index.htm

利用这个模板可以分析基因表达数据

<p><font color="#FF0000">N.B. The graph classes command syntax will be
revised in the 3.0beta version</font>
<br>&nbsp;
<ul>
<li>
<a href="#BTL_Graph">BTL_Graph</a></li>
</ul>
<b>Specializations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<a href="#BTL_Graph3">BTL_Graph3</a></li>

<li>
<a href="#BTL_Graph4">BTL_Graph4</a></li>

<li>
<a href="#BTL_Graph5">BTL_Graph5</a></li>

<li>
<a href="#BTL_Graph6">BTL_Graph6</a></li>
</ul>
<b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_GraphWithEdgesO0">BTL_GraphWithEdges</a> - - <i>Construct
empty undirected graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO1">BTL_GraphWithEdges</a> - - <i>Construct
new undirected or directed graph i.e. BTL_GraphWithEdges g1(directed);
or BTL_Graph g2(undirected);</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO2">~BTL_GraphWithEdges</a> - - <i>Delete
graph and all vertices and edges in it.</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO3">AddVertex</a> - - <i>Add new vertex
to graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO4">RemoveVertex</a> - - <i>Delete vertex
from graph. Return false if vertex not found in this graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO5">AddEdge</a> - - <i>Insert edge into
this graph. Return endEdge() if input is invalid.</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO6">RemoveEdge</a> - - <i>Remove edge from
this graph. Return false if input is invalid.</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO7">BeginEdgeData</a> - - <i>Return iterator
that references first edge data item. (There is a const version of this
function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO8">BeginEdgeData</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO9">EndEdgeData</a> - - <i>Return iterator
that references the position in memory after the last edge data item. (There
is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO10">EndEdgeData</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO11">begin_edge</a> - - <i>Return EdgeIterator
that references first edge in graph. (There is a const version of this
function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO12">begin_edge</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO13">end_edge</a> - - <i>Return EdgeIterator
that references the position in memory after the last edge in graph.(There
is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphWithEdgesO14">end_edge</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_Vertex"></a>
<h2>
BTL_Vertex</h2>

<p><br>This class encapsulates a graph vertex and is designed for use with
the graph class. Each vertex contains a reference to a data object and
pointers to other vertices. It is a template class the single template
parameter is a type of dereferencer.
<br><b>Authors:</b> W.R.Pitt
<br><b>Files:</b> <a href="btl/btl_graph.h">btl_graph.h</a>
<br><b>Dependencies:</b> <a href="#BTL_II">BTL_II</a>, and <a href="#BTL_II">BTL_IteratorDerefencer</a>,
or <a href="#BTL_II">BTL_InDencer</a>
<p><b>Generalizations</b><font color="#FF0000"></font>
<p><font color="#FF0000">N.B. The graph classes command syntax will be
revised in the 3.0beta version</font>
<br>&nbsp;
<ul>
<li>
<a href="#BTL_VertexBase">BTL_VertexBase</a></li>
</ul>
<b>Specializations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<a href="#BTL_VertexWithEdges">BTL_VertexWithEdges</a></li>
</ul>
<b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_VertexO0">BTL_Vertex</a> - - <i>Construct new empty Vertex</i></tt></li>

<li>
<tt><a href="#BTL_VertexO1">BTL_Vertex</a> - - <i>Copy constructor.</i></tt></li>

<li>
<tt><a href="#BTL_VertexO2">~BTL_Vertex</a> - - <i>Destructor</i></tt></li>

<li>
<tt><a href="#BTL_VertexO3">GetIterator</a> - - <i>Get an iterator that
references the data item associated with this vertex. With graphs that
use STL an vector or deque to store data items this iterator may become
invalid after insertions or deletions of vertices. (There is also a const
version of this function.)</i></tt></li>

<li>
<tt><a href="#BTL_VertexO4">GetIterator</a> -</tt></li>

<li>
<tt><a href="#BTL_VertexO5">Visited</a> - - <i>Read/write access to visited
flag. This can be used in Graph searching routines.</i></tt></li>

<li>
<tt><a href="#BTL_VertexO6">begin_vertex</a> - - <i>Return iterator that
references first vertex connected to this vertex.(There is a const version
of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_VertexO7">begin_vertex</a> -</tt></li>

<li>
<tt><a href="#BTL_VertexO8">end_vertex</a> - - <i>Return iterator that
references the position in memory after the last vertex connected to this
vertex.(There is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_VertexO9">end_vertex</a> -</tt></li>

<li>
<tt><a href="#BTL_VertexO10">begin</a> - - <i>Return iterator that references
first vertex connected to this vertex. (There is a const version of this
function as well)</i></tt></li>

<li>
<tt><a href="#BTL_VertexO11">begin</a> -</tt></li>

<li>
<tt><a href="#BTL_VertexO12">end</a> - - <i>Return iterator that references
the position in memory after the last vertex connected to this vertex.(There
is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_VertexO13">end</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_Graph"></a>
<h2>
BTL_Graph</h2>

<p><br>Graph container with any type of data at vertices of the graph and
no data associated with edges. The default behaviour is have undirected
edges. This can be changed to directed if specified in the constructor.
No self links (edges from one vertex to itself) are allowed.
<br><b>Authors:</b> W.R.Pitt
<br><b>Files:</b> <a href="btl/btl_graph.h">btl_graph.h</a>
<br><b>Friends:</b> operator&lt;&lt;
<br><b>Dependencies:</b> <a href="#BTL_Vertex">BTL_VertexBase and its subclasses.</a>
<p><font color="#FF0000">N.B. The graph classes command syntax will be
revised in the 3.0beta version</font>
<br>&nbsp;
<p><b>Specializations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<a href="#BTL_GraphWithEdges">BTL_GraphWithEdges</a></li>

<li>
<a href="#BTL_Graph1">BTL_Graph1</a></li>

<li>
<a href="#BTL_Graph2">BTL_Graph2</a></li>
</ul>
<b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_GraphO0">BTL_Graph</a> - - <i>Construct new undirected
graph</i></tt></li>

<li>
<tt><a href="#BTL_GraphO1">BTL_Graph</a> - - <i>Construct new undirected
or directed graph i.e. BTL_Graph g1(directed); or BTL_Graph g2(undirected);</i></tt></li>

<li>
<tt><a href="#BTL_GraphO2">~BTL_Graph</a> - - <i>Delete Graph and all the
vertices in it</i></tt></li>

<li>
<tt><a href="#BTL_GraphO3">GetDirectionality</a> - - <i>Get the edge directionality
of this graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphO4">AddVertex</a> - - <i>Add new vertex to graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphO5">RemoveVertex</a> - - <i>Remove a vertex (and
all pointers to it) from the graph. Return false if vertex was not found
in the graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphO6">AddLink</a> - - <i>Add a pointer between two
vertices. Return false if either vertex is not in this graph or is link
already present</i></tt></li>

<li>
<tt><a href="#BTL_GraphO7">RemoveLink</a> - - <i>Remove pointer/link between
two vertices. Return false if link not there</i></tt></li>

<li>
<tt><a href="#BTL_GraphO8">SetAllVisited</a> - - <i>Set the visited field
of all vertices in this graph.</i></tt></li>

<li>
<tt><a href="#BTL_GraphO9">find</a> - - <i>Find a vertex within this Graph.(There
is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphO10">find</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphO11">begin</a> - - <i>Return iterator that references
first data item.(There is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphO12">begin</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphO13">end</a> - - <i>Return iterator that references
the position in memory after the last data item. (There is a const version
of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphO14">end</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphO15">begin_vertex</a> - - <i>Return iterator that
references the first Vertex. (There is a const version of this function
as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphO16">begin_vertex</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphO17">end_vertex</a> - - <i>Return iterator that
references the position in memory after the last Vertex. (There is a const
version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_GraphO18">end_vertex</a> -</tt></li>

<li>
<tt><a href="#BTL_GraphO19">size</a> - - <i>Give the number of vertices
within the Graph</i></tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_DFSIterator"></a>
<h2>
BTL_DFSIterator</h2>

<p><br>This is a an iterator for iterating over a connected sub-graph in
depth first order. It is designed to work with the BTL_Graph and BTL_GraphWithEdges
but takes that type of graph as its template parameter and could be used
on any graph and vertex type if they have a given set of functions.
<br><b>Authors:</b> W.R.Pitt
<br><b>Files:</b> <a href="btl/DFSIterator.h">DFSIterator.h</a>
<br><b>Dependencies:</b> None
<p><font color="#FF0000">N.B. The graph classes command syntax will be
revised in the 3.0beta version</font>
<br>&nbsp;
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_DFSIteratorO0">BTL_DFSIterator</a> - - <i>Default constructor.</i></tt></li>

<li>
<tt><a href="#BTL_DFSIteratorO1">BTL_DFSIterator</a> - - <i>Construct with
iterator. This is essential if operator++ etc. is to be used.</i></tt></li>

<li>
<tt><a href="#BTL_DFSIteratorO2">operator++</a> - - <i>Move iterator forward
one in depth first search order.</i></tt></li>

<li>
<tt><a href="#BTL_DFSIteratorO3">operator!</a> - - <i>Returns false when
current position is one past the end of the last element in the container.</i></tt></li>

<li>
<tt><a href="#BTL_DFSIteratorO4">operator++</a> - - <i>Move iterator forward
one in depth first search order.</i></tt></li>

<li>
<tt><a href="#BTL_DFSIteratorO5">operator==</a> - - <i>Equality operator</i></tt></li>

<li>
<tt><a href="#BTL_DFSIteratorO6">operator*</a> - - <i>Dereference operator</i></tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_ConstDFSIterator"></a>
<h2>
BTL_ConstDFSIterator</h2>

<p><br>The const version of the BTL_DFSIterator.
<br><b>Authors:</b> W.R.Pitt
<br><b>Files:</b> <a href="btl/DFSIterator.h">DFSIterator.h</a>
<br><b>Dependencies:</b> None
<p><font color="#FF0000">N.B. The graph classes command syntax will be
revised in the 3.0beta version</font>
<br>&nbsp;
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_ConstDFSIteratorO0">BTL_ConstDFSIterator</a> - - <i>Default
constructor.</i></tt></li>

<li>
<tt><a href="#BTL_ConstDFSIteratorO1">BTL_ConstDFSIterator</a> - - <i>Construct
with iterator. This is essential if operator++ etc. is to be used.</i></tt></li>

<li>
<tt><a href="#BTL_ConstDFSIteratorO2">operator++</a> - - <i>Move iterator
forward one in depth first search order.</i></tt></li>

<li>
<tt><a href="#BTL_ConstDFSIteratorO3">operator!</a> - - <i>Returns false
when current position is one past the end of the last element in the container.</i></tt></li>

<li>
<tt><a href="#BTL_ConstDFSIteratorO4">operator++</a> - - <i>Move iterator
forward one in depth first search order.</i></tt></li>

<li>
<tt><a href="#BTL_ConstDFSIteratorO5">operator==</a> - - <i>Equality operator</i></tt></li>

<li>
<tt><a href="#BTL_ConstDFSIteratorO6">operator*</a> - - <i>Dereference
operator</i></tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr><!--END	PAGE -->
<h3>
<a href="#ATOM_processor"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>&nbsp;<a href="#Classes"><img SRC="uupb.gif" ALT="up" BORDER=0 ></a>
ATOM_processor</h3>

<ul><a NAME="ATOM_processorO0"></a>
<li>
<b><tt>void CloseFile(const char* fileName, ifstream&amp; fileStream);</tt></b></li>

<br>&nbsp;
<p>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<p><a NAME="ATOM_processorO1"></a>
<li>
<b><tt>NameStore&amp; Alternate()</tt></b></li>

<br>&nbsp;
<p>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<p><a NAME="ATOM_processorO2"></a>
<li>
<b><tt>ATOM_processor()</tt></b></li>

<br>Default constructor (does nothing)
<p><a NAME="ATOM_processorO3"></a>
<li>
<b><tt>~ATOM_processor()</tt></b></li>

<br>Default destructor (does nothing)
<p><a NAME="ATOM_processorO4"></a>
<li>
<b><tt>bool empty() const</tt></b></li>

<br>Returns true if no coordinates have been read
<p><a NAME="ATOM_processorO5"></a>
<li>
<b><tt>void ReadFile(const char *fileName, const char *chains = " ", const
char alternate = ' ');</tt></b></li>

<br>Read a PDB format file with the given name, selecting only those chains
whose id letter occurs in a given string and using the alternate set of
coordinates identified by the user-supplied character. The default reads
records with any chain id and either no alternate id or the first encounterd
alternate id.
<p><a NAME="ATOM_processorO6"></a>
<li>
<b><tt>IdStore&amp; AtomNo()</tt></b></li>

<br>Return a reference to the atom number in a STL vector of int.
<p><a NAME="ATOM_processorO7"></a>
<li>
<b><tt>NameStore&amp; Atom