</ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="PPM_processor"></a><h2>PPM_processor</h2><p><br>This class is a simple ascii PPM image file processor. It is notcomplete and is only included for use by the demo programs that come withthis library.<br><b>Authors:</b> W.R.Pitt<br><b>Friends:</b> ostream operator<br><b>Files:</b> <a href="btl/PPM_processor.h">PPM_processor.h</a><br><b>Dependencies:</b> none<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#PPM_processorO0">ReadFile</a> - - <i>Read in a file witha given name.</i></tt></li><li><tt><a href="#PPM_processorO1">ReadImageData</a> - - <i>Get image data.</i></tt></li><li><tt><a href="#PPM_processorO2">WriteImageData</a> - - <i>Write image data.</i></tt></li><li><tt><a href="#PPM_processorO3">ReadWidth</a> - - <i>Read width of image.</i></tt></li><li><tt><a href="#PPM_processorO4">ReadHeight</a> - - <i>Read image height.</i></tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="XYZ_processor"></a><h2>XYZ_processor</h2><p><br>This is simple class for reading xyz format files. It is reallyonly included in the library so that real data can be used in the testprograms.<br><b>Friends:</b> an output operator<br><b>Authors:</b> W.R.Pitt<br><b>Files:</b> <a href="btl/XYZ_processor.h">XYZ_processor.h</a><br><b>Dependencies:</b> None<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#XYZ_processorO0">XYZ_processor</a> - - <i>Default constructor(does nothing)</i></tt></li><li><tt><a href="#XYZ_processorO1">empty</a> - - <i>Returns true if no coordinateshave been read</i></tt></li><li><tt><a href="#XYZ_processorO2">ReadFile</a> - - <i>Read an xyz format filewith the given name</i></tt></li><li><tt><a href="#XYZ_processorO3">Coords</a> - - <i>Return a reference tothe read coordinates in a STL vector of float. Coordinates are stored inthe following order: x,y,z,x,y,z,x,...</i></tt></li><li><tt><a href="#XYZ_processorO4">Elements</a> - - <i>Return a reference tothe read atomic elements in a STL vector of char. Each element is storedas 2 chars.</i></tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="needleman_wunsch_similarity"></a><h2>needleman_wunsch_similarity</h2><p><br>Pairwise similarity score for two sequences.<br><b><font color="#FF0000">Restrictions:</font></b> The containers holdingthe sequences must have at least forward iterators and an equality operator(==) should be defined for pairs of elements. The score for any pair ofelements is match_score (or mismatch_score) - total gap penalty. The totalgap penalty = gap_penalty + (length_of_gap * gap_length_multiplier)<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#needleman_wunsch_similarityO0">needleman_wunsch_similarity</a>-</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="needleman_wusch_align"></a><h2>needleman_wusch_align</h2><p><br>Pairwise alignment for two complete sequences. The score for anypair of elements is match_score (or mismatch_score) - total gap penalty.The total gap penalty = gap_penalty + (length_of_gap * gap_length_multiplier).The aligned sequence elements are placed alternately in the output containeri.e with the odd elements representing the first sequence.<br><b><font color="#FF0000">Restrictions:</font></b> The containers holdingthe sequences must have at least forward iterators and an equality operator(==) should be defined for pairs of elements. The result container shouldeither have no fixed size or be created at least twice the size of thelonger sequence.<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#needleman_wusch_alignO0">needleman_wunsch_align</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="fourier_transform"></a><h2>fourier_transform</h2><p><br>Two dimensional FFT. 1D and 3D versions also available<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#fourier_transformO0">fourier_transform</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="mean"></a><h2>mean</h2><p><br>Calculate the mean value of the elements in a container.<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#meanO0">mean</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="mean_absolute_deviation"></a><h2>mean_absolute_deviation</h2><p><br>Calculate mean absolute deviation from the mean of the elementsin a container.<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#mean_absolute_deviationO0">mean_absolute_deviation</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="variance"></a><h2>variance</h2><p><br>Calculate the sample variance of the elements in a container.<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#varianceO0">variance</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="normal_statistics"></a><h2>normal_statistics</h2><p><br>Calculate the mean, mean absolute deviation from mean, sample variance,skew and kurtosis of the distribution of the elements in a container.<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#normal_statisticsO0">normal_statistics</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="max_mismatch"></a><h2>max_mismatch</h2><p><br>Returns the maximum difference between equivalent elements in twocontainers in the sense of (a-b)<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#max_mismatchO0">max_mismatch</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="max_absolute_mismatch"></a><h2>max_absolute_mismatch</h2><p><br>Returns the largest absolute difference between equivalent elementsin two containers<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#max_absolute_mismatchO0">max_absolute_mismatch</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="min_mismatch"></a><h2>min_mismatch</h2><p><br>Returns the minimum difference between equivalent elements in twocontainers in the sense of (a-b)<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#min_mismatchO0">min_mismatch</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="min_absolute_mismatch"></a><h2>min_absolute_mismatch</h2><p><br>Returns the smallest absolute difference between equivalent elementsin two containers<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#min_absolute_mismatchO0">min_absolute_mismatch</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="every_less_equal"></a><h2>every_less_equal</h2><p><br>Returns true if every element of a is less than or equal to theequivalent element of b<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#every_less_equalO0">every_less_equal</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="every_less"></a><h2>every_less</h2><p><br>Returns true if every element of a is less than the equivalent elementof b<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#every_lessO0">every_less</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="less_absolute"></a><h2>less_absolute</h2><p><br>Compare the absolute values of two arguements true if |x| &lt; |y|<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#less_absoluteO0">operator()</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="random_uniform"></a><h2>random_uniform</h2><p><br>Portable random number generator that produces float,double, intand long random numbers. In the case of float &amp; double the numbersare uniformly distributed in the range 0 to 1. In the case of long theyare uniformly distributed in the range 0 to 2**31 and in the int case from0 to 2**15. It is an implementation of Donald Knuth's floating point ranf_arraygenerator, a lagged additive generator x(i) = (x(i-KK) + x(i-LL))mod 1.0for float and double numbers and Knuth's lagged subtractive generator x(i)= (x(i-KK) - x(i-LL))mod 2**MM where MM = 15 for int and MM=30 for long.An object containing random numbers is constructed and used by random_uniform<T>numbers(seed); T temp = numbers(); The seed integer should be &lt; 1073741822for float, double and long numbers and &lt; 32765 in the case of of intdata. N.B. it is best not to generate a sequence of more than 2**70 numbersusing the same seed. This generator fails the birthday spacings test i.esome differences between pairs of numbers occur more often than desired.See Knuth's Art of Computer Programming 3rd Edition for solutions<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#random_uniformO0">random_uniform</a> -</tt></li><li><tt><a href="#random_uniformO1">operator()</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="random_normal"></a><h2>random_normal</h2><p><br>Portable random number generator that produces float or double precisionrandom numbers from a normal distibution using the ratio method of Kinderman&amp; Monahan (see Knuth TAOCP).<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#random_normalO0">random_normal</a> -</tt></li><li><tt><a href="#random_normalO1">random_normal</a> -</tt></li><li><tt><a href="#random_normalO2">operator()</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="random_exponential"></a><h2>random_exponential</h2><p><br>Portable random number generator that produces float or double precisionrandom numbers from an exponential distibution.<p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#random_exponentialO0">random_exponential</a> -</tt></li><li><tt><a href="#random_exponentialO1">random_exponential</a> -</tt></li><li><tt><a href="#random_exponentialO2">operator()</a> -</tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="numeric_vector"></a><h2>numeric_vector</h2><p><br>this template class represents a numerical vector of any size.<p>&nbsp;V = xi + yj + zk + ...<p>&nbsp;However, its primary use will probably in representing the positionof atoms in three dimensions. The default contructor contructs a 3 elementnumeric_vector.<p>&nbsp;There are several types associated with this class:<p>&nbsp;<tt>value_type</tt> : by default the same as the type BTL_REALwhich is defined in BTL.h<p>&nbsp;<tt>iterator</tt> : this is a STL type iterator. It can be usedto randomly access the elements of the numeric_vector e.g.<p><tt>&nbsp;numeric_vector&lt;> v1; ... for (numeric_vector&lt;>::iteratori = v1.begin(); i != v1.end(); i++) cout &lt;&lt; *i;</tt><p><tt>const_iterator</tt> : used to access a const numeric_vector.<p>&nbsp;<tt>size_type</tt> : this is an unsigned integer type that representsthe size of any numeric_vector object.<br><b>Authors:</b> D.S.Moss, W.R.Pitt, M.A.Williams<br><b>Files:</b> <a href="btl/btl_numeric_vector.h">btl_numeric_vector.h</a><br><b>Friends:</b> Friend equivalents to some functions are availableand are documented with these functions. Also available is: friend ostream&amp;operator&lt;&lt;(ostream &amp;os, const numeric_vector<T> &amp;m);<br><b>Dependencies:</b> <a href="#NumericLimits">NumericLimits.h</a><p><b>Operations</b><br>&nbsp;<br>&nbsp;<ul><li><tt><a href="#numeric_vectorO0">numeric_vector</a> - - <i>Constructs a3D vector and initialises each value to zero.</i></tt></li><li><tt><a href="#numeric_vectorO1">numeric_vector</a> - - <i>Constructs a3D vector with initialization and initialises the values with the numbersgiven.</i></tt></li><li><tt><a href="#numeric_vectorO2">numeric_vector</a> - - <i>Constructor fora vector of n elements. All n values initiated to a value v. The defaultvalue is zero .</i></tt></li><li><tt><a href="#numeric_vectorO3">numeric_vector</a> - - <i>Construct froman array given a value_type*. This constructor is obsolete and will bedeleted in future releases.</i></tt></li><li><tt><a href="#numeric_vectorO4">numeric_vector</a> - - <i>Copy constructor.</i></tt></li><li><tt><a href="#numeric_vectorO5">~numeric_vector</a> - - <i>Destructor.</i></tt></li><li><tt><a href="#numeric_vectorO6">begin</a> - - <i>Returns iterator thatcan be used to begin traversing through all elements of the numeric_vector.(There is also a const version of this function.)</i></tt></li><li><tt><a href="#numeric_vectorO7">begin</a> -</tt></li><li><tt><a href="#numeric_vectorO8">end</a> - - <i>Returns an iterator canbe used in comparison for ending traversal through the numeric_vector.(There is also a const version of this function.)</i></tt></li><li><tt><a href="#numeric_vectorO9">end</a> -</tt></li><li><tt><a href="#numeric_vectorO10">operator[]</a> - - <i>Returns the element,i positions from the beginning of the numeric_vector, in constant time.