data/admin/documentation/CodeGuidelines_main.xml

<chapter id="NamingConventions" xreflabel="Naming Conventions">
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<title>Naming Conventions</title>
<para>
The intent of naming conventions is to allow programmers, which are
not familiar with the code to easily grasp the meaning and scope of
symbols in the source code. Each programmer of COPASI should adhere
for its own benefit and to the advantage of the project to the
following conventions.
</para>

<sect1 id="ClassNames" xreflabel="Class Names">
<title>Class Names</title>
<para>
Class names must all start with a capital letter <literal>C</literal>. This is
followed by a descriptive name. This name might be composed by
different words. These words must all start with capital letters and
are concatenated without underscores. Good examples for class names
include: 
  <literal>CCopasiXMLParser</literal> , <literal>CExpatTemplate</literal>, and <literal>CMathModel</literal>.
</para>
</sect1>

<sect1 id="VariableNames" xreflabel="Variable Names">
<title>Variable Names</title>
<para>
In general a variable name should be descriptive. This name might be
composed by different words. These words must all start with capital
letters and are concatenated without underscores. In addition the
following standards should be followed:  
</para>

<simplelist type="horiz" columns="2">
<member><command>Counters</command></member>
<member>might be used such as <literal>i</literal>, <literal>k</literal>,
and <literal>l</literal>, which may be used in loops.
</member>
<member><command>Iterators</command></member><member> might be used such as <literal>it</literal> and <literal>end</literal>, which may be used in loops. 
</member>
<member><command>Pointers</command></member><member> are prepended with a lower case letter <literal>p</literal>. 
</member>
<member><command>Method Parameters</command></member><member> must start with a lower case letter.
</member>
<member><command>Class Member Variables</command></member><member> are prepended with a lower case
  letter <literal>m</literal>.
</member>
<member><command>Class Member Pointers</command></member><member> must have the
  prefix <literal>mp</literal>.
</member>
</simplelist>

</sect1>

<sect1 id="MethodName" xreflabel="Method Name">
<title>Method Name</title>
<para>
Method names should have a descriptive name starting with a lower case
letter. This name might be composed by different words. These words
beginning with the second must start with capital letters and
are concatenated without underscores. Good examples for method names
include: 
   <literal>createMetabolite</literal>, <literal>compileIfNecessary</literal>, and <literal>buildMoieties</literal>
</para>

<para>
In addition the following standards should be followed:  
</para>

<simplelist type="horiz" columns="2">

<member><command>Retrieval Methods</command></member><member> must start with <literal>get</literal> followed by
  the member variable name without the prefix.
</member>

<member><command>Set Methods</command></member><member> must start with <literal>set</literal> followed by
  the member variable name without the prefix.
</member>

<member><command>Boolean Query Functions</command></member><member> should start if applicable with
  <literal>is</literal>.
</member>
</simplelist>
</sect1>
</chapter>

<chapter id="ProgramCodeGuidelines" xreflabel="Program Code Guidelines">
<title>Program Code Guidelines</title>

<sect1 id="include" xreflabel="include">
<title>Use of #include </title>
<para>
To minimize compilation problems on the different platforms and with
the libraries COPASI depends on it is necessary to define some rules,
which need to be followed when specifying include files in the COPASI
code.  
</para>
<para> The #include statement distinguishes between two different type
of include files. 
</para>

<itemizedlist>
<listitem><para><command>Global Includes: </command>Global include files are
indicated by surrounding the filename with &lt; and &gt;, i.e. the
statements looks like: <literal>#include &lt;filename&gt;</literal>. 
All files not located in the COPASI source tree are considered global includes.
</para></listitem>

<listitem><para><command>Local Includes: </command>Local include files are
indicated by surrounding the filename with double quotes, i.e. the
statements looks like: <literal>#include "filename"</literal>. 
All files located in the COPASI source tree are considered local includes.
</para></listitem>
</itemizedlist>

<sect2 id="includeHeader" xreflabel="include Header">
<title>Order of #include in Header Files</title>
<para>
The number of include statements in header files should be kept to the
minimum necessary to compile the header file, i.e., a COPASI code file
just containing the following two lines of code must compile successfully:
</para>
<programlisting>
#include "copasi.h"
#include "filename"
</programlisting>
<para>
To achieve the minimal list of includes one should replace all not
needed includes with forward declarations as often as possible. Please
note that it should never be necessary to include <literal>copasi.h
</literal> in a header file.
</para>
<orderedlist>
<listitem><para><command>Qt Header Files: </command>Qt header
files must appear first. Please note that the Qt header file names are
all lowercase.</para></listitem>
<listitem><para><command>Global Header Files: </command>Other
global header files must appear next.</para></listitem>
<listitem><para><command>COPASI Header Files: </command>All COPASI
header files must be included with the full filename starting with the
<literal>copasi </literal> directory, i.e., the include statement
looks like <literal>#include "copasi/.." </literal></para></listitem>
</orderedlist>

</sect2>
<sect2 id="includeCode" xreflabel="include Code">
<title>Order of #include in Code Files</title>
<orderedlist>
<listitem><para><command>Qt Header Files: </command>Qt header
files must appear first. Please note that the Qt header file names are
all lowercase.</para></listitem>
<listitem><para><command>Global Header Files: </command>Other
global header files must appear next.</para></listitem>
<listitem><para><command>copasi.h: </command>This file must precede
all other local includes since they depend on the defines
of <literal>copasi.h </literal> to be present. </para></listitem>
<listitem><para><command>COPASI Header Files: </command>COPASI
header files must be included after
<literal>copasi.h</literal>. </para></listitem> 
<listitem><para><command>blaswrap.h or clapackwrap.h: </command>These two
wrapper files must appear last as their defines often conflict with
other includes.</para></listitem>
</orderedlist>
<para>

</para>
</sect2>

</sect1>

<sect1 id="Loops" xreflabel="Loops">
<title>Loops</title>
<para>
Counter or iterators used in loops must not be declared in the
<literal>for</literal> statement as the scope of the variables
declared within is not well defined in C and C++ standard and thus
leads to compile problems. The solution is to define those variables
prior to the <literal>for</literal> statement. 
</para>
</sect1>
</chapter>

<chapter id="CodeDocumentation" xreflabel="Code Documentation">
<title>Code Documentation</title>
<sect1 id="ClassDocumentation" xreflabel="Class Documentation">
<title>Class Documentation</title>
<para>
The COPASI team uses doxygen to generate API documentation. It is
therefore necessary that the classes, methods, and variables or
documented completely.
</para>
</sect1>

<sect1 id="VariableDocumentation" xreflabel="Variable Documentation">
<title>Variable Documentation</title>
<para></para>
</sect1>

<sect1 id="MethodDocumentation" xreflabel="Method Documentation">
<title>Method Documentation</title>
<para></para>
</sect1>

<sect1 id="InclineCodeDocumentation" xreflabel="Incline Code Documentation">
<title>Incline Code Documentation</title>
<para></para>
</sect1>
</chapter>

<chapter id="COPASIObjectStructure" xreflabel="COPASI Object Structure">
<title>COPASI Object Structure</title>
<para>
COPASI has an object structure which is used to access all objects
which can be calculated, plotted, or printed. Objects can be grouped to
larger objects called containers. COPASI itself functions as a root
container, i.e., it contains all objects which might be of interest
for calculation or output. The access to any object is provided with
an LDAP like common name (CN) which can be resolved starting from any
container.
</para>

<sect1 id="Object" xreflabel="Object">
<title>Object</title>
<para>
The object (<literal>class CCopasiObject</literal>) is the main
building block of the object structure. Each object has the following
main attributes: 

<variablelist><title>Attribute List</title>

<varlistentry><term><literal>std::string mObjectName</literal></term>
<listitem><para>The name of the object.
</para></listitem></varlistentry>

<varlistentry>
<term><literal>std::string mObjectType</literal></term>
<listitem><para>The type of the object, e.g. Compartment.
</para></listitem></varlistentry>

<varlistentry>
<term><literal>CCopasiContainer * mpObjectParent</literal></term>
<listitem><para>A pointer to the objects parent container.
</para></listitem></varlistentry>

<varlistentry>
<term><literal>unsigned int mObjectFlag</literal></term>
<listitem><para>A flag indicating object properties.
</para></listitem></varlistentry>
</variablelist>

</para>

<para>
In addition to the expected <literal>get</literal> and
<literal>set</literal> methods the objects provides the following
methods: 

<variablelist><title>Method List</title>
<varlistentry>
<term><literal>CCopasiContainer * getObjectAncestor(const std::string
&amp;type) const</literal></term>
<listitem><para>This method retrieves the closest ancestor of the object of
the specified type. 
</para></listitem></varlistentry>

<varlistentry>
<term><literal>virtual CCopasiObjectName getCN() const</literal></term>
<listitem><para>This method retrieve the common name (CN) of the object.
</para></listitem></varlistentry>

<varlistentry>
<term><literal>

</literal></term>
<listitem><para>

</para></listitem></varlistentry>

</variablelist>

</para>
</sect1>

<sect1 id="Container" xreflabel="Container">
<title>Container</title>
<para></para>
</sect1>

<sect1 id="COPASIVector" xreflabel="COPASI Vector">
<title>COPASI Vector</title>
<para></para>
</sect1>

<sect1 id="Parameter" xreflabel="Parameter">
<title>Parameter</title>
<para></para>
</sect1>

<sect1 id="ParameterGroup" xreflabel="Parameter Group">
<title>Parameter Group</title>
<para></para>
</sect1>

<sect1 id="Dependencies" xreflabel="Dependencies">
<title>Dependencies</title>
<para></para>
</sect1>
</chapter>

<chapter id="TheModelState" xreflabel="The Model State">
<title>The Model State</title>
<sect1 id="StateTemplateOrder" xreflabel="State Template Order">
<title>State Template Order</title>
<para>
This section describes whether and in which order the above calculated
simulation objects appear in the initial and current state of the
model. The order is described by the class CStateTemplate. Please note
that all objects with the type "Fixed" are marked "Unused" as there is
no need to calculate them during simulation.
</para>
<table frame="all"><title>State Template Order</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="2*" />
<colspec colwidth="2*" />
<thead>
 <row>
   <entry>Object</entry>
   <entry>Type</entry>
   <entry>Status</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Model</entry>
   <entry>Time</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Model Value</entry>
   <entry>ODE</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Compartment</entry>
   <entry>ODE</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Metabolite</entry>
   <entry>ODE</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Metabolite</entry>
   <entry>Reaction</entry>
   <entry>Independent</entry>
 </row>
 <row>
   <entry>Metabolite</entry>
   <entry>Reaction</entry>
   <entry>Dependent</entry>
 </row>
 <row>
   <entry>Metabolite</entry>
   <entry>Assignment</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Compartment</entry>
   <entry>Assignment</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Model Value</entry>
   <entry>Assignment</entry>
   <entry>Used</entry>
 </row>
 <row>
   <entry>Any</entry>
   <entry>Any</entry>
   <entry>Unused</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect1>

<sect1 id="SettingTheInitialState" xreflabel="Setting the Initial State">
<title>Setting the Initial State</title>
<para>
The initial state of a COPASI model is due to the introduction of
assignments for all model entities no longer determined through fixed
values. To calculate the current initial values those assignments have
to be evaluated at <inlineequation><mml:math>
<mml:mi>t</mml:mi>
<mml:mo>=</mml:mo>
<mml:msub>
 <mml:mi>T</mml:mi>
 <mml:mn>0</mml:mn>
</mml:msub>
</mml:math></inlineequation>. These evaluation will effect in many cases
other initial values. For example the initial particle numbers of
metabolites will change when a compartment's initial volume
changes. To detemine the initial values, which need to be recalculated
as well as the functions used for their calculation COPASI uses a
dependecy system. In this system each initial value stores the
information on which values it depends and which method to call to
recalculated its value. 
</para>
<para>
Since the change of one initial value may now result in a complicated
chain of updates for other initial values it no longer suffices to
use its update method to set its value. We need to add an additional
step which will update all values effected by the change. To retrive
the list of needed refreshes in the proper order the class CModel
provides the following method.
</para>
<variablelist>
<varlistentry>
<term><literal>vector&lt;Refresh *&gt;
buildInitialRefreshSequence(set&lt;const CCopasiObject *&gt; &amp;changedObjects);</literal></term>
<listitem><para>
This method retrieves a vector of refresh methods, which must be called
to update all other initial values given a set of changed objects. If
the set of changed objects is empty the method will return a vector
of refresh method, which suffices to synchronize all initial values.
</para></listitem></varlistentry>
e
</variablelist>
</sect1>

<sect1 id="SettingTheState" xreflabel="Setting the State">
<title>Setting the State</title>
<para></para>
</sect1>

<sect1 id="ApplyingAssignemets" xreflabel="Applying Assignemets">
<title>Applying Assignments</title>
<para></para>
</sect1>

<sect1 id="CalculatingCurrentValues" xreflabel="Calculating Current Values">
<title>Calculating Current Values</title>
<para></para>
</sect1>

<sect1 id="DependencySpecifications" xreflabel="Dependency Specifications">
<title>Dependency Specifications</title>

<sect2 id="InitialValues" xreflabel="Initial Values">
<title>Initial Values</title>
<sect3 id="MetaboliteWithAssignment" 
 xreflabel="Metabolite with Assignment">
<title>Metabolite with Assignment</title>

<table frame="all"><title>Metabolite with Assignment</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Initial Particle Number</entry>
   <entry>Initial Concentration, parent compartment Volume</entry>
   <entry>refreshInititalValue</entry>
 </row>
 <row>
   <entry>Initial Concentration</entry>
   <entry>all objects in implicit expression</entry>
   <entry>refreshInitialConcentration</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="MetaboliteWithoutAssignment" 
 xreflabel="Metabolite without Assignment">
<title>Metabolite without Assignment</title>

<table frame="all"><title>Metabolite without Assignment</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Initial Particle Number</entry>
   <entry>initial concentration, parent compartment volume</entry>
   <entry>refreshInitialValue</entry>
 </row>
 <row>
   <entry>Initial Concentration</entry>
   <entry>parent compartment Volume</entry>
   <entry>refreshInititalConcentration</entry>
 </row>
</tbody>
</tgroup>
</table>
<para>
The initial concentration is of course dependent on the initial
particle number. This must be taken into account manually to avoid
circular depencies. However, this is straight forward as the initial
particle number may only be set directly, in which case no further
dependencies are encountered or calculated from the initial
concentration in the case the concentration is given the normal 
dependecies take care of the problem.
</para>
</sect3>

<sect3 id="CompartmentGlobalQuantityWithAssignment" 
 xreflabel="Compartment, Global Quantity with Assignment">
<title>Compartment, Global Quantity with Assignment</title>

<table frame="all">
<title>Compartment, Global Quantity with Assignment</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Initial Value</entry>
   <entry>all objects in implicit expression</entry>
   <entry>refreshInitialValue</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="CompartmentGlobalQuantityWithoutAssignment" 
 xreflabel="Compartment, Global Quantity without Assignment">
<title>Compartment, Global Quantity without Assignment</title>

<table frame="all">
<title>Compartment, Global Quantity without Assignment</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Initial Value</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="MoietyInitial" xreflabel="MoietyInitial">
<title>Moiety</title>

<table frame="all">
<title>Moiety</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Initial Number</entry>
   <entry>Particle numbers of all involved metabolites</entry>
   <entry>refreshInitialValue</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

</sect2>

<sect2 id="TransientValues" xreflabel="Transient Values">
<title>Transient Values</title>

<sect3 id="MetaboliteReaction" xreflabel="Metabolite Reaction">
<title>Metabolite Reaction (Independent)</title>
<table frame="all"><title>Metabolite Reaction (Independent)</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Particle Number</entry>
   <entry>Self (state controlled)</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Concentration</entry>
   <entry>Particle Number, parent compartment Volume</entry>
   <entry>refreshConcentration</entry>
 </row>
 <row>
   <entry>Particle Rate</entry>
   <entry>All particle fluxes of reactions the metabolites participates in</entry>
   <entry>refreshRate</entry>
 </row>
 <row>
   <entry>Concentration Rate</entry>
   <entry>Particle Rate, Concentration, parent compartment Volume and Rate</entry>
   <entry>refreshConcentrationRate</entry>
 </row>
 <row>
   <entry>Transition Time</entry>
   <entry>All particle fluxes of reactions the metabolites participates in</entry>
   <entry>refreshTransitionTime</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="MetaboliteDependent" xreflabel="Metabolite Dependent">
<title>Metabolite Reaction (Dependent)</title>
<table frame="all"><title>Metabolite Reaction (Dependent)</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Particle Number</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Concentration</entry>
   <entry>Particle Number, parent compartment Volume</entry>
   <entry>refreshConcentration</entry>
 </row>
 <row>
   <entry>Particle Rate</entry>
   <entry>All particle fluxes of reactions the metabolites participates in</entry>
   <entry>refreshRate</entry>
 </row>
 <row>
   <entry>Concentration Rate</entry>
   <entry>Particle Rate, Concentration, parent compartment Volume and Rate</entry>
   <entry>refreshConcentrationRate</entry>
 </row>
 <row>
   <entry>Transition Time</entry>
   <entry>All particle fluxes of reactions the metabolites participates in</entry>
   <entry>refreshTransitionTime</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="MetaboliteAssignmentConcentration" xreflabel="Metabolite Assignment (Concentration)">
<title>Metabolite Assignment (Concentration)</title>
<table frame="all"><title>Metabolite Assignment (Concentration)</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Particle Number</entry>
   <entry>Concentration, parent compartment Volume</entry>
   <entry>refreshNumber</entry>
 </row>
 <row>
   <entry>Concentration</entry>
   <entry>all objects in expression</entry>
   <entry>calculate</entry>
 </row>
 <row>
   <entry>Particle Rate (NA)</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Concentration Rate (NA)</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Transition Time (NA)</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
</tbody>
</tgroup>
</table>
<para>This will be implemented later</para>
</sect3>

<sect3 id="MetaboliteODEConcentration" xreflabel="Metabolite ODE (Concentration)">
<title>Metabolite ODE (Concentration)</title>
<table frame="all"><title>Metabolite ODE (Concentration)</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Particle Number</entry>
   <entry>Self (state controlled)</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Concentration</entry>
   <entry>Particle Number, parent compartment Volume</entry>
   <entry>refreshConcentration</entry>
 </row>
 <row>
   <entry>Particle Rate</entry>
   <entry>all objects in expression, parent compartment Volume</entry>
   <entry>calculate</entry>
 </row>
 <row>
   <entry>Concentration Rate</entry>
   <entry>Particle Rate, Concentration, parent compartment Volume and Rate</entry>
   <entry>refreshConcentrationRate</entry>
 </row>
 <row>
   <entry>Transition Time</entry>
   <entry>Particle Number, Particle Rate</entry>
   <entry>refreshTransitionTime</entry>
 </row>
</tbody>
</tgroup>
</table>
<para>This will be implemented later</para>
</sect3>

<sect3 id="Moiety" xreflabel="Moiety">
<title>Moiety</title>
<table frame="all"><title>Moiety</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>Particle number of participating independent metabolites</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Dependent Number</entry>
   <entry>Self</entry>
   <entry>none</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="Reaction" xreflabel="Reaction">
<title>Reaction</title>
<table frame="all"><title>Reaction</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>
    all variables of the kinetic function,
    associated compartment Volume, kinetic function, 
    all metabolites involved
   </entry>
   <entry>calculate</entry>
 </row>
 <row>
   <entry>ParticleFlux</entry>
   <entry>all variables of the kinetic function,
    associated compartment Volume</entry>
   <entry>calculate</entry>
 </row>
 <row>
   <entry>Flux</entry>
   <entry>all variables of the kinetic function,
    associated compartment Volume</entry>
   <entry>calculate</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="ModelValueAssignment" xreflabel="Model Value Assignment">
<title>Model Value Assignment</title>
<table frame="all"><title>Model Value Assignment</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Value</entry>
   <entry>all objects in expression</entry>
   <entry>calculate</entry>
 </row>
 <row>
   <entry>Rate (not available)</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="ModelValueODE" xreflabel="Model Value ODE">
<title>Model Value ODE</title>
<table frame="all"><title>Model Value ODE</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Value</entry>
   <entry>Self (state controlled)</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Rate</entry>
   <entry>all objects in expression</entry>
   <entry>calculate</entry>
 </row>
</tbody>
</tgroup>
</table>
</sect3>

<sect3 id="CompartmentAssignment" xreflabel="Compartment Assignment">
<title>Compartment Assignment</title>
<table frame="all"><title>Compartment Assignment</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Volume</entry>
   <entry>all objects in expression</entry>
   <entry>calculate</entry>
 </row>
 <row>
   <entry>Rate (not available)</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
</tbody>
</tgroup>
</table>
<para>This will be implemented later</para>
</sect3>

<sect3 id="CompartmentODE" xreflabel="Compartment ODE">
<title>Compartment ODE</title>
<table frame="all"><title>Compartment ODE</title>
<tgroup cols="3" align="left" colsep="1" rowsep="1">
<colspec colwidth="2*" />
<colspec colwidth="6*" />
<colspec colwidth="3*" />
<thead>
 <row>
   <entry>Attribute</entry>
   <entry>Dependencies</entry>
   <entry>Refresh Method</entry>
 </row>
</thead>
<tbody>
 <row>
   <entry>Self</entry>
   <entry>none</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Volume</entry>
   <entry>Self (state controlled)</entry>
   <entry>none</entry>
 </row>
 <row>
   <entry>Rate</entry>
   <entry>all objects in expression</entry>
   <entry>calculate</entry>
 </row>
</tbody>
</tgroup>
</table>
<para>This will be implemented later</para>
</sect3>
</sect2>
</sect1>

</chapter>

<chapter id="InstallationStructure" xreflabel="Installation Structure">
<title>Installation Structure</title>
<para>
This section defines the installation structure for COPASI on
different platforms. Each platform will adhere to the platform
specific requirements. 
</para>

<sect1 id="Unix" xreflabel="Unix">
<title>Unix</title>
<para>
The installation location needs to be available to COPASI at runtime
and therefore the environment variable <literal>COPASIDIR</literal> pointing to this
location must be set by the user. 
</para>
<programlisting>
  $COPASIDIR 
   +- bin 
   |  +- CopasiSE 
   |  +- CopasiUI 
   +- share 
   |  +- copasi 
   |     +- doc 
   |     |  +- html 
   |     |     +- figures 
   |     |     |  +- DefaultPlotAdded.jpg 
   |     |     |  +- ModelSettingsDialog.jpg 
   |     |     |  +- ObjectBrowserSelection.jpg 
   |     |     |  +- ObjectBrowserTree.jpg 
   |     |     |  +- PlotDefinition.jpg 
   |     |     |  +- PlotWindow.jpg 
   |     |     |  +- ReactionDialog.jpg 
   |     |     |  +- ReactionOverview.jpg 
   |     |     |  +- ReactionOverviewEmpty.jpg 
   |     |     |  +- ReportDefinitionDialog.jpg 
   |     |     |  +- TimeCourseDialog.jpg 
   |     |     |  +- ... 
   |     |     +- TutWiz-Step1.html 
   |     |     +- TutWiz-Step2.html 
   |     |     +- TutWiz-Step3.html 
   |     |     +- TutWiz-Step4.html 
   |     |     +- TutWiz-Step5.html 
   |     |     +- TutWiz-Step6.html 
   |     |     +- ... 
   |     +- examples 
   |     |  +- CircadianClock.cps 
   |     |  +- Metabolism-2000Poo.xml 
   |     |  +- YeastGlycolysis.gps 
   |     |  +- brusselator.cps 
   |     |  +- ... 
   |     +- icons 
   |        +- copasi icon small.png 
   +- README 
   +- ChangeLog 
</programlisting>
</sect1>

<sect1 id="MacOSX" xreflabel="MacOS X">
<title>MacOS X</title>
<para>
The installation location must be available to COPASI at
runtime. However it is possible to determine the location through MacOS
X.
</para>
<programlisting>
  $COPASIDIR 
   +- CopasiSE.app 
   |  +- Contents 
   |  |  +- MacOS 
   |  |     +- CopasiSE 
   +- CopasiUI.app 
   |  +- Contents 
   |  |  +- MacOS 
   |  |  |  +- CopasiUI 
   |  |  +- Resources 
   |  |  |  +- doc 
   |  |  |     +- html 
   |  |  |        +- figures 
   |  |  |        |  +- DefaultPlotAdded.jpg 
   |  |  |        |  +- ModelSettingsDialog.jpg 
   |  |  |        |  +- ObjectBrowserSelection.jpg 
   |  |  |        |  +- ObjectBrowserTree.jpg 
   |  |  |        |  +- PlotDefinition.jpg 
   |  |  |        |  +- PlotWindow.jpg 
   |  |  |        |  +- ReactionDialog.jpg 
   |  |  |        |  +- ReactionOverview.jpg 
   |  |  |        |  +- ReactionOverviewEmpty.jpg 
   |  |  |        |  +- ReportDefinitionDialog.jpg 
   |  |  |        |  +- TimeCourseDialog.jpg 
   |  |  |        |  +- ... 
   |  |  |        +- TutWiz-Step1.html 
   |  |  |        +- TutWiz-Step2.html 
   |  |  |        +- TutWiz-Step3.html 
   |  |  |        +- TutWiz-Step4.html 
   |  |  |        +- TutWiz-Step5.html 
   |  |  |        +- TutWiz-Step6.html 
   |  |  |        +- ... 
   |  |  +- Info.plist 
   +- examples 
   |  +- CircadianClock.cps 
   |  +- Metabolism-2000Poo.xml 
   |  +- YeastGlycolysis.gps 
   |  +- brusselator.cps 
   |  +- ... 
   +- COPASI-README.rtf 
</programlisting>
</sect1>

<sect1 id="Windows" xreflabel="Windows">
<title>Windows</title>
<para>
The installation location must be available to COPASI at
runtime. However it is possible to determine the location through
Windows specific means.
</para>
<programlisting>
  $COPASIDIR 
   +- bin 
   |  +- CopasiSE 
   |  +- CopasiUI 
   +- share 
   |  +- copasi 
   |     +- doc 
   |     |  +- html 
   |     |     +- figures 
   |     |     |  +- DefaultPlotAdded.jpg 
   |     |     |  +- ModelSettingsDialog.jpg 
   |     |     |  +- ObjectBrowserSelection.jpg 
   |     |     |  +- ObjectBrowserTree.jpg 
   |     |     |  +- PlotDefinition.jpg 
   |     |     |  +- PlotWindow.jpg 
   |     |     |  +- ReactionDialog.jpg 
   |     |     |  +- ReactionOverview.jpg 
   |     |     |  +- ReactionOverviewEmpty.jpg 
   |     |     |  +- ReportDefinitionDialog.jpg 
   |     |     |  +- TimeCourseDialog.jpg 
   |     |     |  +- ... 
   |     |     +- TutWiz-Step1.html 
   |     |     +- TutWiz-Step2.html 
   |     |     +- TutWiz-Step3.html 
   |     |     +- TutWiz-Step4.html 
   |     |     +- TutWiz-Step5.html 
   |     |     +- TutWiz-Step6.html 
   |     |     +- ... 
   |     +- examples 
   |     |  +- CircadianClock.cps 
   |     |  +- Metabolism-2000Poo.xml 
   |     |  +- YeastGlycolysis.gps 
   |     |  +- brusselator.cps 
   |     |  +- ... 
   |     +- icons
   |        +- Copasi.ico
   |        +- CopasiDoc.ico
   +- LICENSE.txt 
   +- README.txt
   +- ChangeLog 
</programlisting>
</sect1>

<sect1 id="HandlingInstallationDifferences" xreflabel="Handling Installation Differences">
<title>Handling Installation Differences</title>
<para>
The handling of differences in the installation structure must be
dealt with in one place within the COPASI code. The place for this is
the class <literal>COptions</literal>. In this class the method:
<literallayout>
   template&lt;class CType&gt; static void getValue(const std::string &amp;name, CType &amp;value)
</literallayout>
provides access to common options within COPASI. The following values
will deal with installation dependent settings:
<literal>CopasiDir</literal>, <literal>TempDir</literal>, <literal>ExampleDir</literal>, and <literal>WizardDir</literal>. The following code
shows how to retrieve the location of the examples files for COPASI: 
<literallayout>
   std::string ExampleDir;
   COptions::getValue(``ExampleDir'', ExampleDir); 
</literallayout>
To assure that the values are correctly set any main program must
call: 
<literallayout>
   COptions::init(argc, argv);
</literallayout>
</para>


</sect1>
</chapter>