TEST_PARTIAL_DIGEST
Test Problems for Partial Digest

TEST_PARTIAL_DIGEST is a C++ library which can generate example cases of the partial digest problem.

In the partial digest problem, we assume that there are N objects arranged along a line. We denote the position of object I by X(I). The positions of the objects are unknown. Instead, we have a list of the distances between every distinct pair of objects. Note that the distances are not "tagged"; that is, if there is a 175 on the list of distances, we don't know which two objects are separated by that distance. In the partial digest problem, we start with the (N*(N-1))/2 distances D, and must come up with at least one linear arrangement of N objects that corresponds to the distances.

To use this library, the user specifies a number of objects N, and a maximum separation DMAX. The library will generate N object locations in an array called LOCATE, and the corresponding list of distances D.

• N must be at least 2.
• DMAX must be at least N - 1.
• The entries in LOCATE will be distinct integers in ascending order.
• LOCATE(1) = 0 and LOCATE(N) = DMAX.

Licensing:

The computer code and data files made available on this web page are distributed under the GNU LGPL license.

Languages:

TEST_PARTIAL_DIGEST is available in a C version and a C++ version and a FORTRAN90 version and a MATLAB version and a Python version.

Related Software and Data:

SUBSET, a C++ library which carries out various combinatorial computations.

Reference:

1. Pavel Pevzner,
   Computational Molecular Biology,
   MIT Press, 2000,
   ISBN: 0-262-16197-4,
   LC: QH506.P47.

Source Code:

• test_partial_digest.cpp, the source code.
• test_partial_digest.hpp, the include file.
• test_partial_digest.txt, the output file.

List of Routines:

• MAIN tests the TEST_PARTIAL_DIGEST library.
• I4_UNIFORM_AB returns a scaled pseudorandom I4 between A and B.
• I4_UNIFORM_AB_TEST tests I4_UNIFORM_AB.
• I4VEC_DISTANCES computes a pairwise distance table.
• I4VEC_DISTANCES_TEST tests I4VEC_DISTANCES.
• I4VEC_HEAP_D reorders an I4VEC into an descending heap.
• I4VEC_HEAP_D_TEST tests I4VEC_HEAP_D.
• I4VEC_PRINT prints an I4VEC, with an optional title.
• I4VEC_PRINT_TEST tests I4VEC_PRINT.
• I4VEC_SORT_HEAP_A ascending sorts an I4VEC using heap sort.
• I4VEC_SORT_HEAP_A_TEST tests I4VEC_SORT_HEAP_A.
• KSUB_RANDOM selects a random subset of size K from a set of size N.
• KSUB_RANDOM_TEST tests KSUB_RANDOM.
• TEST_PARTIAL_DIGEST returns a partial digest test problem.
• TEST_PARTIAL_DIGEST_TEST tests TEST_PARTIAL_DIGEST.
• TIMESTAMP prints the current YMDHMS date as a time stamp.

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