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            /* Sparse matrices in compressed column-oriented form */
#include "Csparse.h"
#include "chm_common.h"

SEXP Csparse_validate(SEXP x)
{
    SEXP pslot = GET_SLOT(x, Matrix_pSym),
    islot = GET_SLOT(x, Matrix_iSym);
    int j, ncol = length(pslot) - 1,
    *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
    nrow, *xp = INTEGER(pslot),
    *xi = INTEGER(islot);

    nrow = dims[0];
    if (length(pslot) <= 0)
    return mkString(_("slot p must have length > 0"));
    if (xp[0] != 0)
    return mkString(_("first element of slot p must be zero"));
    if (length(islot) != xp[ncol])
    return mkString(_("last element of slot p must match length of slots i and x"));
    for (j = 0; j < ncol; j++) {
    if (xp[j] > xp[j+1])
        return mkString(_("slot p must be non-decreasing"));
    }
    for (j = 0; j < length(islot); j++) {
    if (xi[j] < 0 || xi[j] >= nrow)
        return mkString(_("all row indices must be between 0 and nrow-1"));
    }
    return ScalarLogical(1);
}

SEXP Csparse_to_dense(SEXP x)
{
    cholmod_sparse *chxs = as_cholmod_sparse(x);
    cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);

    Free(chxs);
    return chm_dense_to_SEXP(chxd, 1);
}

SEXP Csparse_to_logical(SEXP x, SEXP tri)
{
    cholmod_sparse *chxs = as_cholmod_sparse(x);
    cholmod_sparse
    *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
    int uploT = 0; char *diag = "";

    Free(chxs);
    if (asLogical(tri)) {   /* triangular sparse matrices */
    uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?
        -1 : 1;
    diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
    }
    return chm_sparse_to_SEXP(chxcp, 1, uploT, diag,
                GET_SLOT(x, Matrix_DimNamesSym));
}

SEXP Csparse_to_matrix(SEXP x)
{
    cholmod_sparse *chxs = as_cholmod_sparse(x);
    cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);

    Free(chxs);
    return chm_dense_to_matrix(chxd, 1,
                   GET_SLOT(x, Matrix_DimNamesSym));
}

SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
{
    cholmod_sparse *chxs = as_cholmod_sparse(x);
    cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);
    int uploT = 0; char *diag = "";

    Free(chxs);
    if (asLogical(tri)) {   /* triangular sparse matrices */
    uploT = (*uplo_P(x) == 'U') ? -1 : 1;
    diag = diag_P(x);
    }
    return chm_triplet_to_SEXP(chxt, 1, uploT, diag,
                   GET_SLOT(x, Matrix_DimNamesSym));
}

/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
SEXP Csparse_symmetric_to_general(SEXP x)
{
    cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;

    if (!(chx->stype))
    error(_("Nonsymmetric matrix in Csparse_symmeteric_to_general"));
    chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
    /* xtype: pattern, "real", complex or .. */
    Free(chx);
    return chm_sparse_to_SEXP(chgx, 1, 0, "",
                  GET_SLOT(x, Matrix_DimNamesSym));
}

SEXP Csparse_transpose(SEXP x, SEXP tri)
{
    cholmod_sparse *chx = as_cholmod_sparse(x);
    cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
    SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
    int uploT = 0; char *diag = "";

    Free(chx);
    tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
    SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
    SET_VECTOR_ELT(dn, 1, tmp);
    UNPROTECT(1);
    if (asLogical(tri)) {   /* triangular sparse matrices */
    uploT = (*uplo_P(x) == 'U') ? -1 : 1;
    diag = diag_P(x);
    }
    return chm_sparse_to_SEXP(chxt, 1, uploT, diag, dn);
}

SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
{
    cholmod_sparse *cha = as_cholmod_sparse(a),
    *chb = as_cholmod_sparse(b);
    cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
    SEXP dn = allocVector(VECSXP, 2);

    Free(cha); Free(chb);
    SET_VECTOR_ELT(dn, 0,   /* establish dimnames */
           duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
    SET_VECTOR_ELT(dn, 1,
           duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
    return chm_sparse_to_SEXP(chc, 1, 0, "", dn);
}

SEXP Csparse_dense_prod(SEXP a, SEXP b)
{
    cholmod_sparse *cha = as_cholmod_sparse(a);
    cholmod_dense *chb = as_cholmod_dense(b);
    cholmod_dense *chc = 
    cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);
    double alpha[] = {1,0}, beta[] = {0,0};

    cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);
    Free(cha); Free(chb);
    return chm_dense_to_SEXP(chc, 1);
}

SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
{
    cholmod_sparse *cha = as_cholmod_sparse(a);
    cholmod_dense *chb = as_cholmod_dense(b);
    cholmod_dense *chc =
    cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);
    double alpha[] = {1,0}, beta[] = {0,0};

    cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);
    Free(cha); Free(chb);
    return chm_dense_to_SEXP(chc, 1);
}

SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
{
    int trip = asLogical(triplet),
    tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
    cholmod_triplet
    *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;
    cholmod_sparse *chcp, *chxt,
    *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)
    : as_cholmod_sparse(x);
    SEXP dn = PROTECT(allocVector(VECSXP, 2));

    if (!tr)
    chxt = cholmod_transpose(chx, chx->xtype, &c);
    chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
    if(!chcp)
    error("Csparse_crossprod(): error return from cholmod_aat()");
    cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
    chcp->stype = 1;
    if (trip) {
    cholmod_free_sparse(&chx, &c);
    Free(cht);
    } else {
    Free(chx);
    }
    if (!tr) cholmod_free_sparse(&chxt, &c);
                /* create dimnames */
    SET_VECTOR_ELT(dn, 0,
           duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
                    (tr) ? 1 : 0)));
    SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
    UNPROTECT(1);
    return chm_sparse_to_SEXP(chcp, 1, 0, "", dn);
}

SEXP Csparse_horzcat(SEXP x, SEXP y)
{
    cholmod_sparse *chx = as_cholmod_sparse(x),
    *chy = as_cholmod_sparse(y), *ans;

    ans = cholmod_horzcat(chx, chy, 1, &c);
    Free(chx); Free(chy);
    /* FIXME: currently drops dimnames */
    return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);
}

SEXP Csparse_vertcat(SEXP x, SEXP y)
{
    cholmod_sparse *chx = as_cholmod_sparse(x),
    *chy = as_cholmod_sparse(y), *ans;

    ans = cholmod_vertcat(chx, chy, 1, &c);
    Free(chx); Free(chy);
    /* FIXME: currently drops dimnames */
    return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);
}

SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
{
    cholmod_sparse *chx = as_cholmod_sparse(x), *ans;

    ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
    Free(chx);
    return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);
}

SEXP Csparse_diagU2N(SEXP x)
{
    cholmod_sparse *chx = as_cholmod_sparse(x);
    cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
    double one[] = {1, 0};
    cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
    int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?
    -1 : 1;

    Free(chx); cholmod_free_sparse(&eye, &c);
    return chm_sparse_to_SEXP(ans, 1, uploT, "N",
                  duplicate(GET_SLOT(x, Matrix_DimNamesSym)));
}

SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
{
    cholmod_sparse *chx = as_cholmod_sparse(x);
    int rsize = (isNull(i)) ? -1 : LENGTH(i),
    csize = (isNull(j)) ? -1 : LENGTH(j);

    if (rsize >= 0 && !isInteger(i))
    error(_("Index i must be NULL or integer"));
    if (csize >= 0 && !isInteger(j))
    error(_("Index j must be NULL or integer"));
    return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
                        INTEGER(j), csize,
                        TRUE, TRUE, &c),
                  1, 0, "", R_NilValue);
}