : modules
+%      solution    : solution sequence
+%      solver      : solver info (extensive)
+%      convergence : convergence criteria
+%      control     : control method
+%      qmu         : sensitivity analysis
+%
+%   Usage:
+%      pairoptions=pairoptions();
+%      pairoptions=pairoptions('module',true,'solver',false);
+
+classdef pairoptions
+	properties (SetAccess=public) 
+		functionname = '';
+		list         = cell(0,2);
+	end
+	%}}}
+	methods
+		function obj = pairoptions(varargin) % {{{
+
+			%get calling function name
+			a=dbstack;
+			if length(a)>1,
+				obj.functionname=a(2).file(1:end-2);
+			else
+				obj.functionname='';
+			end
+
+			%initialize list
+			if nargin==0,
+				%Do nothing,
+			else
+				obj=buildlist(obj,varargin{:});
+			end
+		end % }}}
+		function obj = buildlist(obj,varargin) % {{{
+		%BUILDLIST - build list of obj from input
+
+			%check length of input
+			if mod((nargin-1),2),
+				error('error: an even number of options is required') 
+			end
+			numoptions = (nargin-1)/2;
+
+			%Allocate memory
+			obj.list=cell(numoptions,2);
+
+			%go through varargin and build list of obj
+			for i=1:numoptions,
+				if ischar(varargin{2*i-1}),
+					obj.list{i,1}=varargin{2*i-1};
+					obj.list{i,2}=varargin{2*i};
+				else
+					%option is not a string, ignore it
+					disp(['WARNING: option number ' num2str(i) ' is not a string, it will be ignored']);
+					obj.list(i,:)=[];
+					continue
+				end
+			end
+		end % }}}
+		function obj = addfield(obj,field,value) % {{{
+			if ischar(field),
+				obj.list{end+1,1} = field;
+				obj.list{end,2}   = value;
+			end
+		end % }}}
+		function obj = addfielddefault(obj,field,value) % {{{
+		%ADDFIELDDEFAULT - add a field to an options list if it does not exist
+			if ischar(field),
+				if ~exist(obj,field),
+					obj.list{end+1,1} = field;
+					obj.list{end,2}   = value;
+				end
+			end
+		end % }}}
+		function obj = changefieldvalue(obj,field,newvalue) % {{{
+		%CHANGEOPTIONVALUE - change the value of an option in an option list
+
+			%track occurance of field
+			lines=find(strcmpi(obj.list(:,1),field));
+
+			%replace value
+			if isempty(lines),
+				%add new field if not found
+				obj=addfield(obj,field,newvalue);
+			else
+				for i=1:length(lines),
+					obj.list{lines(i),2}=newvalue;
+				end
+			end
+		end % }}}
+		function obj = deleteduplicates(obj,warn) % {{{
+		%DELETEDUPLICATES - delete duplicates in an option list
+
+			%track the first occurance of each option
+			[dummy lines]=unique(obj.list(:,1),'first');
+			clear dummy
+
+			%warn user if requested
+			if warn,
+				numoptions=size(obj.list,1);
+				for i=1:numoptions,
+					if ~ismember(i,lines),
+						disp(['WARNING: option ' obj.list{i,1} ' appeared more than once. Only its first occurence will be kept'])
+					end
+				end
+			end
+
+			%remove duplicates from the options list
+			obj.list=obj.list(lines,:);
+		end % }}}
+		function disp(obj) % {{{
+			disp(sprintf('   functionname: %s',obj.functionname));
+			if ~isempty(obj.list),
+				disp(sprintf('   list: (%ix%i)\n',size(obj.list,1),size(obj.list,2)));
+				for i=1:size(obj.list,1),
+					if ischar(obj.list{i,2}),
+						disp(sprintf('     field: %-10s value: ''%s''',obj.list{i,1},obj.list{i,2}));
+					elseif isnumeric(obj.list{i,2}) & length(obj.list{i,2})==1,
+						disp(sprintf('     field: %-10s value: %g',obj.list{i,1},obj.list{i,2}));
+					elseif isnumeric(obj.list{i,2}) & length(obj.list{i,2})==2,
+						disp(sprintf('     field: %-10s value: [%g %g]',obj.list{i,1},obj.list{i,2}));
+					else
+						disp(sprintf('     field: %-10s value: (%ix%i)',obj.list{i,1},size(obj.list{i,2},1),size(obj.list{i,2},2)));
+					end
+				end
+			else
+				disp(sprintf('   list: empty'));
+			end
+		end % }}}
+		function bool = exist(obj,field) % {{{
+		%EXIST - check if the option exist
+
+			%some argument checking: 
+			if ((nargin~=2) | (nargout~=1)),
+				error('exist error message: bad usage');
+			end
+			if ~ischar(field),
+				error('exist error message: field should be a string');
+			end
+
+			%Recover option
+			bool=any(strcmpi(field,obj.list(:,1)));
+		end % }}}
+		function num = fieldoccurences(obj,field), % {{{
+		%FIELDOCCURENCES - get number of occurence of a field
+
+			%check input 
+			if ~ischar(field),
+				error('fieldoccurences error message: field should be a string');
+			end
+
+			%get number of occurence
+			num=sum(strcmpi(field,obj.list(:,1)));
+		end % }}}
+		function value = getfieldvalue(obj,field,varargin), % {{{
+		%GETOPTION - get the value of an option
+		%
+		%   Usage:
+		%      value=getfieldvalue(obj,field,varargin)
+		%
+		%   Find an option value from a field. A default option
+		%   can be given in input if the field does not exist
+		%
+		%   Examples:
+		%      value=getfieldvalue(options,'caxis');
+		%      value=getfieldvalue(options,'caxis',[0 2]);
+
+			%some argument checking: 
+			if ((nargin~=2 & nargin~=3) | (nargout~=1)),
+				help getfieldvalue
+				error('getfieldvalue error message: bad usage');
+			end
+
+			if ~ischar(field),
+				error('getfieldvalue error message: field should be a string');
+			end
+
+			%Recover option
+			for i=1:size(obj.list,1),
+				if strcmpi(obj.list{i,1},field)
+					value=obj.list{i,2};
+					return
+				end
+			end
+
+			%The option has not been found, output default if provided
+			if nargin==3,
+				value=varargin{1};
+			else
+				error(['error message: field ' field ' has not been provided by user (and no default value has been specified)'])
+			end
+		end % }}}
+		function obj = removefield(obj,field,warn)% {{{
+		%REMOVEFIELD - delete a field in an option list
+		%
+		%   Usage:
+		%      obj=removefield(obj,field,warn)
+		%
+		%   if warn==1 display an info message to wan user that
+		%   some of his options have been removed.
+
+			%check is field exist
+			if exist(obj,field),
+
+				%find where the field is located
+				lines=find(~strcmpi(obj.list(:,1),field));
+
+				%remove duplicates from the options list
+				obj.list=obj.list(lines,:);
+
+				%warn user if requested
+				if warn
+					disp(['removefield info: option ' field ' has been removed from the list of options.'])
+				end
+			end
+		end % }}}
+	end
+end