diff --git a/api/Log_h.html b/api/Log_h.html
deleted file mode 100644
index 8b366650951a36f66a87a3024e886f9695562578..0000000000000000000000000000000000000000
--- a/api/Log_h.html
+++ /dev/null
@@ -1,184 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>Source: Log.h</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>Source: Log.h</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<pre>
-/* Log.h
-
- Mark Woolrich, FMRIB Image Analysis Group
-
- Copyright (C) 1999-2000 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#if !defined(Log_h)
-#define Log_h
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include "newmatap.h"
-#include "newmatio.h"
-
-using namespace NEWMAT;
-
-namespace Utilities{
-
- template<class t> string tostring(const t obj);
-
- class Log
- {
- public:
- static Log& getInstance();
- ~Log() { delete logger; }
-
- /** Makes a directory to place results into:
- keeps adding "+" to pdirname until unique directory is made: */
- void makeDir(const string& pdirname, const string& plogfilename = "logfile");
-
- /** Sets an existing directory to place results into: */
- void setDir(const string& pdirname, const string& plogfilename = "logfile");
-
- const string& getDir() const { return dir; }
- const string& getLogFileName() const { return logfilename; }
- const string appendDir(const string& filename) const { return dir + "/" + filename;}
-
- void out(const string& p_fname, const Matrix& p_mat);
- void out(const string& p_fname, const RowVector& p_mat);
- void out(const string& p_fname, const ColumnVector& p_mat);
-
- static int counter() { return count++; }
- ofstream& str();
-
- private:
- Log():logEstablished(false) {}
-
- const Log& operator=(Log&);
- Log(Log&);
-
- static Log* logger;
- string dir;
- ofstream logfileout;
- string logfilename;
- static int count;
-
- bool logEstablished;
- };
-
- inline void Log::out(const string& p_fname, const Matrix& p_mat)
- {
-
- if(!logEstablished)
- {
- logfilename = "logfile";
- setDir(".");
- }
-
- ofstream out;
- out.open((dir + "/" + p_fname).c_str(), ios::out);
- out.setf(ios::scientific, ios::floatfield);
-
- for(int i=1; i<=p_mat.Nrows(); i++)
- {
- for(int j=1; j<=p_mat.Ncols(); j++)
- {
- out << p_mat(i,j) << " ";
- }
- out << endl;
- }
-
- out.close();
- }
-
- inline void Log::out(const string& p_fname, const ColumnVector& p_mat)
- {
- if(!logEstablished)
- {
- logfilename = "logfile";
- setDir(".");
- }
-
- ofstream out;
- out.open((dir + "/" + p_fname).c_str(), ios::out);
- out.setf(ios::scientific, ios::floatfield);
- for(int j=1; j<=p_mat.Nrows(); j++)
- {
- out << p_mat(j);
- out << endl;
- }
-
- out.close();
- }
-
- inline void Log::out(const string& p_fname, const RowVector& p_mat)
- {
-
- if(!logEstablished)
- {
- logfilename = "logfile";
- setDir(".");
- }
-
- ofstream out;
- out.open((dir + "/" + p_fname).c_str(), ios::out);
- out.setf(ios::scientific, ios::floatfield);
-
- for(int j=1; j<=p_mat.Ncols(); j++)
- {
- out << p_mat(j) << " ";
- }
- out << endl;
- out.close();
- }
-
- inline Log& Log::getInstance(){
- if(logger == NULL)
- logger = new Log();
-
- return *logger;
- }
-
- inline ofstream& Log::str() {
-
- if(!logEstablished)
- {
- logfilename = "logfile";
- setDir(".");
- }
-
- return logfileout;
- }
-
-}
-
-#endif
-
-</pre>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities.html b/api/Utilities.html
deleted file mode 100644
index c85582a1626044581ba1af739a55b9bbf19f0b3a..0000000000000000000000000000000000000000
--- a/api/Utilities.html
+++ /dev/null
@@ -1,187 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>namespace Utilities</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>namespace Utilities</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH><A HREF="full-list-Utilities.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Types</h4><ul><LI>class <A HREF="Utilities__Log.html">Log</A>
-</LI>
-<LI>typedef enum <A HREF="#ref7">argflag</A>
-</LI>
-<LI>class <i><A HREF="Utilities__BaseOption.html">BaseOption</A></i>
-</LI>
-<LI>class <A HREF="Utilities__Option.html">Option</A>
-</LI>
-<LI>class <A HREF="Utilities__X_OptionError.html">X_OptionError</A>
-</LI>
-<LI>class <A HREF="Utilities__X_UnknownOption.html">X_UnknownOption</A>
-</LI>
-<LI>class <A HREF="Utilities__X_AlreadySet.html">X_AlreadySet</A>
-</LI>
-<LI>class <A HREF="Utilities__X_MissingArgument.html">X_MissingArgument</A>
-</LI>
-<LI>class <A HREF="Utilities__X_InvalidArgument.html">X_InvalidArgument</A>
-</LI>
-<LI>class <A HREF="Utilities__OptionParser.html">OptionParser</A>
-</LI>
-<LI>class <A HREF="Utilities__TimingFunction.html">TimingFunction</A>
-</LI>
-<LI>class <A HREF="Utilities__Time_Tracer.html">Time_Tracer</A>
-</LI>
-<LI>class <A HREF="Utilities__Tracer_Plus.html">Tracer_Plus</A>
-</LI>
-</ul><h4>Public Methods</h4><ul><LI>template<class t> string <b><A HREF="#ref1">tostring</A></b> (const t obj)
-</LI>
-<LI>bool <b><A HREF="#ref3">string_to_T</A></b> (bool &b, const string& s)
-</LI>
-<LI>bool <b><A HREF="#ref4">string_to_T</A></b> (string& d, const string& s)
-</LI>
-<LI>bool <b><A HREF="#ref5">string_to_T</A></b> (int& i, const string& s)
-</LI>
-<LI>bool <b><A HREF="#ref6">string_to_T</A></b> (float& v, const string& s)
-</LI>
-<LI>ostream& <b><A HREF="#ref9">operator<<</A></b> (ostream &os, const BaseOption& o)
-</LI>
-<LI>inline ostream& <b><A HREF="#ref18">operator<<</A></b> (ostream& ostr, const TimingFunction* t)
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="tostring"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>template<class t> string <underline>tostring</underline> (const t obj)
-</strong></td></tr></table><p></p><A NAME="Utilities__Log.html"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>Log</underline> <small>(class)</small></strong></td></tr></table><p></p><A NAME="string_to_T"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>string_to_T</underline> (bool &b, const string& s)
-</strong></td></tr></table><p></p><A NAME="string_to_T"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>string_to_T</underline> (string& d, const string& s)
-</strong></td></tr></table><p></p><A NAME="string_to_T"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>string_to_T</underline> (int& i, const string& s)
-</strong></td></tr></table><p></p><A NAME="string_to_T"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>string_to_T</underline> (float& v, const string& s)
-</strong></td></tr></table><p></p><A NAME="argflag"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>typedef enum <underline>argflag</underline></strong></td></tr></table><p></p><A NAME="Utilities__BaseOption.html"></A><A NAME="ref8"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>BaseOption</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- Provides behaviour common to all option types. Actual options are
- declared using the templated Option class. The
- OptionParser class can be used to parse command lines.
-</p>
-<p><b>See also</b>: Option, OptionParser</p>
-<A NAME="operator%253C%253C"></A><A NAME="ref9"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>ostream& <underline>operator<<</underline> (ostream &os, const BaseOption& o)
-</strong></td></tr></table><p></p><A NAME="Utilities__Option.html"></A><A NAME="ref10"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>Option</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- Template class adding type specific behaviour to BaseOption. Define
- one of these per program supported option.
-</p>
-<A NAME="Utilities__X_OptionError.html"></A><A NAME="ref11"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>X_OptionError</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- Throw this exception if an error occured inside the Options package.
- </p>
-<A NAME="Utilities__X_UnknownOption.html"></A><A NAME="ref12"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>X_UnknownOption</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- Throw this exception if no matching option was found during parsing.
- </p>
-<A NAME="Utilities__X_AlreadySet.html"></A><A NAME="ref13"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>X_AlreadySet</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- </p>
-<A NAME="Utilities__X_MissingArgument.html"></A><A NAME="ref14"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>X_MissingArgument</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- If an option should have had an argument but didn't then throw this
- exception.
- </p>
-<A NAME="Utilities__X_InvalidArgument.html"></A><A NAME="ref15"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>X_InvalidArgument</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- </p>
-<A NAME="Utilities__OptionParser.html"></A><A NAME="ref16"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>OptionParser</underline> <small>(class)</small></strong></td></tr></table><p></p><p>
- A class for parsing command line arguments into Option objects. The
- following example demonstrates the principle:
-</p>
-
-<pre>
-
-#include "options.h"
-
-// $Id$
-
-using namespace Utilities;
-
-Option<bool> verbose(string("-V,--verbose"), false,
- string("switch on diagnostic messages"),
- false, BaseOption::no_argument);
-Option<bool> help(string("-h,--help"), false,
- string("display this message"),
- false, BaseOption::no_argument);
-Option<float> dof(string("-d,--dof"), 100.0,
- string("number of degrees of freedom"),
- true, BaseOption::requires_argument);
-Option<string> mask(string("-m,--mask"), string("mask"),
- string("brain mask volume"),
- true, BaseOption::requires_argument);
-Option<string> resid(string("-r,--res"), string("res4d"),
- string("4d `residual-of-fit' image"),
- true, BaseOption::requires_argument);
-Option<int> segid(string("-s,--shared-seg-id"), -1,
- "shared memory segment ID",
- false, BaseOption::requires_argument);
-
-string title =
-"opttst (Version 1.0)\n\n\
-Copyright(c) 2000, University of Oxford\n\
-Dave Flitney";
-
-string examples =
-"opttst --dof=<number> --mask=<filename> --res=<filename>\n\
-opttst -d <number> -m <filename> -r <filename>\n\
-opttst --verbose\n";
-
-int main(unsigned int argc, char **argv) {
-
- OptionParser options(title, examples);
-
- try {
-
- options.add(verbose);
- options.add(help);
- options.add(segid);
- options.add(dof);
- options.add(mask);
- options.add(resid);
-
- for(unsigned int a = options.parse_command_line(argc, argv);
- a < argc; a++)
- cout << argv[a] << endl;
-
- if(help.value() ||
- !options.check_compulsory_arguments())
- options.usage();
-
- if(verbose.value()) {
- cout << "verbose = " << verbose.value() << endl;
- cout << "help = " << help.value() << endl;
- cout << "segid = " << segid.value() << endl;
- cout << "dof = " << dof.value() << endl;
- cout << "mask = " << mask.value() << endl;
- cout << "resid = " << resid.value() << endl;
- }
-
- } catch(X_OptionError& e) {
- options.usage();
- cerr << endl << e.what() << endl;
- } catch(std::exception &e) {
- cerr << e.what() << endl;
- }
-}
-
-</pre>
-
-<p> </p>
-<p><b>See also</b>: BaseOption, Option</p>
-<A NAME="Utilities__TimingFunction.html"></A><A NAME="ref17"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>TimingFunction</underline> <small>(class)</small></strong></td></tr></table><p></p><A NAME="operator%253C%253C"></A><A NAME="ref18"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>inline ostream& <underline>operator<<</underline> (ostream& ostr, const TimingFunction* t)
-</strong></td></tr></table><p></p><A NAME="Utilities__Time_Tracer.html"></A><A NAME="ref19"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>Time_Tracer</underline> <small>(class)</small></strong></td></tr></table><p></p><A NAME="Utilities__Tracer_Plus.html"></A><A NAME="ref20"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>Tracer_Plus</underline> <small>(class)</small></strong></td></tr></table><p></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__BaseOption.html b/api/Utilities__BaseOption.html
deleted file mode 100644
index 1d1a90ce99f13332fc099ee8324cd9a9be664560..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption.html
+++ /dev/null
@@ -1,116 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class BaseOption</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class BaseOption</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Provides behaviour common to all option types. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH colspan="2">Contains pure virtuals</TH></TR><TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::BaseOption</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherited by</TH><TD><A HREF="Utilities__Option.html">Option</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">BaseOption</A></b> (const string& k, const string& ht, bool c, ArgFlag f): key_(k), help_text_(ht), arg_flag_(f), unset_(true), compulsory_(c)
-</LI>
-<LI>bool <b><A HREF="#ref2">compulsory</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref3">required</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref4">optional</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref5">has_arg</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref6">set</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref7">unset</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref8">matches</A></b> (const string& arg)
-</LI>
-<LI>const string& <b><A HREF="#ref9">key</A></b> () const
-</LI>
-<LI>const string& <b><A HREF="#ref10">help_text</A></b> () const
-</LI>
-<LI>virtual bool <b><i><A HREF="#ref11">set_value</A></i></b> (const string& vs)
-</LI>
-<LI>virtual ~ <b><A HREF="#ref12">BaseOption</A></b> ()
-</LI>
-</ul><h4>Protected Members</h4><ul><LI>bool <b><A HREF="#ref16">unset_</A></b></LI>
-<LI>bool <b><A HREF="#ref17">compulsory_</A></b></LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Provides behaviour common to all option types. Actual options are
- declared using the templated Option class. The
- OptionParser class can be used to parse command lines.
-</p>
-<p><b>See also</b>: Option, OptionParser</p>
-<A NAME="BaseOption"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>BaseOption</underline> (const string& k, const string& ht, bool c, ArgFlag f): key_(k), help_text_(ht), arg_flag_(f), unset_(true), compulsory_(c)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>k</i></TD><TD align="left" valign="top">comma seperated list of key aliases
-</TD></TR>
-<TR><TD align="left" valign="top"><i>ht</i></TD><TD align="left" valign="top">the help text to be printed for this option
-</TD></TR>
-<TR><TD align="left" valign="top"><i>c</i></TD><TD align="left" valign="top">if true then this option is compulsory
-</TD></TR>
-<TR><TD align="left" valign="top"><i>f</i></TD><TD align="left" valign="top">one of no_argument, requires_argument, optional_argument
- to indicate what arguments should be supplied
- </TD></TR>
-</TABLE></P>
-<A NAME="compulsory"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>compulsory</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: true if the option is compulsory
- </p>
-<A NAME="required"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>required</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: true if the option requires an argument
- </p>
-<A NAME="optional"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>optional</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: true if the option has an optional argument
- </p>
-<A NAME="has_arg"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>has_arg</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: true if the option has an argument at all
- </p>
-<A NAME="set"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>set</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: true if the option has been set
- </p>
-<A NAME="unset"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>unset</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: true if the option remains unset
- </p>
-<A NAME="matches"></A><A NAME="ref8"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>matches</underline> (const string& arg)
-</strong></td></tr></table><p></p><A NAME="key"></A><A NAME="ref9"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const string& <underline>key</underline> ()
-</strong></td></tr></table><p> <small>[const]</small></p><A NAME="help_text"></A><A NAME="ref10"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const string& <underline>help_text</underline> ()
-</strong></td></tr></table><p> <small>[const]</small></p><A NAME="set_value"></A><A NAME="ref11"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> bool <i><underline>set_value</underline></i> (const string& vs)
-</strong></td></tr></table><p> <small>[pure virtual]</small></p><A NAME="BaseOption"></A><A NAME="ref12"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>BaseOption</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><A NAME="unset_"></A><A NAME="ref16"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>unset_</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="compulsory_"></A><A NAME="ref17"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>compulsory_</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><HR><UL><LI><i>Version</i>: 1.0b, Nov., 2000.
- </LI><LI><i>Author</i>: Dave Flitney
-</LI><LI><i>Generated</i>: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</LI></UL></BODY></HTML>
diff --git a/api/Utilities__BaseOption__Option.html b/api/Utilities__BaseOption__Option.html
deleted file mode 100644
index 58e3d2b43a586d7f62b86bdc5f81a492c477f9eb..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__Option.html
+++ /dev/null
@@ -1,83 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Option</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Option</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Template class adding type specific behaviour to BaseOption. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::Option</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Template form</TH><TD>Option<templateclass T> </code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__BaseOption.html">Utilities::BaseOption</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__Option.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">Option</A></b> (const string& k, const T& v, const string& ht, bool c, ArgFlag f = no_argument): BaseOption(k, ht, c, f), default_(v), value_(v)
-</LI>
-<LI>bool <b><A HREF="#ref2">set_value</A></b> (const string& vs)
-</LI>
-<LI>const T& <b><A HREF="#ref3">value</A></b> ()
-</LI>
-<LI>const T& <b><A HREF="#ref4">default_value</A></b> ()
-</LI>
-<LI>virtual ~ <b><A HREF="#ref5">Option</A></b> ()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Template class adding type specific behaviour to BaseOption. Define
- one of these per program supported option.
-</p>
-<A NAME="Option"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>Option</underline> (const string& k, const T& v, const string& ht, bool c, ArgFlag f = no_argument): BaseOption(k, ht, c, f), default_(v), value_(v)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>k</i></TD><TD align="left" valign="top">Comma seperated list of key aliases
-</TD></TR>
-<TR><TD align="left" valign="top"><i>v</i></TD><TD align="left" valign="top">Default value for this option
-</TD></TR>
-<TR><TD align="left" valign="top"><i>ht</i></TD><TD align="left" valign="top">Help text to be printed when outputting usage
-</TD></TR>
-<TR><TD align="left" valign="top"><i>c</i></TD><TD align="left" valign="top">If true then this option is compulsory
-</TD></TR>
-<TR><TD align="left" valign="top"><i>f</i></TD><TD align="left" valign="top">This options argument requirements
- </TD></TR>
-</TABLE></P>
-<A NAME="set_value"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>set_value</underline> (const string& vs)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>vs</i></TD><TD align="left" valign="top">The value string which needs to be parsed to set
- this options value. The overloaded function string_to_T must be defined
- for type T.
- </TD></TR>
-</TABLE></P>
-<A NAME="value"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const T& <underline>value</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: The options value.
- </p>
-<A NAME="default_value"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const T& <underline>default_value</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: The options default value.
- </p>
-<A NAME="Option"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>Option</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><HR><UL><LI><i>Version</i>: 1.0b, Nov., 2000.
-</LI><LI><i>Author</i>: Dave Flitney
-</LI><LI><i>Generated</i>: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</LI></UL></BODY></HTML>
diff --git a/api/Utilities__BaseOption__OptionParser.html b/api/Utilities__BaseOption__OptionParser.html
deleted file mode 100644
index 6dd7fc2dab7c79efedae7cd8d354b7b5346f7763..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__OptionParser.html
+++ /dev/null
@@ -1,164 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class OptionParser</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class OptionParser</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- A class for parsing command line arguments into Option objects. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::OptionParser</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__OptionParser.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">OptionParser</A></b> (const string& p, const string& e): progname_(p), example_(e)
-</LI>
-<LI>void <b><A HREF="#ref2">add</A></b> (BaseOption& o)
-</LI>
-<LI>void <b><A HREF="#ref3">usage</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref4">check_compulsory_arguments</A></b> (bool verbose=false)
-</LI>
-<LI>unsigned int <b><A HREF="#ref5">parse_command_line</A></b> (unsigned int argc, char **argv)
-</LI>
-<LI>virtual ~ <b><A HREF="#ref6">OptionParser</A></b> ()
-</LI>
-</ul><h4>Protected Methods</h4><ul><LI> <b><A HREF="#ref7">OptionParser</A></b> ()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- A class for parsing command line arguments into Option objects. The
- following example demonstrates the principle:
-</p>
-
-<pre>
-
-#include "options.h"
-
-// $Id$
-
-using namespace Utilities;
-
-Option<bool> verbose(string("-V,--verbose"), false,
- string("switch on diagnostic messages"),
- false, BaseOption::no_argument);
-Option<bool> help(string("-h,--help"), false,
- string("display this message"),
- false, BaseOption::no_argument);
-Option<float> dof(string("-d,--dof"), 100.0,
- string("number of degrees of freedom"),
- true, BaseOption::requires_argument);
-Option<string> mask(string("-m,--mask"), string("mask"),
- string("brain mask volume"),
- true, BaseOption::requires_argument);
-Option<string> resid(string("-r,--res"), string("res4d"),
- string("4d `residual-of-fit' image"),
- true, BaseOption::requires_argument);
-Option<int> segid(string("-s,--shared-seg-id"), -1,
- "shared memory segment ID",
- false, BaseOption::requires_argument);
-
-string title =
-"opttst (Version 1.0)\n\n\
-Copyright(c) 2000, University of Oxford\n\
-Dave Flitney";
-
-string examples =
-"opttst --dof=<number> --mask=<filename> --res=<filename>\n\
-opttst -d <number> -m <filename> -r <filename>\n\
-opttst --verbose\n";
-
-int main(unsigned int argc, char **argv) {
-
- OptionParser options(title, examples);
-
- try {
-
- options.add(verbose);
- options.add(help);
- options.add(segid);
- options.add(dof);
- options.add(mask);
- options.add(resid);
-
- for(unsigned int a = options.parse_command_line(argc, argv);
- a < argc; a++)
- cout << argv[a] << endl;
-
- if(help.value() ||
- !options.check_compulsory_arguments())
- options.usage();
-
- if(verbose.value()) {
- cout << "verbose = " << verbose.value() << endl;
- cout << "help = " << help.value() << endl;
- cout << "segid = " << segid.value() << endl;
- cout << "dof = " << dof.value() << endl;
- cout << "mask = " << mask.value() << endl;
- cout << "resid = " << resid.value() << endl;
- }
-
- } catch(X_OptionError& e) {
- options.usage();
- cerr << endl << e.what() << endl;
- } catch(std::exception &e) {
- cerr << e.what() << endl;
- }
-}
-
-</pre>
-
-<p> </p>
-<p><b>See also</b>: BaseOption, Option, @example</p>
-<A NAME="OptionParser"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>OptionParser</underline> (const string& p, const string& e): progname_(p), example_(e)
-</strong></td></tr></table><p></p><A NAME="add"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>add</underline> (BaseOption& o)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>o</i></TD><TD align="left" valign="top">An option to be added to the parser
- </TD></TR>
-</TABLE></P>
-<A NAME="usage"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>usage</underline> ()
-</strong></td></tr></table><p></p><A NAME="check_compulsory_arguments"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>check_compulsory_arguments</underline> (bool verbose=false)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>verbose</i></TD><TD align="left" valign="top">If set then this method will carp about any option which
- is marked as compulsory but hasn't been set
-</TD></TR>
-</TABLE></P>
-<p><b>Returns</b>: true if all compulsory arguments have been set and false otherwise
- </p>
-<A NAME="parse_command_line"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>unsigned int <underline>parse_command_line</underline> (unsigned int argc, char **argv)
-</strong></td></tr></table><p></p><p>
- The parameters, argc and argv, should normally be those passed to
- main via the command line shell.
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>argc</i></TD><TD align="left" valign="top">The argument count.
-</TD></TR>
-<TR><TD align="left" valign="top"><i>argv</i></TD><TD align="left" valign="top">The vector of argument strings.
- </TD></TR>
-</TABLE></P>
-<A NAME="OptionParser"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>OptionParser</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><A NAME="OptionParser"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>OptionParser</underline> ()
-</strong></td></tr></table><p> <small>[protected]</small></p><p>
- </p>
-<HR><UL><LI><i>Version</i>: 1.0b, Nov., 2000.
-</LI><LI><i>Author</i>: Dave Flitney
-</LI><LI><i>Generated</i>: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</LI></UL></BODY></HTML>
diff --git a/api/Utilities__BaseOption__X_AlreadySet.html b/api/Utilities__BaseOption__X_AlreadySet.html
deleted file mode 100644
index 204a63eb2a3093a54ef6df9d8e0fd20f296e0bf7..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__X_AlreadySet.html
+++ /dev/null
@@ -1,45 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_AlreadySet</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_AlreadySet</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::X_AlreadySet</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__BaseOption__X_OptionError.html">Utilities::BaseOption::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__X_AlreadySet.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_AlreadySet</A></b> (const string& s) throw(): str_(s+":already set!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- </p>
-<A NAME="X_AlreadySet"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_AlreadySet</underline> (const string& s) throw(): str_(s+":already set!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__BaseOption__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__BaseOption__X_InvalidArgument.html b/api/Utilities__BaseOption__X_InvalidArgument.html
deleted file mode 100644
index c1a07358b6fdeb3de3e09d5cdf9238752825b8fb..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__X_InvalidArgument.html
+++ /dev/null
@@ -1,45 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_InvalidArgument</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_InvalidArgument</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::X_InvalidArgument</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__BaseOption__X_OptionError.html">Utilities::BaseOption::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__X_InvalidArgument.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_InvalidArgument</A></b> (const string& o, const string& v) throw(): str_(o+":invalid argument "+v+"!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- </p>
-<A NAME="X_InvalidArgument"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_InvalidArgument</underline> (const string& o, const string& v) throw(): str_(o+":invalid argument "+v+"!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__BaseOption__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__BaseOption__X_MissingArgument.html b/api/Utilities__BaseOption__X_MissingArgument.html
deleted file mode 100644
index fdb90700ff76df75432ed060f08c375f8b4fe2cc..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__X_MissingArgument.html
+++ /dev/null
@@ -1,48 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_MissingArgument</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_MissingArgument</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- If an option should have had an argument but didn't then throw this
- exception. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::X_MissingArgument</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__BaseOption__X_OptionError.html">Utilities::BaseOption::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__X_MissingArgument.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_MissingArgument</A></b> (const string& s) throw(): str_(s+":missing argument!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- If an option should have had an argument but didn't then throw this
- exception.
- </p>
-<A NAME="X_MissingArgument"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_MissingArgument</underline> (const string& s) throw(): str_(s+":missing argument!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__BaseOption__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__BaseOption__X_OptionError.html b/api/Utilities__BaseOption__X_OptionError.html
deleted file mode 100644
index 83ccc7e5f6f075f2fd27f2092569613c001eda87..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__X_OptionError.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_OptionError</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_OptionError</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Throw this exception if an error occured inside the Options package. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::X_OptionError</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD>std::exception</TD></TR>
-<TR><TH>Inherited by</TH><TD><A HREF="Utilities__BaseOption__X_AlreadySet.html">X_AlreadySet</A>, <A HREF="Utilities__BaseOption__X_InvalidArgument.html">X_InvalidArgument</A>, <A HREF="Utilities__BaseOption__X_MissingArgument.html">X_MissingArgument</A>, <A HREF="Utilities__BaseOption__X_UnknownOption.html">X_UnknownOption</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__X_OptionError.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_OptionError</A></b> () throw()
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Throw this exception if an error occured inside the Options package.
- </p>
-<A NAME="X_OptionError"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_OptionError</underline> () throw()
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__BaseOption__X_UnknownOption.html b/api/Utilities__BaseOption__X_UnknownOption.html
deleted file mode 100644
index ef2850c49346681403f14697ecfcaff7db9c7db8..0000000000000000000000000000000000000000
--- a/api/Utilities__BaseOption__X_UnknownOption.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_UnknownOption</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_UnknownOption</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Throw this exception if no matching option was found during parsing. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__BaseOption.html">BaseOption</A>::X_UnknownOption</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__BaseOption__X_OptionError.html">Utilities::BaseOption::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__BaseOption__X_UnknownOption.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_UnknownOption</A></b> (const string& s) throw(): str_(s+":unknown option!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Throw this exception if no matching option was found during parsing.
- </p>
-<A NAME="X_UnknownOption"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_UnknownOption</underline> (const string& s) throw(): str_(s+":unknown option!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__BaseOption__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__Log.html b/api/Utilities__Log.html
deleted file mode 100644
index 02256fb5099aeb31a48dc3fbfaca6f2f65b3a566..0000000000000000000000000000000000000000
--- a/api/Utilities__Log.html
+++ /dev/null
@@ -1,73 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Log</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Log</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::Log</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="Log_h.html">Log.h</A>></code></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__Log.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI>~ <b><A HREF="#ref2">Log</A></b> ()
-</LI>
-<LI>void <b><A HREF="#ref3">makeDir</A></b> (const string& pdirname, const string& plogfilename = "logfile")
-</LI>
-<LI>void <b><A HREF="#ref4">setDir</A></b> (const string& pdirname, const string& plogfilename = "logfile")
-</LI>
-<LI>const string& <b><A HREF="#ref5">getDir</A></b> () const
-</LI>
-<LI>const string& <b><A HREF="#ref6">getLogFileName</A></b> () const
-</LI>
-<LI>const string <b><A HREF="#ref7">appendDir</A></b> (const string& filename) const
-</LI>
-<LI>void <b><A HREF="#ref8">out</A></b> (const string& p_fname, const Matrix& p_mat)
-</LI>
-<LI>void <b><A HREF="#ref9">out</A></b> (const string& p_fname, const RowVector& p_mat)
-</LI>
-<LI>void <b><A HREF="#ref10">out</A></b> (const string& p_fname, const ColumnVector& p_mat)
-</LI>
-<LI>ofstream& <b><A HREF="#ref12">str</A></b> ()
-</LI>
-</ul><h4>Public Static Methods</h4><ul><LI>static Log& <b><A HREF="#ref1">getInstance</A></b> ()
-</LI>
-<LI>static int <b><A HREF="#ref11">counter</A></b> ()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="getInstance"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> Log& <underline>getInstance</underline> ()
-</strong></td></tr></table><p> <small>[static]</small></p><A NAME="Log"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>~ <underline>Log</underline> ()
-</strong></td></tr></table><p></p><A NAME="makeDir"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>makeDir</underline> (const string& pdirname, const string& plogfilename = "logfile")
-</strong></td></tr></table><p></p><p> Makes a directory to place results into:
- keeps adding "+" to pdirname until unique directory is made: </p>
-<A NAME="setDir"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>setDir</underline> (const string& pdirname, const string& plogfilename = "logfile")
-</strong></td></tr></table><p></p><p> Sets an existing directory to place results into: </p>
-<A NAME="getDir"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const string& <underline>getDir</underline> ()
-</strong></td></tr></table><p> <small>[const]</small></p><A NAME="getLogFileName"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const string& <underline>getLogFileName</underline> ()
-</strong></td></tr></table><p> <small>[const]</small></p><A NAME="appendDir"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const string <underline>appendDir</underline> (const string& filename)
-</strong></td></tr></table><p> <small>[const]</small></p><A NAME="out"></A><A NAME="ref8"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>out</underline> (const string& p_fname, const Matrix& p_mat)
-</strong></td></tr></table><p></p><A NAME="out"></A><A NAME="ref9"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>out</underline> (const string& p_fname, const RowVector& p_mat)
-</strong></td></tr></table><p></p><A NAME="out"></A><A NAME="ref10"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>out</underline> (const string& p_fname, const ColumnVector& p_mat)
-</strong></td></tr></table><p></p><A NAME="counter"></A><A NAME="ref11"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> int <underline>counter</underline> ()
-</strong></td></tr></table><p> <small>[static]</small></p><A NAME="str"></A><A NAME="ref12"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>ofstream& <underline>str</underline> ()
-</strong></td></tr></table><p></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__Option.html b/api/Utilities__Option.html
deleted file mode 100644
index 7a14ebccfa48fab4475b74b3a07900dcda96d6fb..0000000000000000000000000000000000000000
--- a/api/Utilities__Option.html
+++ /dev/null
@@ -1,84 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Option</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Option</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Template class adding type specific behaviour to BaseOption. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::Option</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Template form</TH><TD>Option<templateclass T> </code></TD></TR>
-<TR><TH>Inherits</TH><TD><i><A HREF="Utilities__BaseOption.html">Utilities::BaseOption</A></i></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__Option.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">Option</A></b> (const string& k, const T& v, const string& ht, bool c, ArgFlag f = no_argument): BaseOption(k, ht, c, f), default_(v), value_(v)
-</LI>
-<LI>bool <b><A HREF="#ref2">set_value</A></b> (const string& vs)
-</LI>
-<LI>const T& <b><A HREF="#ref3">value</A></b> ()
-</LI>
-<LI>const T& <b><A HREF="#ref4">default_value</A></b> ()
-</LI>
-<LI>virtual ~ <b><A HREF="#ref5">Option</A></b> ()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Template class adding type specific behaviour to BaseOption. Define
- one of these per program supported option.
-</p>
-<A NAME="Option"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>Option</underline> (const string& k, const T& v, const string& ht, bool c, ArgFlag f = no_argument): BaseOption(k, ht, c, f), default_(v), value_(v)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>k</i></TD><TD align="left" valign="top">Comma seperated list of key aliases
-</TD></TR>
-<TR><TD align="left" valign="top"><i>v</i></TD><TD align="left" valign="top">Default value for this option
-</TD></TR>
-<TR><TD align="left" valign="top"><i>ht</i></TD><TD align="left" valign="top">Help text to be printed when outputting usage
-</TD></TR>
-<TR><TD align="left" valign="top"><i>c</i></TD><TD align="left" valign="top">If true then this option is compulsory
-</TD></TR>
-<TR><TD align="left" valign="top"><i>f</i></TD><TD align="left" valign="top">This options argument requirements
- </TD></TR>
-</TABLE></P>
-<A NAME="set_value"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>set_value</underline> (const string& vs)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>vs</i></TD><TD align="left" valign="top">The value string which needs to be parsed to set
- this options value. The overloaded function string_to_T must be defined
- for type T.
- </TD></TR>
-</TABLE></P>
-<p>Reimplemented from <i><A HREF="Utilities__BaseOption.html">BaseOption</A></i>.</p>
-<A NAME="value"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const T& <underline>value</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: The options value.
- </p>
-<A NAME="default_value"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const T& <underline>default_value</underline> ()
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Returns</b>: The options default value.
- </p>
-<A NAME="Option"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>Option</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><HR><UL><LI><i>Version</i>: 1.0b, Nov., 2000.
-</LI><LI><i>Author</i>: Dave Flitney
-</LI><LI><i>Generated</i>: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</LI></UL></BODY></HTML>
diff --git a/api/Utilities__OptionParser.html b/api/Utilities__OptionParser.html
deleted file mode 100644
index 647d04e4498406697809c41d478087cc989581c8..0000000000000000000000000000000000000000
--- a/api/Utilities__OptionParser.html
+++ /dev/null
@@ -1,164 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class OptionParser</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class OptionParser</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- A class for parsing command line arguments into Option objects. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::OptionParser</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__OptionParser.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">OptionParser</A></b> (const string& p, const string& e): progname_(p), example_(e)
-</LI>
-<LI>void <b><A HREF="#ref2">add</A></b> (BaseOption& o)
-</LI>
-<LI>void <b><A HREF="#ref3">usage</A></b> ()
-</LI>
-<LI>bool <b><A HREF="#ref4">check_compulsory_arguments</A></b> (bool verbose=false)
-</LI>
-<LI>unsigned int <b><A HREF="#ref5">parse_command_line</A></b> (unsigned int argc, char **argv)
-</LI>
-<LI>virtual ~ <b><A HREF="#ref6">OptionParser</A></b> ()
-</LI>
-</ul><h4>Protected Methods</h4><ul><LI> <b><A HREF="#ref7">OptionParser</A></b> ()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- A class for parsing command line arguments into Option objects. The
- following example demonstrates the principle:
-</p>
-
-<pre>
-
-#include "options.h"
-
-// $Id$
-
-using namespace Utilities;
-
-Option<bool> verbose(string("-V,--verbose"), false,
- string("switch on diagnostic messages"),
- false, BaseOption::no_argument);
-Option<bool> help(string("-h,--help"), false,
- string("display this message"),
- false, BaseOption::no_argument);
-Option<float> dof(string("-d,--dof"), 100.0,
- string("number of degrees of freedom"),
- true, BaseOption::requires_argument);
-Option<string> mask(string("-m,--mask"), string("mask"),
- string("brain mask volume"),
- true, BaseOption::requires_argument);
-Option<string> resid(string("-r,--res"), string("res4d"),
- string("4d `residual-of-fit' image"),
- true, BaseOption::requires_argument);
-Option<int> segid(string("-s,--shared-seg-id"), -1,
- "shared memory segment ID",
- false, BaseOption::requires_argument);
-
-string title =
-"opttst (Version 1.0)\n\n\
-Copyright(c) 2000, University of Oxford\n\
-Dave Flitney";
-
-string examples =
-"opttst --dof=<number> --mask=<filename> --res=<filename>\n\
-opttst -d <number> -m <filename> -r <filename>\n\
-opttst --verbose\n";
-
-int main(unsigned int argc, char **argv) {
-
- OptionParser options(title, examples);
-
- try {
-
- options.add(verbose);
- options.add(help);
- options.add(segid);
- options.add(dof);
- options.add(mask);
- options.add(resid);
-
- for(unsigned int a = options.parse_command_line(argc, argv);
- a < argc; a++)
- cout << argv[a] << endl;
-
- if(help.value() ||
- !options.check_compulsory_arguments())
- options.usage();
-
- if(verbose.value()) {
- cout << "verbose = " << verbose.value() << endl;
- cout << "help = " << help.value() << endl;
- cout << "segid = " << segid.value() << endl;
- cout << "dof = " << dof.value() << endl;
- cout << "mask = " << mask.value() << endl;
- cout << "resid = " << resid.value() << endl;
- }
-
- } catch(X_OptionError& e) {
- options.usage();
- cerr << endl << e.what() << endl;
- } catch(std::exception &e) {
- cerr << e.what() << endl;
- }
-}
-
-</pre>
-
-<p> </p>
-<p><b>See also</b>: BaseOption, Option</p>
-<A NAME="OptionParser"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>OptionParser</underline> (const string& p, const string& e): progname_(p), example_(e)
-</strong></td></tr></table><p></p><A NAME="add"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>add</underline> (BaseOption& o)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>o</i></TD><TD align="left" valign="top">An option to be added to the parser
- </TD></TR>
-</TABLE></P>
-<A NAME="usage"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>usage</underline> ()
-</strong></td></tr></table><p></p><A NAME="check_compulsory_arguments"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>check_compulsory_arguments</underline> (bool verbose=false)
-</strong></td></tr></table><p></p><p>
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>verbose</i></TD><TD align="left" valign="top">If set then this method will carp about any option which
- is marked as compulsory but hasn't been set
-</TD></TR>
-</TABLE></P>
-<p><b>Returns</b>: true if all compulsory arguments have been set and false otherwise
- </p>
-<A NAME="parse_command_line"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>unsigned int <underline>parse_command_line</underline> (unsigned int argc, char **argv)
-</strong></td></tr></table><p></p><p>
- The parameters, argc and argv, should normally be those passed to
- main via the command line shell.
-</p>
-<p><b>Parameters</b>:<TABLE BORDER="0" CELLPADDING="5">
-<TR><TD align="left" valign="top"><i>argc</i></TD><TD align="left" valign="top">The argument count.
-</TD></TR>
-<TR><TD align="left" valign="top"><i>argv</i></TD><TD align="left" valign="top">The vector of argument strings.
- </TD></TR>
-</TABLE></P>
-<A NAME="OptionParser"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>OptionParser</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><A NAME="OptionParser"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>OptionParser</underline> ()
-</strong></td></tr></table><p> <small>[protected]</small></p><p>
- </p>
-<HR><UL><LI><i>Version</i>: 1.0b, Nov., 2000.
-</LI><LI><i>Author</i>: Dave Flitney
-</LI><LI><i>Generated</i>: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</LI></UL></BODY></HTML>
diff --git a/api/Utilities__Time_Tracer.html b/api/Utilities__Time_Tracer.html
deleted file mode 100644
index 33aacb963b80e7fab6d5094f551ef21ecec5f4f0..0000000000000000000000000000000000000000
--- a/api/Utilities__Time_Tracer.html
+++ /dev/null
@@ -1,62 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Time_Tracer</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Time_Tracer</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::Time_Tracer</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="time__tracer_h.html">time_tracer.h</A>></code></TD></TR>
-<TR><TH>Inherited by</TH><TD><A HREF="Utilities__Tracer_Plus.html">Tracer_Plus</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__Time_Tracer.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">Time_Tracer</A></b> (char* str)
-</LI>
-<LI>virtual ~ <b><A HREF="#ref2">Time_Tracer</A></b> ()
-</LI>
-</ul><h4>Public Static Methods</h4><ul><LI>static void <b><A HREF="#ref3">dump_times</A></b> (const string& dir)
-</LI>
-<LI>static void <b><A HREF="#ref4">setdebugon</A></b> ()
-</LI>
-<LI>static void <b><A HREF="#ref5">settimingon</A></b> ()
-</LI>
-</ul><h4>Protected Members</h4><ul><LI>static bool <b><A HREF="#ref6">debug</A></b></LI>
-<LI>static bool <b><A HREF="#ref7">timingon</A></b></LI>
-<LI>static unsigned int <b><A HREF="#ref8">pad</A></b></LI>
-<LI>static set<TimingFunction*, TimingFunction::comparer_name> <b><A HREF="#ref9">timingFunctions</A></b></LI>
-<LI>string <b><A HREF="#ref10">tmp</A></b></LI>
-<LI>TimingFunction*<b><A HREF="#ref11">timingFunction</A></b></LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="Time_Tracer"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>Time_Tracer</underline> (char* str)
-</strong></td></tr></table><p></p><A NAME="Time_Tracer"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>Time_Tracer</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><A NAME="dump_times"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> void <underline>dump_times</underline> (const string& dir)
-</strong></td></tr></table><p> <small>[static]</small></p><A NAME="setdebugon"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> void <underline>setdebugon</underline> ()
-</strong></td></tr></table><p> <small>[static]</small></p><A NAME="settimingon"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> void <underline>settimingon</underline> ()
-</strong></td></tr></table><p> <small>[static]</small></p><A NAME="debug"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>static bool <underline>debug</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="timingon"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>static bool <underline>timingon</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="pad"></A><A NAME="ref8"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>static unsigned int <underline>pad</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="timingFunctions"></A><A NAME="ref9"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>static set<TimingFunction*, TimingFunction::comparer_name> <underline>timingFunctions</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="tmp"></A><A NAME="ref10"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>string <underline>tmp</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="timingFunction"></A><A NAME="ref11"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>TimingFunction* <underline>timingFunction</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__TimingFunction.html b/api/Utilities__TimingFunction.html
deleted file mode 100644
index e3df0fe33e82b64f5f6be14fa8953a103182e140..0000000000000000000000000000000000000000
--- a/api/Utilities__TimingFunction.html
+++ /dev/null
@@ -1,62 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class TimingFunction</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class TimingFunction</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::TimingFunction</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="time__tracer_h.html">time_tracer.h</A>></code></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__TimingFunction.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Types</h4><ul><LI>class <A HREF="Utilities__TimingFunction__comparer_name.html">comparer_name</A>
-</LI>
-<LI>class <A HREF="Utilities__TimingFunction__comparer_time_taken.html">comparer_time_taken</A>
-</LI>
-</ul><h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">TimingFunction</A></b> (const char * pstr): str(pstr), time_taken(0), times_called(0)
-</LI>
-<LI>void <b><A HREF="#ref4">start</A></b> ()
-</LI>
-<LI>void <b><A HREF="#ref5">end</A></b> ()
-</LI>
-<LI>friend ostream& <b><A HREF="#ref8">operator<<</A></b> (ostream& ostr, const TimingFunction* t)
-</LI>
-</ul><h4>Public Members</h4><ul><LI>friend <b><A HREF="#ref6">comparer_name</A></b></LI>
-<LI>friend <b><A HREF="#ref7">comparer_time_taken</A></b></LI>
-</ul><h4>Protected Members</h4><ul><LI>const char*<b><A HREF="#ref9">str</A></b></LI>
-<LI>clock_t <b><A HREF="#ref10">time_taken</A></b></LI>
-<LI>int <b><A HREF="#ref11">times_called</A></b></LI>
-<LI>clock_t <b><A HREF="#ref12">start_time</A></b></LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="TimingFunction"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>TimingFunction</underline> (const char * pstr): str(pstr), time_taken(0), times_called(0)
-</strong></td></tr></table><p></p><A NAME="Utilities__TimingFunction__comparer_name.html"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>comparer_name</underline> <small>(class)</small></strong></td></tr></table><p></p><A NAME="Utilities__TimingFunction__comparer_time_taken.html"></A><A NAME="ref3"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong><underline>comparer_time_taken</underline> <small>(class)</small></strong></td></tr></table><p></p><A NAME="start"></A><A NAME="ref4"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>start</underline> ()
-</strong></td></tr></table><p></p><A NAME="end"></A><A NAME="ref5"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>void <underline>end</underline> ()
-</strong></td></tr></table><p></p><A NAME="comparer_name"></A><A NAME="ref6"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>friend <underline>comparer_name</underline>
-</strong></td></tr></table><p></p><A NAME="comparer_time_taken"></A><A NAME="ref7"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>friend <underline>comparer_time_taken</underline>
-</strong></td></tr></table><p></p><A NAME="operator%253C%253C"></A><A NAME="ref8"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>friend ostream& <underline>operator<<</underline> (ostream& ostr, const TimingFunction* t)
-</strong></td></tr></table><p></p><A NAME="str"></A><A NAME="ref9"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>const char* <underline>str</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="time_taken"></A><A NAME="ref10"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>clock_t <underline>time_taken</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="times_called"></A><A NAME="ref11"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>int <underline>times_called</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><A NAME="start_time"></A><A NAME="ref12"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>clock_t <underline>start_time</underline>
-</strong></td></tr></table><p> <small>[protected]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__TimingFunction__comparer_name.html b/api/Utilities__TimingFunction__comparer_name.html
deleted file mode 100644
index 61bfa2fd73aefa0e4ca6766aa8e8e1d744208a98..0000000000000000000000000000000000000000
--- a/api/Utilities__TimingFunction__comparer_name.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class comparer_name</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class comparer_name</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__TimingFunction.html">TimingFunction</A>::comparer_name</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="time__tracer_h.html">time_tracer.h</A>></code></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__TimingFunction__comparer_name.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI>bool <b><A HREF="#ref1">operator()</A></b> (const TimingFunction* t1, const TimingFunction* t2) const
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="operator()"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>operator()</underline> (const TimingFunction* t1, const TimingFunction* t2)
-</strong></td></tr></table><p> <small>[const]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__TimingFunction__comparer_time_taken.html b/api/Utilities__TimingFunction__comparer_time_taken.html
deleted file mode 100644
index 4b462cd3b6e5f5efd69829cd34ce96ea109e6d90..0000000000000000000000000000000000000000
--- a/api/Utilities__TimingFunction__comparer_time_taken.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class comparer_time_taken</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class comparer_time_taken</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::<A HREF="Utilities__TimingFunction.html">TimingFunction</A>::comparer_time_taken</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="time__tracer_h.html">time_tracer.h</A>></code></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__TimingFunction__comparer_time_taken.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI>bool <b><A HREF="#ref1">operator()</A></b> (const TimingFunction* t1, const TimingFunction* t2) const
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="operator()"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong>bool <underline>operator()</underline> (const TimingFunction* t1, const TimingFunction* t2)
-</strong></td></tr></table><p> <small>[const]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__Tracer_Plus.html b/api/Utilities__Tracer_Plus.html
deleted file mode 100644
index 5aa6bea3aa6d1d69e3f8b10d0ddd5b6984f54d9e..0000000000000000000000000000000000000000
--- a/api/Utilities__Tracer_Plus.html
+++ /dev/null
@@ -1,41 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Tracer_Plus</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Tracer_Plus</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::Tracer_Plus</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="tracer__plus_h.html">tracer_plus.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__Time_Tracer.html">Utilities::Time_Tracer</A>, Tracer</TD></TR>
-<TR><TH><A HREF="full-list-Utilities__Tracer_Plus.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">Tracer_Plus</A></b> (char* str) : Tracer(str), Time_Tracer(str)
-</LI>
-<LI>virtual ~ <b><A HREF="#ref2">Tracer_Plus</A></b> ()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><A NAME="Tracer_Plus"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>Tracer_Plus</underline> (char* str) : Tracer(str), Time_Tracer(str)
-</strong></td></tr></table><p></p><A NAME="Tracer_Plus"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> ~ <underline>Tracer_Plus</underline> ()
-</strong></td></tr></table><p> <small>[virtual]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__X_AlreadySet.html b/api/Utilities__X_AlreadySet.html
deleted file mode 100644
index e8e12276a23ffdf04c121d455c1e9508b83b0c52..0000000000000000000000000000000000000000
--- a/api/Utilities__X_AlreadySet.html
+++ /dev/null
@@ -1,45 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_AlreadySet</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_AlreadySet</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::X_AlreadySet</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__X_AlreadySet.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_AlreadySet</A></b> (const string& s) throw(): str_(s+":already set!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- </p>
-<A NAME="X_AlreadySet"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_AlreadySet</underline> (const string& s) throw(): str_(s+":already set!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__X_InvalidArgument.html b/api/Utilities__X_InvalidArgument.html
deleted file mode 100644
index e9328c52bbbf51befcb279782f11f846fe625e36..0000000000000000000000000000000000000000
--- a/api/Utilities__X_InvalidArgument.html
+++ /dev/null
@@ -1,45 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_InvalidArgument</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_InvalidArgument</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::X_InvalidArgument</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__X_InvalidArgument.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_InvalidArgument</A></b> (const string& o, const string& v) throw(): str_(o+":invalid argument "+v+"!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- </p>
-<A NAME="X_InvalidArgument"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_InvalidArgument</underline> (const string& o, const string& v) throw(): str_(o+":invalid argument "+v+"!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__X_MissingArgument.html b/api/Utilities__X_MissingArgument.html
deleted file mode 100644
index 861ed9da329c36f0a7d12b753da7c82467dcbc7e..0000000000000000000000000000000000000000
--- a/api/Utilities__X_MissingArgument.html
+++ /dev/null
@@ -1,48 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_MissingArgument</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_MissingArgument</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- If an option should have had an argument but didn't then throw this
- exception. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::X_MissingArgument</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__X_MissingArgument.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_MissingArgument</A></b> (const string& s) throw(): str_(s+":missing argument!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- If an option should have had an argument but didn't then throw this
- exception.
- </p>
-<A NAME="X_MissingArgument"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_MissingArgument</underline> (const string& s) throw(): str_(s+":missing argument!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__X_OptionError.html b/api/Utilities__X_OptionError.html
deleted file mode 100644
index b9e423dd6d1b55729d9f7aea94bd89d99872855b..0000000000000000000000000000000000000000
--- a/api/Utilities__X_OptionError.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_OptionError</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_OptionError</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Throw this exception if an error occured inside the Options package. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::X_OptionError</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD>std::exception</TD></TR>
-<TR><TH>Inherited by</TH><TD><A HREF="Utilities__X_AlreadySet.html">X_AlreadySet</A>, <A HREF="Utilities__X_InvalidArgument.html">X_InvalidArgument</A>, <A HREF="Utilities__X_MissingArgument.html">X_MissingArgument</A>, <A HREF="Utilities__X_UnknownOption.html">X_UnknownOption</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__X_OptionError.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_OptionError</A></b> () throw()
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Throw this exception if an error occured inside the Options package.
- </p>
-<A NAME="X_OptionError"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_OptionError</underline> () throw()
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/Utilities__X_UnknownOption.html b/api/Utilities__X_UnknownOption.html
deleted file mode 100644
index 1c3ac898ccbcb4d457b98559398b47d854efa0e1..0000000000000000000000000000000000000000
--- a/api/Utilities__X_UnknownOption.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_UnknownOption</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_UnknownOption</h1>
- </TD>
- <TD valign="top" align="right" colspan="1">
- Throw this exception if no matching option was found during parsing. <small><A HREF="#longdesc">More...</A></small></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
- <TR><TH>Full name</TH><TD><code><A HREF="Utilities.html">Utilities</A>::X_UnknownOption</code></TD></TR>
-<TR><TH>Definition</TH><TD><code>#include <<A HREF="options_h.html">options.h</A>></code></TD></TR>
-<TR><TH>Inherits</TH><TD><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A></TD></TR>
-<TR><TH><A HREF="full-list-Utilities__X_UnknownOption.html">List of all Methods</A></TH></TR>
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<h4>Public Methods</h4><ul><LI> <b><A HREF="#ref1">X_UnknownOption</A></b> (const string& s) throw(): str_(s+":unknown option!")
-</LI>
-<LI>virtual const char * <b><A HREF="#ref2">what</A></b> () const throw()
-</LI>
-</ul><HR><A NAME="longdesc"><H2>Detailed Description</H2><p>
- Throw this exception if no matching option was found during parsing.
- </p>
-<A NAME="X_UnknownOption"></A><A NAME="ref1"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> <underline>X_UnknownOption</underline> (const string& s) throw(): str_(s+":unknown option!")
-</strong></td></tr></table><p></p><A NAME="what"></A><A NAME="ref2"></A><table width="100%"><tr bgcolor="#eeeeee"><td><strong> const char * <underline>what</underline> () const throw()
-</strong></td></tr></table><p> <small>[virtual]</small></p><p>Reimplemented from <A HREF="Utilities__X_OptionError.html">X_OptionError</A>.</p>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/all-globals.html b/api/all-globals.html
deleted file mode 100644
index 457bed0a7d31446b98cd0eb5ef8b817061e32680..0000000000000000000000000000000000000000
--- a/api/all-globals.html
+++ /dev/null
@@ -1,32 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE> Globals</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1> Globals</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities.html b/api/full-list-Utilities.html
deleted file mode 100644
index 62d25ab1da24f72f22591ff5305e66e4fc7540d5..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>namespace Utilities: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>namespace Utilities: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>operator<< - tostring</TH></TR><TR ><TD><A HREF="Utilities.html#operator%25253C%25253C">Utilities::operator<<</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities.html#string_to_T">Utilities::string_to_T</A></TD></TR>
-<TR ><TD><A HREF="Utilities.html#tostring">Utilities::tostring</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption.html b/api/full-list-Utilities__BaseOption.html
deleted file mode 100644
index 8c10012edb486269dde1796d197d286cc9678c84..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption.html
+++ /dev/null
@@ -1,43 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class BaseOption: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class BaseOption: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>BaseOption - help_text</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#BaseOption">Utilities::BaseOption::BaseOption</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#compulsory">Utilities::BaseOption::compulsory</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#has_arg">Utilities::BaseOption::has_arg</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#help_text">Utilities::BaseOption::help_text</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>key - required</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#key">Utilities::BaseOption::key</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#matches">Utilities::BaseOption::matches</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#optional">Utilities::BaseOption::optional</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#required">Utilities::BaseOption::required</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>set - unset</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#set">Utilities::BaseOption::set</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#set_value">Utilities::BaseOption::set_value</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#unset">Utilities::BaseOption::unset</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__Option.html b/api/full-list-Utilities__BaseOption__Option.html
deleted file mode 100644
index bf908604f991fa54f30e14c1a1738a5ce8f4a544..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__Option.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Option: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Option: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Option - default_value</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__Option.html#Option">Utilities::BaseOption::Option::Option</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__Option.html#default_value">Utilities::BaseOption::Option::default_value</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>operator<< - value</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#operator%25253C%25253C">Utilities::BaseOption::operator<<</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__Option.html#set_value">Utilities::BaseOption::Option::set_value</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__Option.html#value">Utilities::BaseOption::Option::value</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__OptionParser.html b/api/full-list-Utilities__BaseOption__OptionParser.html
deleted file mode 100644
index 7a3b8b889dc4a605c7a92d8e55bfc5068781808c..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__OptionParser.html
+++ /dev/null
@@ -1,40 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class OptionParser: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class OptionParser: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>OptionParser - check_compulsory_arguments</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__OptionParser.html#OptionParser">Utilities::BaseOption::OptionParser::OptionParser</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__OptionParser.html#add">Utilities::BaseOption::OptionParser::add</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__OptionParser.html#check_compulsory_arguments">Utilities::BaseOption::OptionParser::check_compulsory_arguments</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>find_matching_option - usage</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__OptionParser.html#find_matching_option">Utilities::BaseOption::OptionParser::find_matching_option</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__OptionParser.html#parse_command_line">Utilities::BaseOption::OptionParser::parse_command_line</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__OptionParser.html#parse_long_option">Utilities::BaseOption::OptionParser::parse_long_option</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__OptionParser.html#parse_option">Utilities::BaseOption::OptionParser::parse_option</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__OptionParser.html#usage">Utilities::BaseOption::OptionParser::usage</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__X_AlreadySet.html b/api/full-list-Utilities__BaseOption__X_AlreadySet.html
deleted file mode 100644
index c360aeddc137b58bf2e190e2d3cb6232bd5b3588..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__X_AlreadySet.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_AlreadySet: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_AlreadySet: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_AlreadySet - what</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__X_AlreadySet.html#X_AlreadySet">Utilities::BaseOption::X_AlreadySet::X_AlreadySet</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__X_OptionError.html#X_OptionError">Utilities::BaseOption::X_OptionError::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__X_AlreadySet.html#what">Utilities::BaseOption::X_AlreadySet::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__X_InvalidArgument.html b/api/full-list-Utilities__BaseOption__X_InvalidArgument.html
deleted file mode 100644
index cf31fa07855b606cb46049e97498a99d052d19be..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__X_InvalidArgument.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_InvalidArgument: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_InvalidArgument: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_InvalidArgument - what</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__X_InvalidArgument.html#X_InvalidArgument">Utilities::BaseOption::X_InvalidArgument::X_InvalidArgument</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__X_OptionError.html#X_OptionError">Utilities::BaseOption::X_OptionError::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__X_InvalidArgument.html#what">Utilities::BaseOption::X_InvalidArgument::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__X_MissingArgument.html b/api/full-list-Utilities__BaseOption__X_MissingArgument.html
deleted file mode 100644
index c90def0cf8f7c405a511f7125dc15840149e6c09..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__X_MissingArgument.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_MissingArgument: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_MissingArgument: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_MissingArgument - what</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__X_MissingArgument.html#X_MissingArgument">Utilities::BaseOption::X_MissingArgument::X_MissingArgument</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__X_OptionError.html#X_OptionError">Utilities::BaseOption::X_OptionError::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__X_MissingArgument.html#what">Utilities::BaseOption::X_MissingArgument::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__X_OptionError.html b/api/full-list-Utilities__BaseOption__X_OptionError.html
deleted file mode 100644
index 19dce22cc2d9d397244cccedfe742913d78ebd7f..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__X_OptionError.html
+++ /dev/null
@@ -1,34 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_OptionError: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_OptionError: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_OptionError - what</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__X_OptionError.html#X_OptionError">Utilities::BaseOption::X_OptionError::X_OptionError</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__X_OptionError.html#what">Utilities::BaseOption::X_OptionError::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__BaseOption__X_UnknownOption.html b/api/full-list-Utilities__BaseOption__X_UnknownOption.html
deleted file mode 100644
index 447676436040a658ee043da892fcef2dc7f4780e..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__BaseOption__X_UnknownOption.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_UnknownOption: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_UnknownOption: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_OptionError - what</TH></TR><TR ><TD><A HREF="Utilities__BaseOption__X_OptionError.html#X_OptionError">Utilities::BaseOption::X_OptionError::X_OptionError</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption__X_UnknownOption.html#X_UnknownOption">Utilities::BaseOption::X_UnknownOption::X_UnknownOption</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption__X_UnknownOption.html#what">Utilities::BaseOption::X_UnknownOption::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:24:46 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__Log.html b/api/full-list-Utilities__Log.html
deleted file mode 100644
index db3252ab4272dea9360742c6f417f7d3789ad5d1..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__Log.html
+++ /dev/null
@@ -1,43 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Log: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Log: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Log - getDir</TH></TR><TR ><TD><A HREF="Utilities__Log.html#Log">Utilities::Log::Log</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Log.html#appendDir">Utilities::Log::appendDir</A></TD></TR>
-<TR ><TD><A HREF="Utilities__Log.html#counter">Utilities::Log::counter</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Log.html#getDir">Utilities::Log::getDir</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>getInstance - operator=</TH></TR><TR ><TD><A HREF="Utilities__Log.html#getInstance">Utilities::Log::getInstance</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Log.html#getLogFileName">Utilities::Log::getLogFileName</A></TD></TR>
-<TR ><TD><A HREF="Utilities__Log.html#makeDir">Utilities::Log::makeDir</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Log.html#operator=">Utilities::Log::operator=</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>out - str</TH></TR><TR ><TD><A HREF="Utilities__Log.html#out">Utilities::Log::out</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Log.html#setDir">Utilities::Log::setDir</A></TD></TR>
-<TR ><TD><A HREF="Utilities__Log.html#str">Utilities::Log::str</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__Option.html b/api/full-list-Utilities__Option.html
deleted file mode 100644
index f85047885e39764e7e0638abd8e073e8f2fc13e2..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__Option.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Option: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Option: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>BaseOption - has_arg</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#BaseOption">Utilities::BaseOption::BaseOption</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Option.html#Option">Utilities::Option::Option</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#compulsory">Utilities::BaseOption::compulsory</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Option.html#default_value">Utilities::Option::default_value</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#has_arg">Utilities::BaseOption::has_arg</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>help_text - required</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#help_text">Utilities::BaseOption::help_text</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#key">Utilities::BaseOption::key</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#matches">Utilities::BaseOption::matches</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__BaseOption.html#optional">Utilities::BaseOption::optional</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#required">Utilities::BaseOption::required</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>set - value</TH></TR><TR ><TD><A HREF="Utilities__BaseOption.html#set">Utilities::BaseOption::set</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Option.html#set_value">Utilities::Option::set_value</A></TD></TR>
-<TR ><TD><A HREF="Utilities__BaseOption.html#unset">Utilities::BaseOption::unset</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Option.html#value">Utilities::Option::value</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__OptionParser.html b/api/full-list-Utilities__OptionParser.html
deleted file mode 100644
index a65ca08ae9cb3c15491474573744b6e76334481e..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__OptionParser.html
+++ /dev/null
@@ -1,40 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class OptionParser: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class OptionParser: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>OptionParser - check_compulsory_arguments</TH></TR><TR ><TD><A HREF="Utilities__OptionParser.html#OptionParser">Utilities::OptionParser::OptionParser</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__OptionParser.html#add">Utilities::OptionParser::add</A></TD></TR>
-<TR ><TD><A HREF="Utilities__OptionParser.html#check_compulsory_arguments">Utilities::OptionParser::check_compulsory_arguments</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>find_matching_option - usage</TH></TR><TR ><TD><A HREF="Utilities__OptionParser.html#find_matching_option">Utilities::OptionParser::find_matching_option</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__OptionParser.html#parse_command_line">Utilities::OptionParser::parse_command_line</A></TD></TR>
-<TR ><TD><A HREF="Utilities__OptionParser.html#parse_long_option">Utilities::OptionParser::parse_long_option</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__OptionParser.html#parse_option">Utilities::OptionParser::parse_option</A></TD></TR>
-<TR ><TD><A HREF="Utilities__OptionParser.html#usage">Utilities::OptionParser::usage</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__Time_Tracer.html b/api/full-list-Utilities__Time_Tracer.html
deleted file mode 100644
index 5b37bb193f618d10fa3b2865cbc16e3d01739a76..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__Time_Tracer.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Time_Tracer: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Time_Tracer: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Time_Tracer - dump_times</TH></TR><TR ><TD><A HREF="Utilities__Time_Tracer.html#Time_Tracer">Utilities::Time_Tracer::Time_Tracer</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Time_Tracer.html#dump_times">Utilities::Time_Tracer::dump_times</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>operator= - settimingon</TH></TR><TR ><TD><A HREF="Utilities__Time_Tracer.html#operator=">Utilities::Time_Tracer::operator=</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Time_Tracer.html#setdebugon">Utilities::Time_Tracer::setdebugon</A></TD></TR>
-<TR ><TD><A HREF="Utilities__Time_Tracer.html#settimingon">Utilities::Time_Tracer::settimingon</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__TimingFunction.html b/api/full-list-Utilities__TimingFunction.html
deleted file mode 100644
index ccb8cf6bc42d3aaf3096dd548aacc6745ae692f4..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__TimingFunction.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class TimingFunction: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class TimingFunction: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>TimingFunction - end</TH></TR><TR ><TD><A HREF="Utilities__TimingFunction.html#TimingFunction">Utilities::TimingFunction::TimingFunction</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__TimingFunction.html#end">Utilities::TimingFunction::end</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>operator<< - start</TH></TR><TR ><TD><A HREF="Utilities__TimingFunction.html#operator%25253C%25253C">Utilities::TimingFunction::operator<<</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__TimingFunction.html#operator=">Utilities::TimingFunction::operator=</A></TD></TR>
-<TR ><TD><A HREF="Utilities__TimingFunction.html#start">Utilities::TimingFunction::start</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__TimingFunction__comparer_name.html b/api/full-list-Utilities__TimingFunction__comparer_name.html
deleted file mode 100644
index 12c827249be2ab5466e2d8a6d70c48030abeaceb..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__TimingFunction__comparer_name.html
+++ /dev/null
@@ -1,33 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class comparer_name: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class comparer_name: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>operator() - operator()</TH></TR><TR ><TD><A HREF="Utilities__TimingFunction__comparer_name.html#operator()">Utilities::TimingFunction::comparer_name::operator()</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__TimingFunction__comparer_time_taken.html b/api/full-list-Utilities__TimingFunction__comparer_time_taken.html
deleted file mode 100644
index 35830be619cdc254eca0e35b49c60dce6b689170..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__TimingFunction__comparer_time_taken.html
+++ /dev/null
@@ -1,33 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class comparer_time_taken: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class comparer_time_taken: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>operator() - operator()</TH></TR><TR ><TD><A HREF="Utilities__TimingFunction__comparer_time_taken.html#operator()">Utilities::TimingFunction::comparer_time_taken::operator()</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__Tracer_Plus.html b/api/full-list-Utilities__Tracer_Plus.html
deleted file mode 100644
index dd3238eaf8daf1e7bf5e5f47c7799f5dfeceb98e..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__Tracer_Plus.html
+++ /dev/null
@@ -1,38 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class Tracer_Plus: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class Tracer_Plus: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Time_Tracer - Tracer_Plus</TH></TR><TR ><TD><A HREF="Utilities__Time_Tracer.html#Time_Tracer">Utilities::Time_Tracer::Time_Tracer</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Tracer_Plus.html#Tracer_Plus">Utilities::Tracer_Plus::Tracer_Plus</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>dump_times - settimingon</TH></TR><TR ><TD><A HREF="Utilities__Time_Tracer.html#dump_times">Utilities::Time_Tracer::dump_times</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Tracer_Plus.html#operator=">Utilities::Tracer_Plus::operator=</A></TD></TR>
-<TR ><TD><A HREF="Utilities__Time_Tracer.html#setdebugon">Utilities::Time_Tracer::setdebugon</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Time_Tracer.html#settimingon">Utilities::Time_Tracer::settimingon</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__X_AlreadySet.html b/api/full-list-Utilities__X_AlreadySet.html
deleted file mode 100644
index 1f03ab93c5900d848df412e2a58ed5699c7a5183..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__X_AlreadySet.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_AlreadySet: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_AlreadySet: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_AlreadySet - what</TH></TR><TR ><TD><A HREF="Utilities__X_AlreadySet.html#X_AlreadySet">Utilities::X_AlreadySet::X_AlreadySet</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_OptionError.html#X_OptionError">Utilities::X_OptionError::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__X_AlreadySet.html#what">Utilities::X_AlreadySet::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__X_InvalidArgument.html b/api/full-list-Utilities__X_InvalidArgument.html
deleted file mode 100644
index 624731a2d216adff8fee2356bb06762621a7ab77..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__X_InvalidArgument.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_InvalidArgument: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_InvalidArgument: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_InvalidArgument - what</TH></TR><TR ><TD><A HREF="Utilities__X_InvalidArgument.html#X_InvalidArgument">Utilities::X_InvalidArgument::X_InvalidArgument</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_OptionError.html#X_OptionError">Utilities::X_OptionError::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__X_InvalidArgument.html#what">Utilities::X_InvalidArgument::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__X_MissingArgument.html b/api/full-list-Utilities__X_MissingArgument.html
deleted file mode 100644
index 28fcb3a527488e313195a50fa3a931e3db67671a..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__X_MissingArgument.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_MissingArgument: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_MissingArgument: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_MissingArgument - what</TH></TR><TR ><TD><A HREF="Utilities__X_MissingArgument.html#X_MissingArgument">Utilities::X_MissingArgument::X_MissingArgument</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_OptionError.html#X_OptionError">Utilities::X_OptionError::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__X_MissingArgument.html#what">Utilities::X_MissingArgument::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__X_OptionError.html b/api/full-list-Utilities__X_OptionError.html
deleted file mode 100644
index 2ad95c63d5b89a89eae2b90833c04e7408aa548b..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__X_OptionError.html
+++ /dev/null
@@ -1,34 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_OptionError: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_OptionError: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_OptionError - what</TH></TR><TR ><TD><A HREF="Utilities__X_OptionError.html#X_OptionError">Utilities::X_OptionError::X_OptionError</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_OptionError.html#what">Utilities::X_OptionError::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/full-list-Utilities__X_UnknownOption.html b/api/full-list-Utilities__X_UnknownOption.html
deleted file mode 100644
index 21c2d8a5c8fc92c23e0d047b1f5a7c73adcfba71..0000000000000000000000000000000000000000
--- a/api/full-list-Utilities__X_UnknownOption.html
+++ /dev/null
@@ -1,35 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>class X_UnknownOption: All methods</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>class X_UnknownOption: All methods</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_OptionError - what</TH></TR><TR ><TD><A HREF="Utilities__X_OptionError.html#X_OptionError">Utilities::X_OptionError::X_OptionError</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_UnknownOption.html#X_UnknownOption">Utilities::X_UnknownOption::X_UnknownOption</A></TD></TR>
-<TR ><TD><A HREF="Utilities__X_UnknownOption.html#what">Utilities::X_UnknownOption::what</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/header-list.html b/api/header-list.html
deleted file mode 100644
index 22e8bd51aa46aacf03344a2e365d6dc591ee5985..0000000000000000000000000000000000000000
--- a/api/header-list.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE> File Index</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
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-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1> File Index</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
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-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
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-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Log.h - tracer_plus.h</TH></TR><TR ><TD><A HREF="Log_h.html">Log.h</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="options_h.html">options.h</A></TD></TR>
-<TR ><TD><A HREF="time__tracer_h.html">time_tracer.h</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="tracer__plus_h.html">tracer_plus.h</A></TD></TR>
-</TABLE></TD></TR></TABLE></UL>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/hier.html b/api/hier.html
deleted file mode 100644
index 9a17725743c75fa3121f36479eadcc16466f36c1..0000000000000000000000000000000000000000
--- a/api/hier.html
+++ /dev/null
@@ -1,58 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE> Class Hierarchy</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1> Class Hierarchy</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
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-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<UL><LI><i><A HREF="Utilities__BaseOption.html">Utilities::BaseOption</A></i>
-<UL><LI><A HREF="Utilities__Option.html">Utilities::Option</A>
-</UL></LI>
-<LI><A HREF="Utilities__Log.html">Utilities::Log</A>
-<LI><A HREF="Utilities__OptionParser.html">Utilities::OptionParser</A>
-<LI><A HREF="Utilities__Time_Tracer.html">Utilities::Time_Tracer</A>
-<UL><LI><A HREF="Utilities__Tracer_Plus.html">Utilities::Tracer_Plus</A>
-</UL></LI>
-<LI><A HREF="Utilities__TimingFunction.html">Utilities::TimingFunction</A>
-<LI><A HREF="Utilities__Tracer_Plus.html">Utilities::Tracer_Plus</A>
-<LI><A HREF="Utilities.html">Utilities</A>
-<LI><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A>
-<UL><LI><A HREF="Utilities__X_AlreadySet.html">Utilities::X_AlreadySet</A>
-<LI><A HREF="Utilities__X_InvalidArgument.html">Utilities::X_InvalidArgument</A>
-<LI><A HREF="Utilities__X_MissingArgument.html">Utilities::X_MissingArgument</A>
-<LI><A HREF="Utilities__X_UnknownOption.html">Utilities::X_UnknownOption</A>
-</UL></LI>
-<LI><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A>
-<UL><LI><A HREF="Utilities__X_AlreadySet.html">Utilities::X_AlreadySet</A>
-<LI><A HREF="Utilities__X_InvalidArgument.html">Utilities::X_InvalidArgument</A>
-<LI><A HREF="Utilities__X_MissingArgument.html">Utilities::X_MissingArgument</A>
-<LI><A HREF="Utilities__X_UnknownOption.html">Utilities::X_UnknownOption</A>
-</UL></LI>
-<LI><A HREF="Utilities__TimingFunction__comparer_name.html">Utilities::TimingFunction::comparer_name</A>
-<LI><A HREF="Utilities__TimingFunction__comparer_time_taken.html">Utilities::TimingFunction::comparer_time_taken</A>
-</UL>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/index-long.html b/api/index-long.html
deleted file mode 100644
index d8429d1e8160dbd3311aaa69667bbc0c38029d94..0000000000000000000000000000000000000000
--- a/api/index-long.html
+++ /dev/null
@@ -1,41 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE> Annotated List</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1> Annotated List</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER=\"0\"><TR ><TD><A HREF="Utilities.html">Utilities</A></TD><TD></TD></TR><TR bgcolor="#eeeeee"><TD><i><A HREF="Utilities__BaseOption.html">Utilities::BaseOption</A></i></TD><TD>
- Provides behaviour common to all option types.</TD></TR><TR ><TD><A HREF="Utilities__Log.html">Utilities::Log</A></TD><TD></TD></TR><TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Option.html">Utilities::Option</A></TD><TD>
- Template class adding type specific behaviour to BaseOption.</TD></TR><TR ><TD><A HREF="Utilities__OptionParser.html">Utilities::OptionParser</A></TD><TD>
- A class for parsing command line arguments into Option objects.</TD></TR><TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Time_Tracer.html">Utilities::Time_Tracer</A></TD><TD></TD></TR><TR ><TD><A HREF="Utilities__TimingFunction.html">Utilities::TimingFunction</A></TD><TD></TD></TR><TR bgcolor="#eeeeee"><TD><A HREF="Utilities__TimingFunction__comparer_name.html">Utilities::TimingFunction::comparer_name</A></TD><TD></TD></TR><TR ><TD><A HREF="Utilities__TimingFunction__comparer_time_taken.html">Utilities::TimingFunction::comparer_time_taken</A></TD><TD></TD></TR><TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Tracer_Plus.html">Utilities::Tracer_Plus</A></TD><TD></TD></TR><TR ><TD><A HREF="Utilities__X_AlreadySet.html">Utilities::X_AlreadySet</A></TD><TD>
- </TD></TR><TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_InvalidArgument.html">Utilities::X_InvalidArgument</A></TD><TD>
- </TD></TR><TR ><TD><A HREF="Utilities__X_MissingArgument.html">Utilities::X_MissingArgument</A></TD><TD>
- If an option should have had an argument but didn't then throw this
- exception.</TD></TR><TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A></TD><TD>
- Throw this exception if an error occured inside the Options package.</TD></TR><TR ><TD><A HREF="Utilities__X_UnknownOption.html">Utilities::X_UnknownOption</A></TD><TD>
- Throw this exception if no matching option was found during parsing.</TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/index.html b/api/index.html
deleted file mode 100644
index 252259a186410682480bb47481b8a73e28e2c2cb..0000000000000000000000000000000000000000
--- a/api/index.html
+++ /dev/null
@@ -1,47 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE> Class Index</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1> Class Index</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<TABLE WIDTH="100%" BORDER="0"><TR><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Utilities - OptionParser</TH></TR><TR ><TD><A HREF="Utilities.html">Utilities</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><i><A HREF="Utilities__BaseOption.html">Utilities::BaseOption</A></i></TD></TR>
-<TR ><TD><A HREF="Utilities__Log.html">Utilities::Log</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__Option.html">Utilities::Option</A></TD></TR>
-<TR ><TD><A HREF="Utilities__OptionParser.html">Utilities::OptionParser</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>Time_Tracer - Tracer_Plus</TH></TR><TR ><TD><A HREF="Utilities__Time_Tracer.html">Utilities::Time_Tracer</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__TimingFunction.html">Utilities::TimingFunction</A></TD></TR>
-<TR ><TD><A HREF="Utilities__TimingFunction__comparer_name.html">Utilities::TimingFunction::comparer_name</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__TimingFunction__comparer_time_taken.html">Utilities::TimingFunction::comparer_time_taken</A></TD></TR>
-<TR ><TD><A HREF="Utilities__Tracer_Plus.html">Utilities::Tracer_Plus</A></TD></TR>
-</TABLE></TD><TD VALIGN="top"><TABLE BORDER="0"><TR bgcolor="b0b0b0"><TH>X_AlreadySet - X_UnknownOption</TH></TR><TR ><TD><A HREF="Utilities__X_AlreadySet.html">Utilities::X_AlreadySet</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_InvalidArgument.html">Utilities::X_InvalidArgument</A></TD></TR>
-<TR ><TD><A HREF="Utilities__X_MissingArgument.html">Utilities::X_MissingArgument</A></TD></TR>
-<TR bgcolor="#eeeeee"><TD><A HREF="Utilities__X_OptionError.html">Utilities::X_OptionError</A></TD></TR>
-<TR ><TD><A HREF="Utilities__X_UnknownOption.html">Utilities::X_UnknownOption</A></TD></TR>
-</TABLE></TD></TR></TABLE><HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/options_h.html b/api/options_h.html
deleted file mode 100644
index 423317bfa176d1b078b15913d31155c3f8e90ea8..0000000000000000000000000000000000000000
--- a/api/options_h.html
+++ /dev/null
@@ -1,403 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>Source: options.h</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>Source: options.h</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<pre>
-// $Id$
-#if !defined(OPTIONS_H)
-#define OPTIONS_H
-
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#define POSIX_SOURCE 1
-
-namespace Utilities {
-
- bool string_to_T(bool &b, const string& s);
- bool string_to_T(string& d, const string& s);
- bool string_to_T(int& i, const string& s);
- bool string_to_T(float& v, const string& s);
-
- typedef enum argflag {
- no_argument = 0, requires_argument, optional_argument
- } ArgFlag;
-
-}
-
-namespace Utilities {
-
- /**
- Provides behaviour common to all option types. Actual options are
- declared using the templated Option class. The
- OptionParser class can be used to parse command lines.
- @see Option
- @see OptionParser
- @author Dave Flitney
- @version 1.0b, Nov., 2000.
- */
- class BaseOption {
- public:
- /**
- @param k comma seperated list of key aliases
- @param ht the help text to be printed for this option
- @param c if true then this option is compulsory
- @param f one of no_argument, requires_argument, optional_argument
- to indicate what arguments should be supplied
- */
- BaseOption(const string& k, const string& ht, bool c, ArgFlag f):
- key_(k), help_text_(ht), arg_flag_(f),
- unset_(true), compulsory_(c) {}
-
- /**
- @return true if the option is compulsory
- */
- bool compulsory() { return compulsory_; }
- /**
- @return true if the option requires an argument
- */
- bool required() { return arg_flag_ == requires_argument; }
- /**
- @return true if the option has an optional argument
- */
- bool optional() { return arg_flag_ == optional_argument; }
- /**
- @return true if the option has an argument at all
- */
- bool has_arg() { return arg_flag_ != no_argument; }
- /**
- @return true if the option has been set
- */
- bool set() { return !unset_; }
- /**
- @return true if the option remains unset
- */
- bool unset() { return unset_; }
- /*
- @param arg A command line argument to be compared against
- the list of possible keys for this option.
- @return True if a match is found.
- */
- bool matches(const string& arg);
- /*
- @return This options key string.
- */
- const string& key() const { return key_; }
- /*
- @return This options help text.
- */
- const string& help_text() const { return help_text_; }
-
- /*
- @param Sets the value for this option. Is overridden in the type
- specific template class Option.
- */
- virtual bool set_value(const string& vs) = 0;
-
- virtual ~BaseOption() {}
-
- private:
- string key_, help_text_;
- ArgFlag arg_flag_;
-
- protected:
- bool unset_, compulsory_;
- };
-
- ostream& operator<<(ostream &os, const BaseOption& o);
-
-
- /**
- Template class adding type specific behaviour to BaseOption. Define
- one of these per program supported option.
- @author Dave Flitney
- @version 1.0b, Nov., 2000.
- @see BaseOption
- */
- template<class T> class Option: public BaseOption {
- public:
- /**
- @param k Comma seperated list of key aliases
- @param v Default value for this option
- @param ht Help text to be printed when outputting usage
- @param c If true then this option is compulsory
- @param f This options argument requirements
- */
- Option(const string& k, const T& v, const string& ht,
- bool c, ArgFlag f = no_argument):
- BaseOption(k, ht, c, f), default_(v), value_(v) {}
-
-
- /**
- @param vs The value string which needs to be parsed to set
- this options value. The overloaded function string_to_T must be defined
- for type T.
- */
- bool set_value(const string& vs) {
- if(string_to_T(value_, vs))
- unset_ = false;
- return !unset_;
- }
-
- /**
- @return The options value.
- */
- const T& value() { return value_; }
- /**
- @return The options default value.
- */
- const T& default_value() { return default_; }
-
- virtual ~Option() {}
-
- private:
- Option() {}
-
- T default_, value_;
- };
-
- /**
- Throw this exception if an error occured inside the Options package.
- */
- class X_OptionError: public std::exception {
- public:
- X_OptionError() throw() {};
- virtual const char * what() const throw() {
- return "There were errors parsing the command line!";
- }
- };
-
- /**
- Throw this exception if no matching option was found during parsing.
- */
- class X_UnknownOption: public X_OptionError {
- public:
- X_UnknownOption(const string& s) throw():
- str_(s+":unknown option!") {};
- virtual const char * what() const throw() {
- return str_.c_str();
- }
-
- private:
- string str_;
- };
-
- /**
- */
- class X_AlreadySet: public X_OptionError {
- public:
- X_AlreadySet(const string& s) throw():
- str_(s+":already set!") {};
- virtual const char * what() const throw() {
- return str_.c_str();
- }
-
- private:
- string str_;
- };
-
- /**
- If an option should have had an argument but didn't then throw this
- exception.
- */
- class X_MissingArgument: public X_OptionError {
- public:
- X_MissingArgument(const string& s) throw():
- str_(s+":missing argument!") {};
- virtual const char * what() const throw() {
- return str_.c_str();
- }
-
- private:
- string str_;
- };
-
- /**
- */
- class X_InvalidArgument: public X_OptionError {
- public:
- X_InvalidArgument(const string& o, const string& v) throw():
- str_(o+":invalid argument "+v+"!") {};
- virtual const char * what() const throw() {
- return str_.c_str();
- }
-
- private:
- string str_;
- };
-
- /**
- A class for parsing command line arguments into Option objects. The
- following example demonstrates the principle:
- @author Dave Flitney
- @version 1.0b, Nov., 2000.
- @see BaseOption
- @see Option
- <pre>
-#include "options.h"
-
-// $Id$
-
-using namespace Utilities;
-
-Option<bool> verbose(string("-V,--verbose"), false,
- string("switch on diagnostic messages"),
- false, BaseOption::no_argument);
-Option<bool> help(string("-h,--help"), false,
- string("display this message"),
- false, BaseOption::no_argument);
-Option<float> dof(string("-d,--dof"), 100.0,
- string("number of degrees of freedom"),
- true, BaseOption::requires_argument);
-Option<string> mask(string("-m,--mask"), string("mask"),
- string("brain mask volume"),
- true, BaseOption::requires_argument);
-Option<string> resid(string("-r,--res"), string("res4d"),
- string("4d `residual-of-fit' image"),
- true, BaseOption::requires_argument);
-Option<int> segid(string("-s,--shared-seg-id"), -1,
- "shared memory segment ID",
- false, BaseOption::requires_argument);
-
-string title =
-"opttst (Version 1.0)\n\n\
-Copyright(c) 2000, University of Oxford\n\
-Dave Flitney";
-
-string examples =
-"opttst --dof=<number> --mask=<filename> --res=<filename>\n\
-opttst -d <number> -m <filename> -r <filename>\n\
-opttst --verbose\n";
-
-int main(unsigned int argc, char **argv) {
-
- OptionParser options(title, examples);
-
- try {
-
- options.add(verbose);
- options.add(help);
- options.add(segid);
- options.add(dof);
- options.add(mask);
- options.add(resid);
-
- for(unsigned int a = options.parse_command_line(argc, argv);
- a < argc; a++)
- cout << argv[a] << endl;
-
- if(help.value() ||
- !options.check_compulsory_arguments())
- options.usage();
-
- if(verbose.value()) {
- cout << "verbose = " << verbose.value() << endl;
- cout << "help = " << help.value() << endl;
- cout << "segid = " << segid.value() << endl;
- cout << "dof = " << dof.value() << endl;
- cout << "mask = " << mask.value() << endl;
- cout << "resid = " << resid.value() << endl;
- }
-
- } catch(X_OptionError& e) {
- options.usage();
- cerr << endl << e.what() << endl;
- } catch(std::exception &e) {
- cerr << e.what() << endl;
- }
-}
- </pre>
- */
- class OptionParser {
- public:
-
- OptionParser(const string& p, const string& e): progname_(p), example_(e) {}
-
- /**
- @param o An option to be added to the parser
- */
- void add(BaseOption& o) { options_.push_back(&o); }
-
- void usage();
- /**
- @param verbose If set then this method will carp about any option which
- is marked as compulsory but hasn't been set
- @return true if all compulsory arguments have been set and false otherwise
- */
- bool check_compulsory_arguments(bool verbose=false);
- /**
- The parameters, argc and argv, should normally be those passed to
- main via the command line shell.
- @param argc The argument count.
- @param argv The vector of argument strings.
- */
- unsigned int parse_command_line(unsigned int argc, char **argv);
-
- virtual ~OptionParser() {}
-
- protected:
- /**
- */
- OptionParser() {}
-
- private:
- /**
- @param optstr A string which should match one of the option strings
- registered with the add method.
- @return Pointer to the matching option or NULL if a match wasn't found.
- */
- BaseOption* find_matching_option(const string& optstr);
- /**
- @param optstr A string which should match one of the option strings
- registered with the add method.
- @param valstr A string which can be used to set the options value
- if applicable.
- @return true on success.
- */
- unsigned int parse_option(const string& optstr, const string& valstr)
- throw(X_AlreadySet, X_UnknownOption,
- X_MissingArgument, X_InvalidArgument);
- /**
- @param str A string of the form --option[=value].
- @return true on success.
- */
- unsigned int parse_long_option(const string& str);
-
- string progname_, example_;
-
- typedef vector<BaseOption *> Options;
- Options options_;
- };
-
-}
-#endif
-</pre>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/time__tracer_h.html b/api/time__tracer_h.html
deleted file mode 100644
index 3bd2866b2c6ba104ebb326d9070d510a74da4368..0000000000000000000000000000000000000000
--- a/api/time__tracer_h.html
+++ /dev/null
@@ -1,190 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>Source: time_tracer.h</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>Source: time_tracer.h</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<pre>
-/* Time_Tracer.h
-
- Mark Woolrich, FMRIB Image Analysis Group
-
- Copyright (C) 1999-2000 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#if !defined(Time_Tracer_h)
-#define Time_Tracer_h
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <time.h>
-#include <set>
-
-namespace Utilities{
-
- class TimingFunction
- {
- public:
- TimingFunction(const char * pstr):
- str(pstr),
- time_taken(0),
- times_called(0)
- {}
-
- class comparer_name
- {
- public:
- bool operator()(const TimingFunction* t1, const TimingFunction* t2) const
- {
- return strcmp(t1->str, t2->str) < 0;
- }
- };
-
- class comparer_time_taken
- {
- public:
- bool operator()(const TimingFunction* t1, const TimingFunction* t2) const
- {
- return t1->time_taken > t2->time_taken;
- }
- };
-
- void start() {start_time = clock();}
- void end() {time_taken += clock()-start_time; times_called++;}
-
- friend comparer_name;
- friend comparer_time_taken;
- friend ostream& operator<<(ostream& ostr, const TimingFunction* t);
-
- protected:
- const char* str;
- clock_t time_taken;
- int times_called;
- clock_t start_time;
-
- private:
- TimingFunction();
- const TimingFunction& operator=(TimingFunction&);
- TimingFunction(TimingFunction&);
- };
-
- inline ostream& operator<<(ostream& ostr, const TimingFunction* t)
- {
- ostr << "<tr><td>" << t->str;
- ostr.setf(0, ios::floatfield);
- ostr << "<td align=center>" << float(t->time_taken)/CLOCKS_PER_SEC;
- ostr.setf(ios::scientific, ios::floatfield);
- ostr << "<td align=center>" << t->times_called << "<td align=center>" << (t->time_taken/float(t->times_called))/CLOCKS_PER_SEC;
- ostr << "</tr>";
- return ostr;
- }
-
- // Non Newmat Tracer:
- class Time_Tracer
- {
- public:
- Time_Tracer(char* str)
- {
- if(debug)
- {
- tmp = "";
- pad++;
- for(unsigned int i = 0; i < pad; i++)
- tmp = tmp + " ";
-
- cout << tmp << str << endl;
- }
- if(timingon)
- {
- // see if already in list:
- timingFunction = new TimingFunction(str);
- set<TimingFunction*, TimingFunction::comparer_name>::iterator it = timingFunctions.find(timingFunction);
- if(it== timingFunctions.end())
- {
- timingFunctions.insert(timingFunction);
- }
- else
- {
- timingFunction = *it;
- }
-
- timingFunction->start();
- }
- }
-
- virtual ~Time_Tracer()
- {
- if(debug && pad > 0)
- {
- cout << tmp << "finished" << endl;
- pad--;
- }
- if(timingon)
- {
- timingFunction->end();
- }
- }
-
- static void dump_times(const string& dir)
- {
- multiset<TimingFunction*, TimingFunction::comparer_time_taken> timingFunctionsByTimeTaken(timingFunctions.begin(), timingFunctions.end());
-
- ofstream out;
- out.open((dir + "/timings.html").c_str(), ios::out);
- out << "<HTML><TITLE>Tracer Timings</TITLE><BODY><table border=3 cellspacing=5>" << endl;
- out << "<tr><td>Function<td align=center>Total Time(secs)<td align=center>Num of calls<td align=center>Time per call(secs)</tr>" << endl;
- copy(timingFunctionsByTimeTaken.begin(), timingFunctionsByTimeTaken.end(), ostream_iterator<TimingFunction*>(out, "\n"));
- out << "</table></BODY></HTML>" << endl;
- out.close();
- }
-
- static void setdebugon() {debug = true;}
- static void settimingon() {timingon = true;}
-
- protected:
- static bool debug;
- static bool timingon;
- static unsigned int pad;
- static set<TimingFunction*, TimingFunction::comparer_name> timingFunctions;
-
- string tmp;
- TimingFunction* timingFunction;
-
- private:
- Time_Tracer();
- const Time_Tracer& operator=(Time_Tracer&);
- Time_Tracer(Time_Tracer&);
- };
-
-}
-#endif
-
-</pre>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>
diff --git a/api/tracer__plus_h.html b/api/tracer__plus_h.html
deleted file mode 100644
index 1dfd9589443b3912dc08578e3d58d5b9197c72f1..0000000000000000000000000000000000000000
--- a/api/tracer__plus_h.html
+++ /dev/null
@@ -1,82 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>Source: tracer_plus.h</TITLE>
-<META NAME="Generator" CONTENT="KDOC ">
-</HEAD>
-<BODY bgcolor="#ffffff" text="#000000" link="#0000ff" vlink="#000099" alink= "#ffffff">
-<TABLE WIDTH="100%" BORDER="0">
-<TR>
-<TD>
- <TABLE BORDER="0">
- <TR><TD valign="top" align="left" cellspacing="10">
- <h1>Source: tracer_plus.h</h1>
- </TD>
- <TD valign="top" align="right" colspan="1"></TD></TR>
- </TABLE>
- <HR>
- <TABLE BORDER="0">
-
- </TABLE>
- </TD>
-<TD align="right"><TABLE BORDER="0"><TR><TD><small><A HREF="index-long.html">Annotated List</small></TD></TR>
-<TR><TD><small><A HREF="header-list.html">Files</small></TD></TR>
-<TR><TD><small><A HREF="all-globals.html">Globals</small></TD></TR>
-<TR><TD><small><A HREF="hier.html">Hierarchy</small></TD></TR>
-<TR><TD><small><A HREF="index.html">Index</small></TD></TR>
-</TABLE></TD></TR></TABLE>
-<pre>
-/* Tracer_Plus.h
-
- Mark Woolrich, FMRIB Image Analysis Group
-
- Copyright (C) 1999-2000 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#if !defined(Tracer_Plus_h)
-#define Tracer_Plus_h
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <time.h>
-#include <set>
-#include "newmatap.h"
-#include "newmatio.h"
-#include "time_tracer.h"
-
-using namespace NEWMAT;
-
-namespace Utilities {
-
- // Newmat version:
- class Tracer_Plus : public Tracer, public Time_Tracer
- {
- public:
- Tracer_Plus(char* str) :
- Tracer(str),
- Time_Tracer(str)
- {
- }
-
- virtual ~Tracer_Plus()
- {
- }
-
- private:
- Tracer_Plus();
- const Tracer_Plus& operator=(Tracer_Plus&);
- Tracer_Plus(Tracer_Plus&);
- };
-
-}
-
-#endif
-
-</pre>
-<HR>
- <table>
- <tr><td><small>Generated by: flitney@mace.fmrib.ox.ac.uk on Thu Feb 22 17:32:45 2001, using kdoc 2.0a36.</small></td></tr>
- </table>
-</BODY>
-</HTML>