dnabasic.c

Go to the documentation of this file.

/*====================================================================*
 -  Copyright (C) 2001 Leptonica.  All rights reserved.
 -
 -  Redistribution and use in source and binary forms, with or without
 -  modification, are permitted provided that the following conditions
 -  are met:
 -  1. Redistributions of source code must retain the above copyright
 -     notice, this list of conditions and the following disclaimer.
 -  2. Redistributions in binary form must reproduce the above
 -     copyright notice, this list of conditions and the following
 -     disclaimer in the documentation and/or other materials
 -     provided with the distribution.
 -
 -  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 -  ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 -  LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 -  A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL ANY
 -  CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 -  EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 -  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 -  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
 -  OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 -  NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 -  SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *====================================================================*/

#include <string.h>
#include <math.h>
#include "allheaders.h"

static const l_int32 INITIAL_PTR_ARRAYSIZE = 50;      
    /* Static functions */
static l_int32 l_dnaExtendArray(L_DNA *da);
static l_int32 l_dnaaExtendArray(L_DNAA *daa);


/*--------------------------------------------------------------------------*
 *                 Dna creation, destruction, copy, clone, etc.             *
 *--------------------------------------------------------------------------*/
L_DNA *
l_dnaCreate(l_int32  n)
{
L_DNA  *da;

    PROCNAME("l_dnaCreate");

    if (n <= 0)
        n = INITIAL_PTR_ARRAYSIZE;

    da = (L_DNA *)LEPT_CALLOC(1, sizeof(L_DNA));
    if ((da->array = (l_float64 *)LEPT_CALLOC(n, sizeof(l_float64))) == NULL) {
        l_dnaDestroy(&da);
        return (L_DNA *)ERROR_PTR("double array not made", procName, NULL);
    }

    da->nalloc = n;
    da->n = 0;
    da->refcount = 1;
    da->startx = 0.0;
    da->delx = 1.0;

    return da;
}


L_DNA *
l_dnaCreateFromIArray(l_int32  *iarray,
                      l_int32   size)
{
l_int32  i;
L_DNA   *da;

    PROCNAME("l_dnaCreateFromIArray");

    if (!iarray)
        return (L_DNA *)ERROR_PTR("iarray not defined", procName, NULL);
    if (size <= 0)
        return (L_DNA *)ERROR_PTR("size must be > 0", procName, NULL);

    da = l_dnaCreate(size);
    for (i = 0; i < size; i++)
        l_dnaAddNumber(da, iarray[i]);

    return da;
}


L_DNA *
l_dnaCreateFromDArray(l_float64  *darray,
                      l_int32     size,
                      l_int32     copyflag)
{
l_int32  i;
L_DNA   *da;

    PROCNAME("l_dnaCreateFromDArray");

    if (!darray)
        return (L_DNA *)ERROR_PTR("darray not defined", procName, NULL);
    if (size <= 0)
        return (L_DNA *)ERROR_PTR("size must be > 0", procName, NULL);
    if (copyflag != L_INSERT && copyflag != L_COPY)
        return (L_DNA *)ERROR_PTR("invalid copyflag", procName, NULL);

    da = l_dnaCreate(size);
    if (copyflag == L_INSERT) {
        if (da->array) LEPT_FREE(da->array);
        da->array = darray;
        da->n = size;
    } else {  /* just copy the contents */
        for (i = 0; i < size; i++)
            l_dnaAddNumber(da, darray[i]);
    }

    return da;
}


L_DNA *
l_dnaMakeSequence(l_float64  startval,
                  l_float64  increment,
                  l_int32    size)
{
l_int32    i;
l_float64  val;
L_DNA     *da;

    PROCNAME("l_dnaMakeSequence");

    if ((da = l_dnaCreate(size)) == NULL)
        return (L_DNA *)ERROR_PTR("da not made", procName, NULL);

    for (i = 0; i < size; i++) {
        val = startval + i * increment;
        l_dnaAddNumber(da, val);
    }

    return da;
}


void
l_dnaDestroy(L_DNA  **pda)
{
L_DNA  *da;

    PROCNAME("l_dnaDestroy");

    if (pda == NULL) {
        L_WARNING("ptr address is NULL\n", procName);
        return;
    }

    if ((da = *pda) == NULL)
        return;

        /* Decrement the ref count.  If it is 0, destroy the l_dna. */
    l_dnaChangeRefcount(da, -1);
    if (l_dnaGetRefcount(da) <= 0) {
        if (da->array)
            LEPT_FREE(da->array);
        LEPT_FREE(da);
    }

    *pda = NULL;
    return;
}


L_DNA *
l_dnaCopy(L_DNA  *da)
{
l_int32  i;
L_DNA   *dac;

    PROCNAME("l_dnaCopy");

    if (!da)
        return (L_DNA *)ERROR_PTR("da not defined", procName, NULL);

    if ((dac = l_dnaCreate(da->n)) == NULL)
        return (L_DNA *)ERROR_PTR("dac not made", procName, NULL);
    dac->startx = da->startx;
    dac->delx = da->delx;

    for (i = 0; i < da->n; i++)
        l_dnaAddNumber(dac, da->array[i]);

    return dac;
}


L_DNA *
l_dnaClone(L_DNA  *da)
{
    PROCNAME("l_dnaClone");

    if (!da)
        return (L_DNA *)ERROR_PTR("da not defined", procName, NULL);

    l_dnaChangeRefcount(da, 1);
    return da;
}


l_ok
l_dnaEmpty(L_DNA  *da)
{
    PROCNAME("l_dnaEmpty");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    da->n = 0;
    return 0;
}



/*--------------------------------------------------------------------------*
 *                  Dna: add/remove number and extend array                 *
 *--------------------------------------------------------------------------*/
l_ok
l_dnaAddNumber(L_DNA     *da,
               l_float64  val)
{
l_int32  n;

    PROCNAME("l_dnaAddNumber");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    n = l_dnaGetCount(da);
    if (n >= da->nalloc)
        l_dnaExtendArray(da);
    da->array[n] = val;
    da->n++;
    return 0;
}


static l_int32
l_dnaExtendArray(L_DNA  *da)
{
    PROCNAME("l_dnaExtendArray");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    if ((da->array = (l_float64 *)reallocNew((void **)&da->array,
                                sizeof(l_float64) * da->nalloc,
                                2 * sizeof(l_float64) * da->nalloc)) == NULL)
            return ERROR_INT("new ptr array not returned", procName, 1);

    da->nalloc *= 2;
    return 0;
}


l_ok
l_dnaInsertNumber(L_DNA      *da,
                  l_int32    index,
                  l_float64  val)
{
l_int32  i, n;

    PROCNAME("l_dnaInsertNumber");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    n = l_dnaGetCount(da);
    if (index < 0 || index > n)
        return ERROR_INT("index not in {0...n}", procName, 1);

    if (n >= da->nalloc)
        l_dnaExtendArray(da);
    for (i = n; i > index; i--)
        da->array[i] = da->array[i - 1];
    da->array[index] = val;
    da->n++;
    return 0;
}


l_ok
l_dnaRemoveNumber(L_DNA   *da,
                  l_int32  index)
{
l_int32  i, n;

    PROCNAME("l_dnaRemoveNumber");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    n = l_dnaGetCount(da);
    if (index < 0 || index >= n)
        return ERROR_INT("index not in {0...n - 1}", procName, 1);

    for (i = index + 1; i < n; i++)
        da->array[i - 1] = da->array[i];
    da->n--;
    return 0;
}


l_ok
l_dnaReplaceNumber(L_DNA     *da,
                   l_int32    index,
                   l_float64  val)
{
l_int32  n;

    PROCNAME("l_dnaReplaceNumber");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    n = l_dnaGetCount(da);
    if (index < 0 || index >= n)
        return ERROR_INT("index not in {0...n - 1}", procName, 1);

    da->array[index] = val;
    return 0;
}


/*----------------------------------------------------------------------*
 *                             Dna accessors                            *
 *----------------------------------------------------------------------*/
l_int32
l_dnaGetCount(L_DNA  *da)
{
    PROCNAME("l_dnaGetCount");

    if (!da)
        return ERROR_INT("da not defined", procName, 0);
    return da->n;
}


l_ok
l_dnaSetCount(L_DNA   *da,
              l_int32  newcount)
{
    PROCNAME("l_dnaSetCount");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    if (newcount > da->nalloc) {
        if ((da->array = (l_float64 *)reallocNew((void **)&da->array,
                         sizeof(l_float64) * da->nalloc,
                         sizeof(l_float64) * newcount)) == NULL)
            return ERROR_INT("new ptr array not returned", procName, 1);
        da->nalloc = newcount;
    }
    da->n = newcount;
    return 0;
}


l_ok
l_dnaGetDValue(L_DNA      *da,
               l_int32     index,
               l_float64  *pval)
{
    PROCNAME("l_dnaGetDValue");

    if (!pval)
        return ERROR_INT("&val not defined", procName, 1);
    *pval = 0.0;
    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    if (index < 0 || index >= da->n)
        return ERROR_INT("index not valid", procName, 1);

    *pval = da->array[index];
    return 0;
}


l_ok
l_dnaGetIValue(L_DNA    *da,
               l_int32   index,
               l_int32  *pival)
{
l_float64  val;

    PROCNAME("l_dnaGetIValue");

    if (!pival)
        return ERROR_INT("&ival not defined", procName, 1);
    *pival = 0;
    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    if (index < 0 || index >= da->n)
        return ERROR_INT("index not valid", procName, 1);

    val = da->array[index];
    *pival = (l_int32)(val + L_SIGN(val) * 0.5);
    return 0;
}


l_ok
l_dnaSetValue(L_DNA     *da,
              l_int32    index,
              l_float64  val)
{
    PROCNAME("l_dnaSetValue");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    if (index < 0 || index >= da->n)
        return ERROR_INT("index not valid", procName, 1);

    da->array[index] = val;
    return 0;
}


l_ok
l_dnaShiftValue(L_DNA     *da,
                l_int32    index,
                l_float64  diff)
{
    PROCNAME("l_dnaShiftValue");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    if (index < 0 || index >= da->n)
        return ERROR_INT("index not valid", procName, 1);

    da->array[index] += diff;
    return 0;
}


l_int32 *
l_dnaGetIArray(L_DNA  *da)
{
l_int32   i, n, ival;
l_int32  *array;

    PROCNAME("l_dnaGetIArray");

    if (!da)
        return (l_int32 *)ERROR_PTR("da not defined", procName, NULL);

    n = l_dnaGetCount(da);
    if ((array = (l_int32 *)LEPT_CALLOC(n, sizeof(l_int32))) == NULL)
        return (l_int32 *)ERROR_PTR("array not made", procName, NULL);
    for (i = 0; i < n; i++) {
        l_dnaGetIValue(da, i, &ival);
        array[i] = ival;
    }

    return array;
}


l_float64 *
l_dnaGetDArray(L_DNA   *da,
               l_int32  copyflag)
{
l_int32     i, n;
l_float64  *array;

    PROCNAME("l_dnaGetDArray");

    if (!da)
        return (l_float64 *)ERROR_PTR("da not defined", procName, NULL);

    if (copyflag == L_NOCOPY) {
        array = da->array;
    } else {  /* copyflag == L_COPY */
        n = l_dnaGetCount(da);
        if ((array = (l_float64 *)LEPT_CALLOC(n, sizeof(l_float64))) == NULL)
            return (l_float64 *)ERROR_PTR("array not made", procName, NULL);
        for (i = 0; i < n; i++)
            array[i] = da->array[i];
    }

    return array;
}


l_int32
l_dnaGetRefcount(L_DNA  *da)
{
    PROCNAME("l_dnaGetRefcount");

    if (!da)
        return ERROR_INT("da not defined", procName, UNDEF);
    return da->refcount;
}


l_ok
l_dnaChangeRefcount(L_DNA   *da,
                    l_int32  delta)
{
    PROCNAME("l_dnaChangeRefcount");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    da->refcount += delta;
    return 0;
}


l_ok
l_dnaGetParameters(L_DNA     *da,
                   l_float64  *pstartx,
                   l_float64  *pdelx)
{
    PROCNAME("l_dnaGetParameters");

    if (pstartx) *pstartx = 0.0;
    if (pdelx) *pdelx = 1.0;
    if (!pstartx && !pdelx)
        return ERROR_INT("neither &startx nor &delx are defined", procName, 1);
    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    if (pstartx) *pstartx = da->startx;
    if (pdelx) *pdelx = da->delx;
    return 0;
}


l_ok
l_dnaSetParameters(L_DNA     *da,
                   l_float64  startx,
                   l_float64  delx)
{
    PROCNAME("l_dnaSetParameters");

    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    da->startx = startx;
    da->delx = delx;
    return 0;
}


l_ok
l_dnaCopyParameters(L_DNA  *dad,
                    L_DNA  *das)
{
l_float64  start, binsize;

    PROCNAME("l_dnaCopyParameters");

    if (!das || !dad)
        return ERROR_INT("das and dad not both defined", procName, 1);

    l_dnaGetParameters(das, &start, &binsize);
    l_dnaSetParameters(dad, start, binsize);
    return 0;
}


/*----------------------------------------------------------------------*
 *                        Serialize Dna for I/O                         *
 *----------------------------------------------------------------------*/
L_DNA *
l_dnaRead(const char  *filename)
{
FILE   *fp;
L_DNA  *da;

    PROCNAME("l_dnaRead");

    if (!filename)
        return (L_DNA *)ERROR_PTR("filename not defined", procName, NULL);

    if ((fp = fopenReadStream(filename)) == NULL)
        return (L_DNA *)ERROR_PTR("stream not opened", procName, NULL);
    da = l_dnaReadStream(fp);
    fclose(fp);
    if (!da)
        return (L_DNA *)ERROR_PTR("da not read", procName, NULL);
    return da;
}


L_DNA *
l_dnaReadStream(FILE  *fp)
{
l_int32    i, n, index, ret, version;
l_float64  val, startx, delx;
L_DNA     *da;

    PROCNAME("l_dnaReadStream");

    if (!fp)
        return (L_DNA *)ERROR_PTR("stream not defined", procName, NULL);

    ret = fscanf(fp, "\nL_Dna Version %d\n", &version);
    if (ret != 1)
        return (L_DNA *)ERROR_PTR("not a l_dna file", procName, NULL);
    if (version != DNA_VERSION_NUMBER)
        return (L_DNA *)ERROR_PTR("invalid l_dna version", procName, NULL);
    if (fscanf(fp, "Number of numbers = %d\n", &n) != 1)
        return (L_DNA *)ERROR_PTR("invalid number of numbers", procName, NULL);

    if ((da = l_dnaCreate(n)) == NULL)
        return (L_DNA *)ERROR_PTR("da not made", procName, NULL);
    for (i = 0; i < n; i++) {
        if (fscanf(fp, "  [%d] = %lf\n", &index, &val) != 2) {
            l_dnaDestroy(&da);
            return (L_DNA *)ERROR_PTR("bad input data", procName, NULL);
        }
        l_dnaAddNumber(da, val);
    }

        /* Optional data */
    if (fscanf(fp, "startx = %lf, delx = %lf\n", &startx, &delx) == 2)
        l_dnaSetParameters(da, startx, delx);
    return da;
}


l_ok
l_dnaWrite(const char  *filename,
           L_DNA       *da)
{
l_int32  ret;
FILE    *fp;

    PROCNAME("l_dnaWrite");

    if (!filename)
        return ERROR_INT("filename not defined", procName, 1);
    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    if ((fp = fopenWriteStream(filename, "w")) == NULL)
        return ERROR_INT("stream not opened", procName, 1);
    ret = l_dnaWriteStream(fp, da);
    fclose(fp);
    if (ret)
        return ERROR_INT("da not written to stream", procName, 1);
    return 0;
}


l_ok
l_dnaWriteStream(FILE   *fp,
                 L_DNA  *da)
{
l_int32    i, n;
l_float64  startx, delx;

    PROCNAME("l_dnaWriteStream");

    if (!fp)
        return ERROR_INT("stream not defined", procName, 1);
    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    n = l_dnaGetCount(da);
    fprintf(fp, "\nL_Dna Version %d\n", DNA_VERSION_NUMBER);
    fprintf(fp, "Number of numbers = %d\n", n);
    for (i = 0; i < n; i++)
        fprintf(fp, "  [%d] = %f\n", i, da->array[i]);
    fprintf(fp, "\n");

        /* Optional data */
    l_dnaGetParameters(da, &startx, &delx);
    if (startx != 0.0 || delx != 1.0)
        fprintf(fp, "startx = %f, delx = %f\n", startx, delx);

    return 0;
}


/*--------------------------------------------------------------------------*
 *                       Dnaa creation, destruction                         *
 *--------------------------------------------------------------------------*/
L_DNAA *
l_dnaaCreate(l_int32  n)
{
L_DNAA  *daa;

    PROCNAME("l_dnaaCreate");

    if (n <= 0)
        n = INITIAL_PTR_ARRAYSIZE;

    daa = (L_DNAA *)LEPT_CALLOC(1, sizeof(L_DNAA));
    if ((daa->dna = (L_DNA **)LEPT_CALLOC(n, sizeof(L_DNA *))) == NULL) {
        l_dnaaDestroy(&daa);
        return (L_DNAA *)ERROR_PTR("l_dna ptr array not made", procName, NULL);
    }
    daa->nalloc = n;
    daa->n = 0;
    return daa;
}


L_DNAA *
l_dnaaCreateFull(l_int32  nptr,
                 l_int32  n)
{
l_int32  i;
L_DNAA  *daa;
L_DNA   *da;

    daa = l_dnaaCreate(nptr);
    for (i = 0; i < nptr; i++) {
        da = l_dnaCreate(n);
        l_dnaaAddDna(daa, da, L_INSERT);
    }

    return daa;
}


l_ok
l_dnaaTruncate(L_DNAA  *daa)
{
l_int32  i, n, nn;
L_DNA   *da;

    PROCNAME("l_dnaaTruncate");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);

    n = l_dnaaGetCount(daa);
    for (i = n - 1; i >= 0; i--) {
        da = l_dnaaGetDna(daa, i, L_CLONE);
        if (!da)
            continue;
        nn = l_dnaGetCount(da);
        l_dnaDestroy(&da);  /* the clone */
        if (nn == 0)
            l_dnaDestroy(&daa->dna[i]);
        else
            break;
    }
    daa->n = i + 1;
    return 0;
}


void
l_dnaaDestroy(L_DNAA  **pdaa)
{
l_int32  i;
L_DNAA  *daa;

    PROCNAME("l_dnaaDestroy");

    if (pdaa == NULL) {
        L_WARNING("ptr address is NULL!\n", procName);
        return;
    }

    if ((daa = *pdaa) == NULL)
        return;

    for (i = 0; i < daa->n; i++)
        l_dnaDestroy(&daa->dna[i]);
    LEPT_FREE(daa->dna);
    LEPT_FREE(daa);
    *pdaa = NULL;

    return;
}


/*--------------------------------------------------------------------------*
 *                             Add Dna to Dnaa                              *
 *--------------------------------------------------------------------------*/
l_ok
l_dnaaAddDna(L_DNAA  *daa,
             L_DNA   *da,
             l_int32  copyflag)
{
l_int32  n;
L_DNA   *dac;

    PROCNAME("l_dnaaAddDna");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);
    if (!da)
        return ERROR_INT("da not defined", procName, 1);

    if (copyflag == L_INSERT) {
        dac = da;
    } else if (copyflag == L_COPY) {
        if ((dac = l_dnaCopy(da)) == NULL)
            return ERROR_INT("dac not made", procName, 1);
    } else if (copyflag == L_CLONE) {
        dac = l_dnaClone(da);
    } else {
        return ERROR_INT("invalid copyflag", procName, 1);
    }

    n = l_dnaaGetCount(daa);
    if (n >= daa->nalloc)
        l_dnaaExtendArray(daa);
    daa->dna[n] = dac;
    daa->n++;
    return 0;
}


static l_int32
l_dnaaExtendArray(L_DNAA  *daa)
{
    PROCNAME("l_dnaaExtendArray");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);

    if ((daa->dna = (L_DNA **)reallocNew((void **)&daa->dna,
                              sizeof(L_DNA *) * daa->nalloc,
                              2 * sizeof(L_DNA *) * daa->nalloc)) == NULL)
            return ERROR_INT("new ptr array not returned", procName, 1);

    daa->nalloc *= 2;
    return 0;
}


/*----------------------------------------------------------------------*
 *                           DNumaa accessors                           *
 *----------------------------------------------------------------------*/
l_int32
l_dnaaGetCount(L_DNAA  *daa)
{
    PROCNAME("l_dnaaGetCount");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 0);
    return daa->n;
}


l_int32
l_dnaaGetDnaCount(L_DNAA   *daa,
                    l_int32  index)
{
    PROCNAME("l_dnaaGetDnaCount");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 0);
    if (index < 0 || index >= daa->n)
        return ERROR_INT("invalid index into daa", procName, 0);
    return l_dnaGetCount(daa->dna[index]);
}


l_int32
l_dnaaGetNumberCount(L_DNAA  *daa)
{
L_DNA   *da;
l_int32  n, sum, i;

    PROCNAME("l_dnaaGetNumberCount");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 0);

    n = l_dnaaGetCount(daa);
    for (sum = 0, i = 0; i < n; i++) {
        da = l_dnaaGetDna(daa, i, L_CLONE);
        sum += l_dnaGetCount(da);
        l_dnaDestroy(&da);
    }

    return sum;
}


L_DNA *
l_dnaaGetDna(L_DNAA  *daa,
             l_int32  index,
             l_int32  accessflag)
{
    PROCNAME("l_dnaaGetDna");

    if (!daa)
        return (L_DNA *)ERROR_PTR("daa not defined", procName, NULL);
    if (index < 0 || index >= daa->n)
        return (L_DNA *)ERROR_PTR("index not valid", procName, NULL);

    if (accessflag == L_COPY)
        return l_dnaCopy(daa->dna[index]);
    else if (accessflag == L_CLONE)
        return l_dnaClone(daa->dna[index]);
    else
        return (L_DNA *)ERROR_PTR("invalid accessflag", procName, NULL);
}


l_ok
l_dnaaReplaceDna(L_DNAA  *daa,
                 l_int32  index,
                 L_DNA   *da)
{
l_int32  n;

    PROCNAME("l_dnaaReplaceDna");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);
    if (!da)
        return ERROR_INT("da not defined", procName, 1);
    n = l_dnaaGetCount(daa);
    if (index < 0 || index >= n)
        return ERROR_INT("index not valid", procName, 1);

    l_dnaDestroy(&daa->dna[index]);
    daa->dna[index] = da;
    return 0;
}


l_ok
l_dnaaGetValue(L_DNAA     *daa,
               l_int32     i,
               l_int32     j,
               l_float64  *pval)
{
l_int32  n;
L_DNA   *da;

    PROCNAME("l_dnaaGetValue");

    if (!pval)
        return ERROR_INT("&val not defined", procName, 1);
    *pval = 0.0;
    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);
    n = l_dnaaGetCount(daa);
    if (i < 0 || i >= n)
        return ERROR_INT("invalid index into daa", procName, 1);
    da = daa->dna[i];
    if (j < 0 || j >= da->n)
        return ERROR_INT("invalid index into da", procName, 1);
    *pval = da->array[j];
    return 0;
}


l_ok
l_dnaaAddNumber(L_DNAA    *daa,
                l_int32    index,
                l_float64  val)
{
l_int32  n;
L_DNA   *da;

    PROCNAME("l_dnaaAddNumber");

    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);
    n = l_dnaaGetCount(daa);
    if (index < 0 || index >= n)
        return ERROR_INT("invalid index in daa", procName, 1);

    da = l_dnaaGetDna(daa, index, L_CLONE);
    l_dnaAddNumber(da, val);
    l_dnaDestroy(&da);
    return 0;
}


/*----------------------------------------------------------------------*
 *                        Serialize Dna for I/O                         *
 *----------------------------------------------------------------------*/
L_DNAA *
l_dnaaRead(const char  *filename)
{
FILE    *fp;
L_DNAA  *daa;

    PROCNAME("l_dnaaRead");

    if (!filename)
        return (L_DNAA *)ERROR_PTR("filename not defined", procName, NULL);

    if ((fp = fopenReadStream(filename)) == NULL)
        return (L_DNAA *)ERROR_PTR("stream not opened", procName, NULL);
    daa = l_dnaaReadStream(fp);
    fclose(fp);
    if (!daa)
        return (L_DNAA *)ERROR_PTR("daa not read", procName, NULL);
    return daa;
}


L_DNAA *
l_dnaaReadStream(FILE  *fp)
{
l_int32    i, n, index, ret, version;
L_DNA     *da;
L_DNAA    *daa;

    PROCNAME("l_dnaaReadStream");

    if (!fp)
        return (L_DNAA *)ERROR_PTR("stream not defined", procName, NULL);

    ret = fscanf(fp, "\nL_Dnaa Version %d\n", &version);
    if (ret != 1)
        return (L_DNAA *)ERROR_PTR("not a l_dna file", procName, NULL);
    if (version != DNA_VERSION_NUMBER)
        return (L_DNAA *)ERROR_PTR("invalid l_dnaa version", procName, NULL);
    if (fscanf(fp, "Number of L_Dna = %d\n\n", &n) != 1)
        return (L_DNAA *)ERROR_PTR("invalid number of l_dna", procName, NULL);
    if ((daa = l_dnaaCreate(n)) == NULL)
        return (L_DNAA *)ERROR_PTR("daa not made", procName, NULL);

    for (i = 0; i < n; i++) {
        if (fscanf(fp, "L_Dna[%d]:", &index) != 1) {
            l_dnaaDestroy(&daa);
            return (L_DNAA *)ERROR_PTR("invalid l_dna header", procName, NULL);
        }
        if ((da = l_dnaReadStream(fp)) == NULL) {
            l_dnaaDestroy(&daa);
            return (L_DNAA *)ERROR_PTR("da not made", procName, NULL);
        }
        l_dnaaAddDna(daa, da, L_INSERT);
    }

    return daa;
}


l_ok
l_dnaaWrite(const char  *filename,
            L_DNAA      *daa)
{
l_int32  ret;
FILE    *fp;

    PROCNAME("l_dnaaWrite");

    if (!filename)
        return ERROR_INT("filename not defined", procName, 1);
    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);

    if ((fp = fopenWriteStream(filename, "w")) == NULL)
        return ERROR_INT("stream not opened", procName, 1);
    ret = l_dnaaWriteStream(fp, daa);
    fclose(fp);
    if (ret)
        return ERROR_INT("daa not written to stream", procName, 1);
    return 0;
}


l_ok
l_dnaaWriteStream(FILE    *fp,
                  L_DNAA  *daa)
{
l_int32  i, n;
L_DNA   *da;

    PROCNAME("l_dnaaWriteStream");

    if (!fp)
        return ERROR_INT("stream not defined", procName, 1);
    if (!daa)
        return ERROR_INT("daa not defined", procName, 1);

    n = l_dnaaGetCount(daa);
    fprintf(fp, "\nL_Dnaa Version %d\n", DNA_VERSION_NUMBER);
    fprintf(fp, "Number of L_Dna = %d\n\n", n);
    for (i = 0; i < n; i++) {
        if ((da = l_dnaaGetDna(daa, i, L_CLONE)) == NULL)
            return ERROR_INT("da not found", procName, 1);
        fprintf(fp, "L_Dna[%d]:", i);
        l_dnaWriteStream(fp, da);
        l_dnaDestroy(&da);
    }

    return 0;
}