/* $Id: masksubj.inl,v 1.1 2009/05/27 20:31:32 kazimird Exp $
 * ===========================================================================
 *
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 *               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.
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 *  warranties of performance, merchantability or fitness for any particular
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 *  Please cite the author in any work or product based on this material.
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 * ===========================================================================
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 */

/**
 * @brief Determines the scanner's offsets taking the database masking
 * restrictions into account (if any). This function should be called from the
 * WordFinder routines only.
 *
 * @param subject The subject sequence [in]
 * @param word_length the real word length [in]
 * @param lut_word_length the lookup table word length [in]
 * @param range the structure to record seq mask index, start and
 *              end of scanning pos, and start and end of current mask [in][out]
 *
 * @return TRUE if the scanning should proceed, FALSE otherwise
 */
static NCBI_INLINE Boolean
s_DetermineScanningOffsets(const BLAST_SequenceBlk* subject,
                           Int4  word_length,
                           Int4  lut_word_length,
                           Int4* range)
{
    /* for masked db, we use (length - word_length) instead */
    for (; range[0] < subject->num_seq_ranges; (range[0])++) {
        /* handle case where s_last is beyond a masked region */
        if (range[2] + word_length > subject->seq_ranges[range[0]].left) {
            range[2] = subject->seq_ranges[range[0]].left - word_length;
            range[4] = range[2] + word_length;
        }

        /* if s_first is in a masked region, try the next one. */
        if (range[1] + lut_word_length >= subject->seq_ranges[range[0]].left) {
            range[1] = subject->seq_ranges[range[0]].right + word_length - lut_word_length;
            range[3] = range[1] - word_length + lut_word_length;
            range[2] = subject->length - word_length;
            range[4] = range[2] + word_length;
            continue;
        }

        /* if the range to scan is smaller than the word size, don't bother. */
        if ( (range[2]-range[1]+1) < word_length ) {
			range[1] = subject->seq_ranges[range[0]].right + word_length - lut_word_length;
            range[3] = range[1] - word_length + lut_word_length;
			range[2] = subject->length - word_length;
			range[4] = range[2] + word_length;
            continue;
            }
 
        break;
    } /* end for */

    if (range[1] + lut_word_length > subject->length) {
        return FALSE;
		}
			
    if ( (range[2]-range[1]+1) < word_length ) {
        return FALSE;
		}

    return TRUE;
}