index.htm

利用这个模板可以分析基因表达数据

each element.</i></tt></li>

<li>
<tt><a href="#matrixO34">operator+</a> - - <i>Addition of a number to each
element.</i></tt></li>

<li>
<tt><a href="#matrixO35">operator-=</a> - - <i>Subtraction of a vector
from the rows of a matrix</i></tt></li>

<li>
<tt><a href="#matrixO36">operator-</a> - - <i>Subtraction of a vector from
the rows of a matrix</i></tt></li>

<li>
<tt><a href="#matrixO37">operator+=</a> - - <i>Addition of a vector to
the rows of a matrix</i></tt></li>

<li>
<tt><a href="#matrixO38">operator+</a> - - <i>Addition of a vector to the
rows of a matrix</i></tt></li>

<li>
<tt><a href="#matrixO39">operator-=</a> - - <i>matrix subtraction</i></tt></li>

<li>
<tt><a href="#matrixO40">operator-</a> - - <i>Matrix subtraction</i></tt></li>

<li>
<tt><a href="#matrixO41">operator+=</a> - - <i>Matrix addition</i></tt></li>

<li>
<tt><a href="#matrixO42">operator+</a> - - <i>Matrix addition</i></tt></li>

<li>
<tt><a href="#matrixO43">operator&amp;</a> - - <i>Matrix multiplication
Transpose(m1) * m2 N.B. this is less efficient than (but not equivalent
to) operator%</i></tt></li>

<li>
<tt><a href="#matrixO44">operator%</a> - - <i>Matrix multiplication m1
* Transpose(m2) N.B. this is more efficient than (but not equivalent to)
operator&amp;</i></tt></li>

<li>
<tt><a href="#matrixO45">operator==</a> - - <i>Equality operator</i></tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="matrix_product"></a>
<h2>
matrix_product</h2>

<p><br>Matrix multiplication. The output matrix is nrows1*ncols2 in size.
<br><b><font color="#FF0000">Restrictions:</font></b> ncols1 must equal
nrows2.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#matrix_productO0">matrix_product</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="matrixtranspose_matrix_product"></a>
<h2>
matrixtranspose_matrix_product</h2>

<p><br>Matrix multiplication: Transpose(M1)*M2. The output matrix is ncols1*ncols2
in size.
<br><b><font color="#FF0000">Restrictions:</font></b> Both matrices must
have the same number of rows
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#matrixtranspose_matrix_productO0">matrixtranspose_matrix_product</a>
-</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="matrix_matrixtranspose_product"></a>
<h2>
matrix_matrixtranspose_product</h2>

<p><br>Matrix multiplication: M1*Transpose(M2) The output matrix is nrows1*nrows2
in size.
<br><b><font color="#FF0000">Restrictions:</font></b> Both matrices must
have the same number of columns
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#matrix_matrixtranspose_productO0">matrix_matrixtranspose_product</a>
-</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="transpose"></a>
<h2>
transpose</h2>

<p><br>Matrix transpose. Can be used in-place.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#transposeO0">transpose</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="column_means"></a>
<h2>
column_means</h2>

<p><br>Calculate the mean of each column of a matrix and store the answers
in a container of size >= ncols.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#column_meansO0">column_means</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="copy_column"></a>
<h2>
copy_column</h2>

<p><br>Copy a column of this matrix into another container. Columns are
numbered from 1. in the FORTRAN manner.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#copy_columnO0">copy_column</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="determinant"></a>
<h2>
determinant</h2>

<p><br>Calculates matrix determinant
<br><b><font color="#FF0000">Restrictions:</font></b> Square matrices only.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#determinantO0">determinant</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="minor"></a>
<h2>
minor</h2>

<p><br>Find the minor of a matrix. The minor denoted by minor(.,.,,.,i,j)
is found by eliminating the row i and column j from the parent matrix.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#minorO0">minor</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="adjoint"></a>
<h2>
adjoint</h2>

<p><br>Matrix adjoint
<br><b><font color="#FF0000">Restrictions:</font></b> Square matrices only.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#adjointO0">adjoint</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="inverse_square"></a>
<h2>
inverse_square</h2>

<p><br>Calculate inverse of a small square matrix (inverse = adjoint/determinant).
The result matrix should be of a floating point type.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#inverse_squareO0">inverse_square</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="eigen_solution"></a>
<h2>
eigen_solution</h2>

<p><br>Eigenvalues and eigenvectors of a symmetric matrix
<br><b><font color="#FF0000">Restrictions:</font></b> The input matrix
must be real, square and symmetric, the output vector of eigen values will
be nrows in size and the output matrix of eigenvectors will be nrows*nrows
in size.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#eigen_solutionO0">eigen_solution</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="inverse_cholesy"></a>
<h2>
inverse_cholesy</h2>

<p><br>Inverts a symmetric positive definite matrix. Employs Cholesky decomposition
in three steps:
<p>&nbsp;(1)M=LL(tr) (2)compute L(-1) (3)M(-1)=L(-1)(tr)L(-1) Input should
contain numerical data that can be interpreted as a symmetric positive
definite matrix. The output is the inverse of this matrix in the form of
a matrix of the same size as the input and probably containing data of
type BTL_REAL.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#inverse_cholesyO0">inverse_cholesky</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="lsqfit_rmsd"></a>
<h2>
lsqfit_rmsd</h2>

<p><br>Calculate the root mean squared deviation after a least squares
fit of the two sets of coordinates using the method of Kearsley(Acta Cryst.
'89, A45, 208-10). Both sets of coordinates remain unchanged by this function
<br><b><font color="#FF0000">Restrictions:</font></b> Each set must have
the same number of coordinates. Each coordinate must be orthogonal and
in three dimensions (i.e. normal x,y,z coordinates). WARNING: if coordinates
with varying dimensions are input then this may well not be detected.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#lsqfit_rmsdO0">lsqfit_rmsd</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="centroid"></a>
<h2>
centroid</h2>

<p><br>Calculate the centroid of a set of x,y,z coordinates held in an
n x 3 matrix.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#centroidO0">centroid</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="rotation_from_fit"></a>
<h2>
rotation_from_fit</h2>

<p><br>Create fitting rotation matrix from the eigen vector that corresponds
to the smallest eigen vector of Kearsley's matrix.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#rotation_from_fitO0">rotation_from_fit</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="rmsd"></a>
<h2>
rmsd</h2>

<p><br>Calculate the root mean squared deviation of two sets of coordinates.
<br><b><font color="#FF0000">Restrictions:</font></b> Each set must have
the same number of coordinates. There is no restriction on the number of
dimensions which the coordinates represent (except that it must be the
same in every case). WARNING: if coordinates with varying dimensions are
input then this may well not be detected.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#rmsdO0">rmsd</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="check_3d_data"></a>
<h2>
check_3d_data</h2>

<p><br>Check that both input containers have the same number of elements
and that number is multiple of 3. Output the number of x,y,z positions.
<p><b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#check_3d_dataO0">check_3d_data</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_VertexWithEdges"></a>
<h2>
BTL_VertexWithEdges</h2>

<p><br>This class represents an vertex that has links to edge objects.
It is to be used in combination with class BTL_GraphWithEdges.
<br><b>Authors:</b> W.R.Pitt
<br><b>Files:</b> <a href="btl/btl_graph_with_edges.h">btl_graph_with_edges.h</a>
<br><b>Friends:</b> friend class BTL_GraphWithEdges&amp;ltT1,T2>>;
<p>friend ostream&amp; operator&lt;&lt;(ostream &amp;os, const BTL_VertexWithEdges
&amp;m);
<br><b>Dependencies:</b> None, except by inheritance.
<p><b>Generalizations</b>
<p><font color="#FF0000">N.B. The graph classes command syntax will be
revised in the 3.0beta version</font>
<ul>
<li>
<a href="#BTL_Vertex">BTL_Vertex</a></li>
</ul>
<b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_VertexWithEdgesO0">BTL_VertexWithEdges</a> - - <i>Constructor
empty vertex.</i></tt></li>

<li>
<tt><a href="#BTL_VertexWithEdgesO1">~BTL_VertexWithEdges</a> - - <i>Delete
vertex and its contents.</i></tt></li>

<li>
<tt><a href="#BTL_VertexWithEdgesO2">begin_edge</a> - - <i>Return iterator
that references first edge connected to Vertex. (There is also a const
version of this function.)</i></tt></li>

<li>
<tt><a href="#BTL_VertexWithEdgesO3">begin_edge</a> -</tt></li>

<li>
<tt><a href="#BTL_VertexWithEdgesO4">end_edge</a> - - <i>Return iterator
that references the position in memory after the last edge connected to
Vertex. (There is also a const version of this function.)</i></tt></li>

<li>
<tt><a href="#BTL_VertexWithEdgesO5">end_edge</a> -</tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_Edge"></a>
<h2>
BTL_Edge</h2>

<p><br>This class represents an edge of a graph. It is to be used in combination
with class BTL_GraphWithEdges.
<br><b>Authors:</b> W.R.Pitt
<br><b>Files:</b> <a href="btl/btl_graph_with_edges.h">btl_graph_with_edges.h</a>
<br><b>Friends:</b> friend class BTL_GraphWithEdges&amp;ltT1,T2>>;
<p>friend ostream&amp; operator&lt;&lt;(ostream &amp;os, const BTL_Edge
&amp;m);
<br><b>Dependencies:</b> <a href="#BTL_VertexWithEdges">BTL_VertexWithEdges</a>
<p><b>Generalizations</b>
<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_EdgeBase">BTL_EdgeBase</a></li>
</ul>
<b>Operations</b>
<br>&nbsp;
<br>&nbsp;
<ul>
<li>
<tt><a href="#BTL_EdgeO0">BTL_Edge</a> - - <i>Construct empty edge</i></tt></li>

<li>
<tt><a href="#BTL_EdgeO1">BTL_Edge</a> - - <i>Copy constructor</i></tt></li>

<li>
<tt><a href="#BTL_EdgeO2">~BTL_Edge</a> - - <i>Destructor</i></tt></li>

<li>
<tt><a href="#BTL_EdgeO3">GetIterator</a> - - <i>Returns an iterator that
can be deferenced to obtain the data object associated with this edge (There
is a const version of this function as well)</i></tt></li>

<li>
<tt><a href="#BTL_EdgeO4">GetIterator</a> -</tt></li>

<li>
<tt><a href="#BTL_EdgeO5">LeftVertex</a> - - <i>Returns pointer to the
first vertex connected to this edge.</i></tt></li>

<li>
<tt><a href="#BTL_EdgeO6">RightVertex</a> - - <i>Returns pointer to the
second vertex connected to this edge.</i></tt></li>
</ul>
<a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a>
<hr>
<p><a NAME="BTL_GraphWithEdges"></a>
<h2>
BTL_GraphWithEdges</h2>

<p><br>Graph container with any type of data at the vertices of the graph
and any type of data at the 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_with_edges.h">btl_graph_with_edges.h</a>
<br><b>Friends:</b> friend ostream&amp; operator&lt;&lt;&lt;(ostream &amp;os,
const BTL_GraphWithEdges &amp;m);
<br><b>Dependencies:</b> <a href="#BTL_Vertex">BTL_Vertex</a>, <a href="#BTL_II">BTL_II</a>
<p><b>Generalizations</b>