lookup_util.c

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/* $Id: lookup_util.c 73100 2016-06-20 15:45:40Z boratyng $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 */
 
/** @file lookup_util.c
 *  Utility functions for lookup table generation.
 */
 
#include <algo/blast/core/lookup_util.h>
 
static void fkm_output(Int4 * a,
                       Int4 n,
                       Int4 p,
                       Uint1 * output,
                       Int4 * cursor,
                       Uint1 * alphabet);
static void fkm(Int4 * a,
                Int4 n,
                Int4 k,
                Uint1 * output,
                Int4 * cursor,
                Uint1 * alphabet);
 
Int4
iexp(Int4 x,
     Int4 n)
{
    Int4 r, y;
 
    r = 1;
    y = x;
 
    if (n == 0)
        return 1;
    if (x == 0)
        return 0;
 
    while (n > 1) {
        if ((n % 2) == 1)
            r *= y;
        n = n >> 1;
        y = y * y;
    }
    r = r * y;
    return r;
}
 
Int4
ilog2(Int8 x)
{
    Int4 lg = 0;
 
    if (x == 0)
        return 0;
 
    while ((x = x >> 1))
        lg++;
 
    return lg;
}
 
/** Output a Lyndon word as part of a de Bruijn sequence.
 *
 *if the length of a lyndon word is divisible by n, print it. 
 * @param a the shift register
 * @param p
 * @param n
 * @param output the output sequence
 * @param cursor current location in the output sequence
 * @param alphabet optional translation alphabet
 */
 
static void
fkm_output(Int4 * a,
           Int4 n,
           Int4 p,
           Uint1 * output,
           Int4 * cursor,
           Uint1 * alphabet)
{
    Int4 i;
 
    if (n % p == 0)
        for (i = 1; i <= p; i++) {
            if (alphabet != NULL)
                output[*cursor] = alphabet[a[i]];
            else
                output[*cursor] = a[i];
            *cursor = *cursor + 1;
        }
}
 
/**
 * iterative fredricksen-kessler-maiorana algorithm
 * to generate de bruijn sequences.
 *
 * generates all lyndon words, in lexicographic order.
 * the concatenation of all lyndon words whose length is 
 * divisible by n yields a de bruijn sequence.
 *
 * further, the sequence generated is of shortest lexicographic length.
 *
 * references: 
 * http://mathworld.wolfram.com/deBruijnSequence.html
 * http://www.theory.csc.uvic.ca/~cos/inf/neck/NecklaceInfo.html
 * http://www.cs.usyd.edu.au/~algo4301/ , chapter 7.2
 * http://citeseer.nj.nec.com/ruskey92generating.html
 *
 * @param a the shift register
 * @param n the number of letters in each word
 * @param k the size of the alphabet
 * @param output the output sequence
 * @param cursor the current location in the output sequence
 * @param alphabet optional translation alphabet
 */
 
static void
fkm(Int4 * a,
    Int4 n,
    Int4 k,
    Uint1 * output,
    Int4 * cursor,
    Uint1 * alphabet)
{
    Int4 i, j;
 
    fkm_output(a, n, 1, output, cursor, alphabet);
 
    i = n;
 
    do {
        a[i] = a[i] + 1;
 
        for (j = 1; j <= n - i; j++)
            a[j + i] = a[j];
 
        fkm_output(a, n, i, output, cursor, alphabet);
 
        i = n;
 
        while (a[i] == k - 1)
            i--;
    }
    while (i > 0);
}
 
void
debruijn(Int4 n,
         Int4 k,
         Uint1 * output,
         Uint1 * alphabet)
{
    Int4 *a;
    Int4 cursor = 0;
 
    /* n+1 because the array is indexed from one, not zero */
    a = (Int4 *) calloc((n + 1), sizeof(Int4));
 
    /* compute the (n,k) de Bruijn sequence and store it in output */
 
    fkm(a, n, k, output, &cursor, alphabet);
 
    sfree(a);
    return;
}
 
Int4
EstimateNumTableEntries(BlastSeqLoc * location, Int4 *max_off)
{
    Int4 num_entries = 0;
    Int4 curr_max = 0;
    BlastSeqLoc *loc = location;
 
    while (loc) {
        num_entries += loc->ssr->right - loc->ssr->left;
        curr_max = MAX(curr_max, loc->ssr->right);
        loc = loc->next;
    }
 
    *max_off = curr_max;
    return num_entries;
}