source: branches/alilink/SL/INSDEL/insdel.cxx

// =============================================================== //
//                                                                 //
//   File      : insdel.cxx                                        //
//   Purpose   : insert/delete columns                             //
//                                                                 //
//   Institute of Microbiology (Technical University Munich)       //
//   http://www.arb-home.de/                                       //
//                                                                 //
// =============================================================== //

// AISC_MKPT_PROMOTE:#ifndef ARBDB_BASE_H
// AISC_MKPT_PROMOTE:#include <arbdb_base.h>
// AISC_MKPT_PROMOTE:#endif

#include "insdel.h"
#include <RangeList.h>

#include <arbdbt.h>
#include <adGene.h>
#include <arb_progress.h>
#include <arb_defs.h>
#include <arb_diff.h>
#include <algorithm>

using namespace std;

#define id_assert(cond) arb_assert(cond)

// --------------------------------------------------------------------------------
// helper to hold any kind of unit (char, int, float)

class UnitPtr {
    const void *ptr;
public:
    UnitPtr() : ptr(NULp) {}
    UnitPtr(const void *ptr_)
        : ptr(ptr_)
    {
        id_assert(ptr);
    }

    void set_pointer(const void *ptr_) {
        id_assert(!ptr);
        ptr = ptr_;
    }
    const void *get_pointer() const { return ptr; }
    const void *expect_pointer() const { id_assert(ptr); return ptr; }
};
struct UnitPair {
    UnitPtr left, right;
};

template <typename T>
inline int compare_type(const T& t1, const T& t2) {
    return t1<t2 ? -1 : (t1>t2 ? 1 : 0);
}

// --------------------------------------------------------------------------------

class AliData;
typedef SmartPtr<AliData> AliDataPtr;

// --------------------------------------------------------------------------------

class AliData {
    size_t          size;
    static GB_ERROR op_error;

public:
    AliData(size_t size_) : size(size_) {}
    virtual ~AliData() {}

    virtual size_t unitsize() const = 0;
    virtual bool has_slice() const = 0;

    enum memop {
        COPY_TO, // always returns 0
        COMPARE_WITH, // returns compare value
        CHECK_DELETE, // return 0 if ok to delete, otherwise op_error is set
    };

    void clear_error() const { op_error = NULp; }
    void set_error(GB_ERROR error) const {
        id_assert(error);
        id_assert(!op_error);
        op_error = error;
    }

    virtual int operate_on_mem(void *mem, size_t start, size_t count, memop op) const           = 0;
    virtual int cmp_data(size_t start, const AliData& other, size_t ostart, size_t count) const = 0;

    void copyPartTo(void *mem, size_t start, size_t count) const { operate_on_mem(mem, start, count, COPY_TO); }
    int cmpPartWith(const void *mem, size_t start, size_t count) const {
        id_assert(is_valid_part(start, count));
        return operate_on_mem(const_cast<void*>(mem), start, count, COMPARE_WITH); // COMPARE_WITH does not modify
    }
    GB_ERROR check_delete_allowed(size_t start, size_t count) const {
        op_error = NULp;
        id_assert(start <= size);
        IF_ASSERTION_USED(int forbidden =) operate_on_mem(NULp, start, std::min(count, size-start), CHECK_DELETE);
        id_assert(correlated(forbidden, op_error));
        return op_error;
    }

    virtual UnitPtr unit_left_of(size_t pos) const  = 0;
    virtual UnitPtr unit_right_of(size_t pos) const = 0;

    virtual AliDataPtr create_gap(size_t gapsize, const UnitPair& gapinfo) const = 0;
    virtual AliDataPtr slice_down(size_t start, size_t count) const = 0;

    size_t elems() const { return size; }
    size_t memsize() const { return unitsize()*elems(); }
    void copyTo(void *mem) const { copyPartTo(mem, 0, elems()); }
    bool empty() const { return !elems(); }

    int cmp_whole_data(const AliData& other) const {
        int cmp = cmp_data(0, other, 0, std::min(elems(), other.elems()));
        if (cmp == 0) { // prefixes are equal
            return compare_type(elems(), other.elems());
        }
        return cmp;
    }

    bool equals(const AliData& other) const {
        if (&other == this) return true;
        if (elems() != other.elems()) return false;

        return cmp_whole_data(other) == 0;
    }
    bool differs_from(const AliData& other) const { return !equals(other); }

    bool is_valid_pos(size_t pos) const { return pos < elems(); }
    bool is_valid_between(size_t pos) const { return pos <= elems(); } // pos == 0 -> before first base; pos == elems() -> after last base

    bool is_valid_part(size_t start, size_t count) const {
        return is_valid_between(start) && is_valid_between(start+count);
    }
};

GB_ERROR AliData::op_error = NULp;

// --------------------------------------------------------------------------------

class AliDataSlice : public AliData {
    AliDataPtr from;
    size_t     offset;

    static int fix_amount(AliDataPtr from, size_t offset, size_t amount) {
        if (amount) {
            size_t from_size = from->elems();
            if (offset>from_size) {
                amount = 0;
            }
            else {
                size_t last_pos  = offset+amount-1;
                size_t last_from = from->elems()-1;

                if (last_pos > last_from) {
                    id_assert(last_from >= offset);
                    amount = last_from-offset+1;
                }
            }
        }
        return amount;
    }

    AliDataSlice(AliDataPtr from_, size_t offset_, size_t amount_)
        : AliData(fix_amount(from_, offset_, amount_)),
          from(from_),
          offset(offset_)
    {
        id_assert(!from->has_slice()); // do not double-slice
    }

public:
    static AliDataPtr make(AliDataPtr from, size_t offset, size_t amount) {
        return (offset == 0 && amount >= from->elems())
            ? from
            : (from->has_slice()
               ? from->slice_down(offset, amount)
               : new AliDataSlice(from, offset, amount));
    }

    size_t unitsize() const OVERRIDE { return from->unitsize(); }
    bool has_slice() const OVERRIDE { return true; }

    AliDataPtr create_gap(size_t gapsize, const UnitPair& gapinfo) const OVERRIDE {
        return from->create_gap(gapsize, gapinfo);
    }
    AliDataPtr slice_down(size_t start, size_t count) const OVERRIDE {
        return new AliDataSlice(from, offset+start, std::min(count, elems()));
    }
    int operate_on_mem(void *mem, size_t start, size_t count, memop op) const OVERRIDE {
        id_assert(is_valid_part(start, count));
        return from->operate_on_mem(mem, start+offset, count, op);
    }
    UnitPtr unit_left_of(size_t pos) const OVERRIDE {
        id_assert(is_valid_between(pos));
        return from->unit_left_of(pos+offset);
    }
    UnitPtr unit_right_of(size_t pos) const OVERRIDE {
        id_assert(is_valid_between(pos));
        return from->unit_right_of(pos+offset);
    }
    int cmp_data(size_t start, const AliData& other, size_t ostart, size_t count) const OVERRIDE {
        id_assert(is_valid_part(start, count));
        id_assert(other.is_valid_part(ostart, count));

        return from->cmp_data(start+offset, other, ostart, count);
    }
};

class ComposedAliData FINAL_TYPE : public AliData {
    AliDataPtr left, right;
    bool       hasSlice;

    ComposedAliData(AliDataPtr l, AliDataPtr r)
        : AliData(l->elems()+r->elems()),
          left(l),
          right(r),
          hasSlice(left->has_slice() || right->has_slice())
    {
        id_assert(l->unitsize() == r->unitsize());
        id_assert(l->elems());
        id_assert(r->elems());
    }
    friend AliDataPtr concat(AliDataPtr left, AliDataPtr right); // for above ctor

    void *inc_by_units(void *mem, size_t units) const { return reinterpret_cast<char*>(mem)+units*unitsize(); }

public:
    size_t unitsize() const OVERRIDE { return left->unitsize(); }
    bool has_slice() const OVERRIDE { return hasSlice; }

    AliDataPtr create_gap(size_t gapsize, const UnitPair& gapinfo) const OVERRIDE {
        return left->create_gap(gapsize, gapinfo);
    }
    AliDataPtr slice_down(size_t start, size_t count) const OVERRIDE {
        size_t left_elems = left->elems();

        if (left_elems <= start) { // left is before slice
            return AliDataSlice::make(right, start-left_elems, count);
        }

        size_t pos_behind = start+count;
        if (left_elems >= pos_behind) { // right is behind slice
            return AliDataSlice::make(left, start, min(count, left_elems));
        }

        size_t take_left  = left_elems-start;
        size_t take_right = count-take_left;

        return new ComposedAliData(
            AliDataSlice::make(left, start, take_left),
            AliDataSlice::make(right, 0, take_right)
            );
    }
    int operate_on_mem(void *mem, size_t start, size_t count, memop op) const OVERRIDE {
        size_t left_elems = left->elems();
        size_t take_left  = 0;
        int    res        = 0;
        if (start<left_elems) {
            take_left = min(count, left_elems-start);
            res       = left->operate_on_mem(mem, start, take_left, op);
        }

        if (res == 0) {
            size_t take_right = count-take_left;
            if (take_right) {
                size_t rstart = start>left_elems ? start-left_elems : 0;
                id_assert(right->is_valid_part(rstart, take_right));
                res = right->operate_on_mem(inc_by_units(mem, take_left), rstart, take_right, op);
            }
        }
        return res;
    }
    int cmp_data(size_t start, const AliData& other, size_t ostart, size_t count) const OVERRIDE {
        size_t left_elems = left->elems();
        size_t take_left  = 0;
        int    cmp        = 0;
        if (start<left_elems) {
            take_left = min(count, left_elems-start);
            cmp       = left->cmp_data(start, other, ostart, take_left);
        }

        if (cmp == 0) {
            size_t take_right = count-take_left;
            if (take_right) {
                size_t rstart  = start>left_elems ? start-left_elems : 0;
                size_t rostart = ostart+take_left;

                id_assert(is_valid_part(rstart, take_right));
                id_assert(other.is_valid_part(rostart, take_right));

                cmp = right->cmp_data(rstart, other, rostart, take_right);
            }
        }
        return cmp;
    }

    UnitPtr unit_left_of(size_t pos) const OVERRIDE {
        id_assert(is_valid_between(pos));
        if (left->elems() == pos) { // split between left and right
            id_assert(pos >= 1);
            return left->unit_right_of(pos-1);
        }
        else if (left->elems() < pos) { // split inside or behind 'right'
            return right->unit_left_of(pos-left->elems());
        }
        else { // split inside or frontof 'left'
            return left->unit_left_of(pos);
        }
    }
    UnitPtr unit_right_of(size_t pos) const OVERRIDE {
        id_assert(is_valid_between(pos));
        if (left->elems() == pos) { // split between left and right
            id_assert(pos >= 1);
            return right->unit_left_of(0);
        }
        else if (left->elems() < pos) { // split inside or behind 'right'
            return right->unit_right_of(pos-left->elems());
        }
        else { // split inside or frontof 'left'
            return left->unit_right_of(pos);
        }
    }
};

// --------------------------------------------------------------------------------

class Deletable { // define characters allowed to delete (only applicable to TypedAliData<char>)
    bool deletable[256];

    void init(bool val) {
        for (int i = 0; i<256; ++i) {
            deletable[i] = val;
        }
    }

public:
    enum DeleteWhat { NOTHING, ANYTHING };
    explicit Deletable(DeleteWhat what) {
        switch (what) {
            case ANYTHING: init(true); break;
            case NOTHING: init(false); break;
        }
    }
    explicit Deletable(const char *allowed) {
        init(false);
        for (int i = 0; allowed[i]; ++i) {
            deletable[safeCharIndex(allowed[i])] = true;
        }
    }

    GB_ERROR get_delete_error(const char *data, size_t start, size_t count) const {
        GB_ERROR error = NULp;
        id_assert(count > 0);
        size_t   end   = start+count-1;
        for (size_t col = start; col <= end && !error; ++col) {
            if (!deletable[safeCharIndex(data[col])]) {
                error = GBS_global_string("You tried to delete '%c' at position %zu  -> Operation aborted", data[col], col);
            }
        }
        return error;
    }
};

// --------------------------------------------------------------------------------

template<typename T>
class TypedAliData : public AliData {
    T gap;

protected:
    static const T *typed_ptr(const UnitPtr& uptr) { return (const T*)uptr.get_pointer(); }
    const T* std_gap_ptr() const { return &gap; }

public:
    TypedAliData(size_t size_, T gap_)
        : AliData(size_),
          gap(gap_)
    {}

    const T& std_gap() const { return gap; }

    size_t unitsize() const OVERRIDE { return sizeof(T); }
    bool has_slice() const OVERRIDE { return false; }

    virtual UnitPtr at_ptr(size_t pos) const = 0;
    AliDataPtr create_gap(size_t gapsize, const UnitPair& /*gapinfo*/) const OVERRIDE;
    __ATTR__NORETURN AliDataPtr slice_down(size_t /*start*/, size_t /*count*/) const OVERRIDE {
        GBK_terminate("logic error: slice_down called for explicit TypedAliData");
    }
    UnitPtr unit_left_of(size_t pos) const OVERRIDE {
        id_assert(is_valid_between(pos));
        return at_ptr(pos-1);
    }
    UnitPtr unit_right_of(size_t pos) const OVERRIDE {
        id_assert(is_valid_between(pos));
        return at_ptr(pos);
    }
};

template<typename T>
struct SpecificGap : public TypedAliData<T> {
    typedef TypedAliData<T> BaseType;

    SpecificGap(size_t gapsize, const T& gap_)
        : BaseType(gapsize, gap_)
    {}
    int operate_on_mem(void *mem, size_t IF_ASSERTION_USED(start), size_t count, AliData::memop op) const OVERRIDE {
        id_assert(BaseType::is_valid_part(start, count));
        switch (op) {
            case AliData::COPY_TO: {
                T *typedMem = (T*)mem;
                for (size_t a = 0; a<count; ++a) { // LOOP_VECTORIZED=3
                    typedMem[a] = BaseType::std_gap();
                }
                break;
            }
            case AliData::COMPARE_WITH: {
                const T *typedMem = (const T*)mem;
                for (size_t a = 0; a<count; ++a) {
                    int cmp = compare_type(BaseType::std_gap(), typedMem[a]);
                    if (cmp) return cmp;
                }
                break;
            }
            case AliData::CHECK_DELETE: {
                break; // deleting an inserted gap is always permitted
            }
        }
        return 0;
    }
    int cmp_data(size_t start, const AliData& other, size_t ostart, size_t count) const OVERRIDE {
        const SpecificGap<T> *other_is_gap = dynamic_cast<const SpecificGap<T>*>(&other);
        if (other_is_gap) {
            return compare_type(BaseType::std_gap(), other_is_gap->std_gap());
        }
        return -other.cmp_data(ostart, *this, start, count);
    }
    UnitPtr at_ptr(size_t pos) const OVERRIDE {
        if (pos<BaseType::elems()) return UnitPtr(BaseType::std_gap_ptr());
        return UnitPtr();
    }
};

template <typename T>
AliDataPtr TypedAliData<T>::create_gap(size_t gapsize, const UnitPair& /*gapinfo*/) const {
    return new SpecificGap<T>(gapsize, std_gap());
}

class SizeAwarable {
    bool   allows_oversize;
    size_t org_ali_size;
public:
    SizeAwarable(bool allows_oversize_, size_t ali_size_)
        : allows_oversize(allows_oversize_),
          org_ali_size(ali_size_)
    {}

    size_t get_allowed_size(size_t term_size, size_t new_ali_size) const {
        size_t allowed_size = new_ali_size;
        if (allows_oversize && term_size>org_ali_size) {
            size_t oversize = term_size-org_ali_size;
            allowed_size    = new_ali_size+oversize;
        }
        return allowed_size;
    }
};
inline SizeAwarable dontAllowOversize(size_t ali_size) { return SizeAwarable(false, ali_size); }

template<typename T>
inline GB_ERROR check_delete_allowed(const T *, size_t, size_t , const Deletable& ) {
    return NULp; // for non-char deleting is always allowed
}
template<>
inline GB_ERROR check_delete_allowed(const char *data, size_t start, size_t count, const Deletable& deletable) {
    return deletable.get_delete_error(data, start, count);
}

template<typename T>
class SpecificAliData : public TypedAliData<T>, public SizeAwarable, virtual Noncopyable {
    const T   *data;
    Deletable  deletable;

public:
    typedef TypedAliData<T> BaseType;

    SpecificAliData(const T *static_data, size_t elements, const T& gap_, const SizeAwarable& sizeAware, const Deletable& deletable_)
        : BaseType(elements, gap_),
          SizeAwarable(sizeAware),
          data(static_data),
          deletable(deletable_)
    {}

    int operate_on_mem(void *mem, size_t start, size_t count, AliData::memop op) const OVERRIDE {
        if (count>0) {
            id_assert(BaseType::is_valid_part(start, count));
            switch (op) {
                case AliData::COPY_TO: {
                    size_t msize = BaseType::unitsize()*count;
                    id_assert(msize>0);
                    memcpy(mem, data+start, msize);
                    break;
                }
                case AliData::COMPARE_WITH: {
                    const T *typedMem = (const T*)mem;
                    for (size_t a = 0; a<count; ++a) {
                        int cmp = compare_type(data[start+a], typedMem[a]);
                        if (cmp) return cmp;
                    }
                    break;
                }
                case AliData::CHECK_DELETE: {
                    const T  *typedMem = (const T*)data;
                    GB_ERROR  error    = check_delete_allowed<T>(typedMem, start, count, deletable);
                    if (error) {
                        BaseType::set_error(error);
                        return 1;
                    }
                    break;
                }
            }
        }
        return 0;
    }
    int cmp_data(size_t start, const AliData& other, size_t ostart, size_t count) const OVERRIDE {
        id_assert(BaseType::is_valid_part(start, count));
        id_assert(other.is_valid_part(ostart, count));

        // if (&other == this && start == ostart) return true; // @@@ why does this fail tests?
        return -other.cmpPartWith(data+start, ostart, count);
    }
    UnitPtr at_ptr(size_t pos) const OVERRIDE {
        if (pos<BaseType::elems()) return UnitPtr(&data[pos]);
        return UnitPtr();
    }
    const T *get_data() const { return data; }
};

class SequenceAliData : public SpecificAliData<char> {
    char dot;

    char preferred_gap(const char *s1, const char *s2) const {
        if (s1 && s2) {
            if (*s1 == std_gap() || *s2 == std_gap()) {
                return std_gap();
            }
            if (*s1 == dot || *s2 == dot) {
                return dot;
            }
            return std_gap();
        }
        else if (s1) {
            id_assert(!s2);
            return *s1 == std_gap() ? std_gap() : dot;
        }
        else if (s2) {
            id_assert(!s1);
            return *s2 == std_gap() ? std_gap() : dot;
        }
        else {
            id_assert(!s1 && !s2);
            return dot;
        }
    }

public:
    SequenceAliData(const char* static_data, size_t elements, char stdgap, char dotgap, const SizeAwarable& sizeAware, const Deletable& deletable_)
        : SpecificAliData<char>(static_data, elements, stdgap, sizeAware, deletable_),
          dot(dotgap)
    {}

    AliDataPtr create_gap(size_t gapsize, const UnitPair& gapinfo) const OVERRIDE {
        char use = preferred_gap(typed_ptr(gapinfo.left), typed_ptr(gapinfo.right));
        return new SpecificGap<char>(gapsize, use);
    }
};

// --------------------------------------------------------------------------------
// @@@ move things below into a class ?

inline AliDataPtr concat(AliDataPtr left, AliDataPtr right) {
    return left->empty() ? right : (right->empty() ? left : new ComposedAliData(left, right));
}
inline AliDataPtr concat(AliDataPtr left, AliDataPtr mid, AliDataPtr right) {
    return concat(left, concat(mid, right));
}

inline AliDataPtr partof(AliDataPtr data, size_t pos, size_t amount) { return AliDataSlice::make(data, pos, amount); }
inline AliDataPtr before(AliDataPtr data, size_t pos) { return partof(data, 0, pos); }
inline AliDataPtr after(AliDataPtr data, size_t pos) { return partof(data, pos+1, data->elems()-pos-1); }

inline AliDataPtr delete_from(AliDataPtr from, size_t pos, size_t amount, GB_ERROR& error) {
    error = from->check_delete_allowed(pos, amount);
    return concat(before(from, pos), after(from, pos+amount-1));
}
inline AliDataPtr insert_at(AliDataPtr dest, size_t pos, AliDataPtr src) {
    return concat(before(dest, pos), src, after(dest, pos-1));
}

inline AliDataPtr insert_gap(AliDataPtr data, size_t pos, size_t count) {
    UnitPair gapinfo;

    id_assert(data->unitsize() <= sizeof(gapinfo.left));

    gapinfo.left  = data->unit_left_of(pos); // @@@ do not perform ALWAYS (put into an object and lazy eval)
    gapinfo.right = data->unit_right_of(pos);

    AliDataPtr gap = data->create_gap(count, gapinfo);
    return insert_at(data, pos, gap);
}

inline AliDataPtr format(AliDataPtr data, const size_t wanted_len, GB_ERROR& error) {
    size_t curr_len = data->elems();
    if (curr_len < wanted_len) {
        data = insert_gap(data, curr_len, wanted_len-curr_len);
    }
    else if (curr_len > wanted_len) {
        data = delete_from(data, wanted_len, curr_len-wanted_len, error);
    }
    id_assert(data->elems() == wanted_len);
    return data;
}


template<typename T> inline AliDataPtr makeAliData(T*& allocated_data, size_t elems, const T& gap) {
    return new SpecificAliData<T>(allocated_data, elems, gap, dontAllowOversize(elems), Deletable(Deletable::ANYTHING));
}
inline AliDataPtr makeAliSeqData(char*& allocated_data, size_t elems, char gap, char dot) {
    return new SequenceAliData(allocated_data, elems, gap, dot, dontAllowOversize(elems), Deletable(Deletable::ANYTHING));
}

// --------------------------------------------------------------------------------

#ifdef UNIT_TESTS
#ifndef TEST_UNIT_H
#include <test_unit.h>
#endif

template<typename T>
inline T*& copyof(const T* const_data, size_t elemsize, size_t elements) { // @@@ elemsize should be derived from type here (if possible)
    static T *copy = NULp;

    size_t memsize = elemsize*elements;
    id_assert(!copy);
    copy = (T*)ARB_alloc<char>(memsize);
    id_assert(copy);
    memcpy(copy, const_data, memsize);
    return copy;
}

#define COPYOF(typedarray) copyof(typedarray, sizeof(*(typedarray)), ARRAY_ELEMS(typedarray))
#define SIZEOF(typedarray) (sizeof(*(typedarray))*ARRAY_ELEMS(typedarray))

#define TEST_EXPECT_COPIES_EQUAL(d1,d2) do{                     \
        size_t  s1 = (d1)->memsize();                           \
        size_t  s2 = (d2)->memsize();                           \
        TEST_EXPECT_EQUAL(s1, s2);                              \
        void   *copy1 = ARB_alloc<char>(s1+s2);                 \
        void   *copy2 = reinterpret_cast<char*>(copy1)+s1;      \
        (d1)->copyTo(copy1);                                    \
        (d2)->copyTo(copy2);                                    \
        TEST_EXPECT_MEM_EQUAL(copy1, copy2, s1);                \
        free(copy1);                                            \
    }while(0)

#define TEST_EXPECT_COPY_EQUALS_ARRAY(adp,typedarray,asize) do{ \
        size_t  size    = (adp)->memsize();                     \
        TEST_EXPECT_EQUAL(size, asize);                         \
        void   *ad_copy = ARB_alloc<char*>(size);               \
        (adp)->copyTo(ad_copy);                                 \
        TEST_EXPECT_MEM_EQUAL(ad_copy, typedarray, size);       \
        free(ad_copy);                                          \
    }while(0)

#define TEST_EXPECT_COPY_EQUALS_STRING(adp,str) do{             \
        size_t  size    = (adp)->memsize();                     \
        char   *ad_copy = ARB_alloc<char>(size+1);              \
        (adp)->copyTo(ad_copy);                                 \
        ad_copy[size]   = 0;                                    \
        TEST_EXPECT_EQUAL(ad_copy, str);                        \
        free(ad_copy);                                          \
    }while(0)

#if defined(ENABLE_CRASH_TESTS) && defined(ASSERTION_USED)
static void illegal_alidata_composition() {
    const int ELEMS = 5;

    int  *i = ARB_alloc<int> (ELEMS);
    char *c = ARB_alloc<char>(ELEMS);

    concat(makeAliData(i, ELEMS, 0), makeAliData(c, ELEMS, '-'));
}
#endif

void TEST_illegal_alidata__crashtest() {
    TEST_EXPECT_CODE_ASSERTION_FAILS(illegal_alidata_composition);
}

template <typename T>
inline T *makeCopy(AliDataPtr d) {
    TEST_EXPECT_EQUAL(d->unitsize(), sizeof(T));
    size_t  size = d->memsize();
    T      *copy = (T*)ARB_alloc<char>(size);
    d->copyTo(copy);
    return copy;
}

template <typename T>
static arb_test::match_expectation compare_works(AliDataPtr d1, AliDataPtr d2, int expected_cmp) {
    int brute_force_compare = 0;
    {
        int minSize = std::min(d1->elems(), d2->elems());

        T *copy1 = makeCopy<T>(d1);
        T *copy2 = makeCopy<T>(d2);

        for (int i = 0; i < minSize && brute_force_compare == 0; ++i) { // compare inclusive terminal zero-element
            brute_force_compare = compare_type(copy1[i], copy2[i]);
        }

        if (brute_force_compare == 0) {
            brute_force_compare = compare_type(d1->elems(), d2->elems());
        }

        free(copy2);
        free(copy1);
    }

    int smart_forward_compare  = d1->cmp_whole_data(*d2);
    int smart_backward_compare = d2->cmp_whole_data(*d1);

    using namespace   arb_test;
    expectation_group expected;

    expected.add(that(brute_force_compare).is_equal_to(expected_cmp));
    expected.add(that(smart_forward_compare).is_equal_to(expected_cmp));
    expected.add(that(smart_backward_compare).is_equal_to(-expected_cmp));

    return all().ofgroup(expected);
}

#define TEST_COMPARE_WORKS(d1,d2,expected) TEST_EXPECTATION(compare_works<char>(d1,d2,expected))

#define TEST_COMPARE_WORKS_ALL_TYPES(tid,d1,d2,expected)                                \
    switch (tid) {                                                              \
        case 0: TEST_EXPECTATION(compare_works<char>(d1,d2,expected)); break;           \
        case 1: TEST_EXPECTATION(compare_works<GB_UINT4>(d1,d2,expected)); break;       \
        case 2: TEST_EXPECTATION(compare_works<float>(d1,d2,expected)); break;          \
    }

#if !defined(ENABLE_CRASH_TESTS)
static void avoid_INVALID_testExport() { avoid_INVALID_testExport(); } // avoids weird symbol-export-bug with stabs + !ENABLE_CRASH_TESTS (encountered with gcc 4.4.3)
#endif

__ATTR__REDUCED_OPTIMIZE void TEST_AliData() {
#define SEQDATA "CGCAC-C-GG-C-GG.A.-C------GG-.C..UCAGU"
    char      chr_src[] = SEQDATA; // also contains trailing 0-byte!
    GB_CUINT4 int_src[] = { 0x01, 0x1213, 0x242526, 0x37383930, 0xffffffff };
    float     flt_src[] = { 0.0, 0.5, 1.0, -5.0, 20.1 };

    AliDataPtr type[] = {
        makeAliSeqData(COPYOF(chr_src), ARRAY_ELEMS(chr_src)-1, '-', '.'),
        makeAliData(COPYOF(int_src), ARRAY_ELEMS(int_src), 0U),
        makeAliData(COPYOF(flt_src), ARRAY_ELEMS(flt_src), 0.0F)
    };
    TEST_EXPECT_COPY_EQUALS_ARRAY(type[0], chr_src, SIZEOF(chr_src)-1);
    TEST_EXPECT_COPY_EQUALS_STRING(type[0], chr_src);
    TEST_EXPECT_COPY_EQUALS_ARRAY(type[1], int_src, SIZEOF(int_src));
    TEST_EXPECT_COPY_EQUALS_ARRAY(type[2], flt_src, SIZEOF(flt_src));

    for (size_t t = 0; t<ARRAY_ELEMS(type); ++t) {
        AliDataPtr data  = type[t];
        AliDataPtr dup = concat(data, data);
        TEST_EXPECT_EQUAL(dup->elems(), 2*data->elems());

        AliDataPtr start = before(data, 3);
        TEST_EXPECT_EQUAL(start->elems(), 3U);

        AliDataPtr end = after(data, 3);
        TEST_EXPECT_EQUAL(end->elems(), data->elems()-4);

        AliDataPtr mid = partof(data, 3, 1);
        TEST_EXPECT_COPIES_EQUAL(concat(start, mid, end), data);

        GB_ERROR   error = NULp;
        AliDataPtr del   = delete_from(data, 3, 1, error);
        TEST_EXPECT_NO_ERROR(error);
        TEST_EXPECT_EQUAL(del->elems(), data->elems()-1);
        TEST_EXPECT_COPIES_EQUAL(concat(start, end), del);

        AliDataPtr empty = before(data, 0);
        TEST_EXPECT_EQUAL(empty->elems(), 0U);

        TEST_EXPECT_COPIES_EQUAL(data, concat(data, empty));
        TEST_EXPECT_COPIES_EQUAL(data, concat(empty, data));
        TEST_EXPECT_COPIES_EQUAL(empty, concat(empty, empty));

        AliDataPtr del_rest = delete_from(data, 3, 999, error);
        TEST_EXPECT_NO_ERROR(error);
        TEST_EXPECT_COPIES_EQUAL(start, del_rest);

        AliDataPtr ins = insert_at(del, 3, mid);
        TEST_EXPECT_COPIES_EQUAL(data, ins);
        TEST_EXPECT_COPIES_EQUAL(del, delete_from(ins, 3, 1, error));
        TEST_EXPECT_NO_ERROR(error);

        TEST_EXPECT_COPIES_EQUAL(insert_at(del, 3, empty), del);
        TEST_EXPECT_COPIES_EQUAL(insert_at(del, 777, empty), del); // append via insert_at
        TEST_EXPECT_COPIES_EQUAL(insert_at(start, 777, end), del); // append via insert_at

        AliDataPtr ins_gap = insert_gap(del, 4, 5);
        TEST_EXPECT_EQUAL(ins_gap->elems(), del->elems()+5);

        AliDataPtr gap_iseq = partof(ins_gap, 4, 5);

        TEST_EXPECT_COPIES_EQUAL(ins_gap, insert_gap(ins_gap, 7, 0)); // insert empty gap

        AliDataPtr start_gap1 = insert_gap(ins_gap, 0, 1); // insert gap at start
        AliDataPtr start_gap3 = insert_gap(ins_gap, 0, 3); // insert gap at start

        AliDataPtr gap_iempty = insert_gap(empty, 0, 5);
        TEST_EXPECT_EQUAL(gap_iempty->elems(), 5U);

        AliDataPtr gap_in_gap = insert_gap(gap_iempty, 3, 2);
        TEST_EXPECT_EQUAL(gap_in_gap->elems(), 7U);

        AliDataPtr end_gap1 = insert_gap(mid, 1, 1);
        TEST_EXPECT_EQUAL(end_gap1->elems(), 2U);

        if (t == 0) {
            AliDataPtr end_gap2 = insert_gap(end, 34, 2);

            TEST_EXPECT_COPY_EQUALS_STRING(start,      "CGC");
            TEST_EXPECT_COPY_EQUALS_STRING(end,        "C-C-GG-C-GG.A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(end_gap2,   "C-C-GG-C-GG.A.-C------GG-.C..UCAGU..");
            TEST_EXPECT_COPY_EQUALS_STRING(mid,        "A");
            TEST_EXPECT_COPY_EQUALS_STRING(end_gap1,   "A-");      // '-' is ok, since before there was a C behind (but correct would be '.')
            TEST_EXPECT_COPY_EQUALS_STRING(del,        "CGCC-C-GG-C-GG.A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(del_rest,   "CGC");
            TEST_EXPECT_COPY_EQUALS_STRING(ins,        "CGCAC-C-GG-C-GG.A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(gap_iseq,   "-----");   // inserted between bases
            TEST_EXPECT_COPY_EQUALS_STRING(gap_iempty, ".....");   // inserted in empty sequence
            TEST_EXPECT_COPY_EQUALS_STRING(gap_in_gap, "......."); // inserted gap in gap
            TEST_EXPECT_COPY_EQUALS_STRING(ins_gap,    "CGCC------C-GG-C-GG.A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(start_gap1, ".CGCC------C-GG-C-GG.A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(start_gap3, "...CGCC------C-GG-C-GG.A.-C------GG-.C..UCAGU");

            AliDataPtr bef_dot     = insert_gap(ins, 15, 2);
            AliDataPtr aft_dot     = insert_gap(ins, 16, 2);
            AliDataPtr bet_dots    = insert_gap(ins, 32, 2);
            AliDataPtr bet_dashes  = insert_gap(ins, 23, 2);
            AliDataPtr bet_dashdot = insert_gap(ins, 29, 2);
            AliDataPtr bet_dotdash = insert_gap(ins, 18, 2);

            TEST_EXPECT_COPY_EQUALS_STRING(ins,        "CGCAC-C-GG-C-GG.A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(bef_dot,    "CGCAC-C-GG-C-GG...A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(aft_dot,    "CGCAC-C-GG-C-GG...A.-C------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(bet_dots,   "CGCAC-C-GG-C-GG.A.-C------GG-.C....UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(bet_dashes, "CGCAC-C-GG-C-GG.A.-C--------GG-.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(bet_dashdot,"CGCAC-C-GG-C-GG.A.-C------GG---.C..UCAGU");
            TEST_EXPECT_COPY_EQUALS_STRING(bet_dotdash,"CGCAC-C-GG-C-GG.A.---C------GG-.C..UCAGU");

            {
                // test comparability of AliData

                AliDataPtr same_as_start_gap1 = after(start_gap3, 1);

                TEST_COMPARE_WORKS(start_gap1, same_as_start_gap1, 0);

                TEST_EXPECT(start_gap1->differs_from(*start_gap3));
                // TEST_EXPECT_EQUAL(strcmp(".CGCC------C-GG-C-GG.A.-C------GG-.C..UCAGU",        // start_gap1
                                         // "...CGCC------C-GG-C-GG.A.-C------GG-.C..UCAGU"), 1); // start_gap3

                TEST_EXPECT_EQUAL(start_gap1->cmp_whole_data(*start_gap3),  1);
                TEST_EXPECT_EQUAL(start_gap3->cmp_whole_data(*start_gap1), -1);

                TEST_COMPARE_WORKS(end, end_gap2, -1);
            }
        }

        {
            // test comparability of AliData (for all types)

            TEST_COMPARE_WORKS_ALL_TYPES(t, start_gap1, start_gap3, 1);
            TEST_COMPARE_WORKS_ALL_TYPES(t, gap_iempty, gap_in_gap, -1);
            TEST_COMPARE_WORKS_ALL_TYPES(t, del, ins, 1);
            TEST_COMPARE_WORKS_ALL_TYPES(t, partof(ins_gap, 0, 17), partof(start_gap3, 3, 17), 0);
            TEST_COMPARE_WORKS_ALL_TYPES(t, start_gap3, start_gap3, 0);
        }
    }

}

#endif // UNIT_TESTS

// --------------------------------------------------------------------------------

enum TerminalType {
    IDT_SPECIES = 0,
    IDT_SAI,
    IDT_SECSTRUCT,
};

static GB_CSTR targetTypeName[] = {
    "Species",
    "SAI",
    "SeceditStruct",
};

class Alignment {
    SmartCharPtr name; // name of alignment
    size_t       len;  // length of alignment
public:
    Alignment(const char *name_, size_t len_) : name(strdup(name_)), len(len_) {}

    const char *get_name() const { return &*name; }
    size_t get_len() const { return len; }
};

// --------------------------------------------------------------------------------

class AliApplicable { // something that can be appied to the whole alignment
    virtual GB_ERROR apply_to_terminal(GBDATA *gb_data, TerminalType term_type, const char *item_name, const Alignment& ali) const = 0;

    GB_ERROR apply_recursive(GBDATA *gb_data, TerminalType term_type, const char *item_name, const Alignment& ali) const;
    GB_ERROR apply_to_childs_named(GBDATA *gb_item_data, const char *item_field, TerminalType term_type, const Alignment& ali) const;
    GB_ERROR apply_to_secstructs(GBDATA *gb_secstructs, const Alignment& ali) const;

public:
    AliApplicable() {}
    virtual ~AliApplicable() {}

    GB_ERROR apply_to_alignment(GBDATA *gb_main, const Alignment& ali) const;
};

GB_ERROR AliApplicable::apply_recursive(GBDATA *gb_data, TerminalType term_type, const char *item_name, const Alignment& ali) const {
    GB_ERROR error = NULp;
    GB_TYPES type  = GB_read_type(gb_data);

    if (type == GB_DB) {
        GBDATA *gb_child;
        for (gb_child = GB_child(gb_data); gb_child && !error; gb_child = GB_nextChild(gb_child)) {
            error = apply_recursive(gb_child, term_type, item_name, ali);
        }
    }
    else {
        error = apply_to_terminal(gb_data, term_type, item_name, ali);
    }

    return error;
}
GB_ERROR AliApplicable::apply_to_childs_named(GBDATA *gb_item_data, const char *item_field, TerminalType term_type, const Alignment& ali) const {
    GBDATA   *gb_item;
    GB_ERROR  error      = NULp;
    long      item_count = GB_number_of_subentries(gb_item_data);

    if (item_count) {
        for (gb_item = GB_entry(gb_item_data, item_field);
             gb_item && !error;
             gb_item = GB_nextEntry(gb_item))
        {
            GBDATA *gb_ali = GB_entry(gb_item, ali.get_name());
            if (gb_ali) {
                const char *item_name = GBT_read_name(gb_item);
                error = apply_recursive(gb_ali, term_type, item_name, ali);
                if (error) error = GBS_global_string("%s '%s': %s", targetTypeName[term_type], item_name, error);
            }
        }
    }
    return error;
}
GB_ERROR AliApplicable::apply_to_secstructs(GBDATA *gb_secstructs, const Alignment& ali) const {
    GB_ERROR  error  = NULp;
    GBDATA   *gb_ali = GB_entry(gb_secstructs, ali.get_name());

    if (gb_ali) {
        long item_count = GB_number_of_subentries(gb_ali)-1;
        if (item_count<1) item_count = 1;

        GBDATA *gb_item;
        for (gb_item = GB_entry(gb_ali, "struct");
             gb_item && !error;
             gb_item = GB_nextEntry(gb_item))
        {
            GBDATA *gb_ref = GB_entry(gb_item, "ref");
            if (gb_ref) {
                error = apply_recursive(gb_ref, IDT_SECSTRUCT, "ref", ali);
                if (error) {
                    const char *item_name = GBT_read_name(gb_item);
                    error = GBS_global_string("%s '%s': %s", targetTypeName[IDT_SECSTRUCT], item_name, error);
                }
            }
        }
    }
    return error;
}

GB_ERROR AliApplicable::apply_to_alignment(GBDATA *gb_main, const Alignment& ali) const {
    GB_ERROR error    = apply_to_childs_named(GBT_find_or_create(gb_main, "extended_data", 7), "extended", IDT_SAI,     ali);
    if (!error) error = apply_to_secstructs(GB_search(gb_main, "secedit/structs", GB_CREATE_CONTAINER), ali);
    if (!error) error = apply_to_childs_named(GBT_find_or_create(gb_main, "species_data",  7), "species",  IDT_SPECIES, ali);
    return error;
}

// --------------------------------------------------------------------------------

class AliEntryCounter : public AliApplicable {
    mutable size_t count;
    GB_ERROR apply_to_terminal(GBDATA *, TerminalType, const char *, const Alignment&) const OVERRIDE { count++; return NULp; }
public:
    AliEntryCounter() : count(0) {}
    size_t get_entry_count() const { return count; }
};

// --------------------------------------------------------------------------------

struct AliEditCommand {
    virtual ~AliEditCommand() {}
    virtual AliDataPtr apply(AliDataPtr to, GB_ERROR& error) const                                 = 0;
    virtual GB_ERROR check_applicable_to(const Alignment& ali, size_t& resulting_ali_length) const = 0;
};

class AliInsertCommand : public AliEditCommand {
    size_t pos; // inserts in front of pos
    size_t amount;
public:
    AliInsertCommand(size_t pos_, size_t amount_) : pos(pos_), amount(amount_) {}
    AliDataPtr apply(AliDataPtr to, GB_ERROR& /*error*/) const OVERRIDE { return insert_gap(to, pos, amount); }
    GB_ERROR check_applicable_to(const Alignment& ali, size_t& resulting_ali_length) const OVERRIDE {
        size_t len = ali.get_len();
        if (pos>len) {
            return GBS_global_string("Can't insert at position %zu (exceeds length %zu of alignment '%s')",
                                     pos, len, ali.get_name());
        }
        resulting_ali_length = len+amount;
        return NULp;
    }
};

class AliDeleteCommand : public AliEditCommand {
    size_t pos;
    size_t amount;
public:
    AliDeleteCommand(size_t pos_, size_t amount_)
        : pos(pos_),
          amount(amount_)
    {}
    AliDataPtr apply(AliDataPtr to, GB_ERROR& error) const OVERRIDE { return delete_from(to, pos, amount, error); }
    GB_ERROR check_applicable_to(const Alignment& ali, size_t& resulting_ali_length) const OVERRIDE {
        size_t len     = ali.get_len();
        size_t end_pos = pos+amount-1;
        if (end_pos >= len) {
            return GBS_global_string("Can't delete positions %zu-%zu (exceeds max. position %zu of alignment '%s')",
                                     pos, end_pos, len-1, ali.get_name());
        }
        resulting_ali_length = len-amount;
        return NULp;
    }
};

class AliFormatCommand FINAL_TYPE : public AliEditCommand {
    size_t wanted_len;

public:
    AliFormatCommand(size_t wanted_len_) : wanted_len(wanted_len_) {}
    AliDataPtr apply(AliDataPtr to, GB_ERROR& error) const OVERRIDE {
        SizeAwarable *knows_size = dynamic_cast<SizeAwarable*>(&*to);

        id_assert(knows_size); // format can only be applied to SpecificAliData
                               // i.e. AliFormatCommand has to be the FIRST of a series of applied commands!

        int allowed_size = knows_size->get_allowed_size(to->elems(), wanted_len);
        return format(to, allowed_size, error);
    }
    GB_ERROR check_applicable_to(const Alignment& IF_ASSERTION_USED(ali), size_t& resulting_ali_length) const OVERRIDE {
        id_assert(ali.get_len() == wanted_len);
        resulting_ali_length     = wanted_len;
        return NULp;
    }
};

class AliAutoFormatCommand : public AliEditCommand {
    mutable SmartPtr<AliFormatCommand> cmd;
public:
    AliDataPtr apply(AliDataPtr to, GB_ERROR& error) const OVERRIDE {
        return cmd->apply(to, error);
    }
    GB_ERROR check_applicable_to(const Alignment& ali, size_t& resulting_ali_length) const OVERRIDE {
        cmd = new AliFormatCommand(ali.get_len()); // late decision on length to format
        return cmd->check_applicable_to(ali, resulting_ali_length);
    }
};

class AliCompositeCommand : public AliEditCommand, virtual Noncopyable {
    AliEditCommand *first;
    AliEditCommand *second;
public:
    AliCompositeCommand(AliEditCommand *cmd1_, AliEditCommand *cmd2_) // takes ownership of commands
        : first(cmd1_),
          second(cmd2_)
    {}
    ~AliCompositeCommand() OVERRIDE { delete second; delete first; }
    AliDataPtr apply(AliDataPtr to, GB_ERROR& error) const OVERRIDE {
        AliDataPtr tmp = first->apply(to, error);
        if (!error) tmp = second->apply(tmp, error);
        return tmp;
    }
    GB_ERROR check_applicable_to(const Alignment& ali, size_t& resulting_ali_length) const OVERRIDE {
        GB_ERROR error = first->check_applicable_to(ali, resulting_ali_length);
        if (!error) {
            Alignment tmp_ali(ali.get_name(), resulting_ali_length);
            error = second->check_applicable_to(tmp_ali, resulting_ali_length);
        }
        return error;
    }
};

// --------------------------------------------------------------------------------

class AliEditor : public AliApplicable {
    const AliEditCommand& cmd;
    Deletable             deletable;

    mutable arb_progress progress;
    mutable size_t       modified_counter;

    GB_ERROR apply_to_terminal(GBDATA *gb_data, TerminalType term_type, const char *item_name, const Alignment& ali) const OVERRIDE;

    bool shall_edit(GBDATA *gb_data, TerminalType term_type) const {
        // defines whether specific DB-elements shall be edited by any AliEditor
        // (true for all data, that contains alignment position specific data)

        const char *key   = GB_read_key_pntr(gb_data);
        bool        shall = key[0] != '_';                                    // general case: don't apply to keys starting with '_'
        if (!shall) shall = term_type == IDT_SAI && strcmp(key, "_REF") == 0; // exception (SAI:_REF needs editing)
        return shall;
    }

public:
    AliEditor(const AliEditCommand& cmd_, const Deletable& deletable_, const char *progress_title, size_t progress_count)
        : cmd(cmd_),
          deletable(deletable_),
          progress(progress_title, progress_count),
          modified_counter(0)
    {}
    ~AliEditor() OVERRIDE {
        progress.done();
    }

    const AliEditCommand& edit_command() const { return cmd; }
};

// --------------------------------------------------------------------------------

static char   *insDelBuffer = NULp;
static size_t  insDelBuffer_size;

inline void free_insDelBuffer() {
    freenull(insDelBuffer);
}
inline char *provide_insDelBuffer(size_t neededSpace) {
    if (insDelBuffer && insDelBuffer_size<neededSpace) free_insDelBuffer();
    if (!insDelBuffer) {
        insDelBuffer_size = neededSpace+10;
        insDelBuffer      = ARB_alloc<char>(insDelBuffer_size);
    }
    return insDelBuffer;
}

inline GB_CSTR alidata2buffer(const AliData& data) { // @@@ DRY vs copying code (above in this file)
    char *buffer = provide_insDelBuffer(data.memsize()+1);

    data.copyTo(buffer);
    buffer[data.memsize()] = 0; // only needed for strings but does not harm otherwise

    return buffer;
}

// --------------------------------------------------------------------------------

class EditedTerminal;

class LazyAliData : public AliData, public SizeAwarable, virtual Noncopyable {
    // internally transforms into SpecificAliData as soon as somebody tries to access the data.
    // (implements lazy loading of sequence data, esp. useful when applying AliFormatCommand; see #702)

    TerminalType       term_type;
    EditedTerminal&    terminal;
    mutable AliDataPtr loaded; // always is TypedAliData<T>

    AliDataPtr loaded_data() const {
        if (loaded.isNull()) load_data();
        return loaded;
    }

public:
    LazyAliData(const SizeAwarable& oversizable, size_t size_, TerminalType term_type_, EditedTerminal& terminal_)
        : AliData(size_),
          SizeAwarable(oversizable),
          term_type(term_type_),
          terminal(terminal_)
    {}

    size_t unitsize() const OVERRIDE {
        // Note: information also known by EditedTerminal (only depends on data-type)
        // No need to load data (doesnt harm atm as data is always used for more atm)
        return loaded_data()->unitsize();
    }
    bool has_slice() const OVERRIDE {
        id_assert(loaded_data()->has_slice() == false); // TypedAliData<T> never has_slice()!
        return false;
    }

    int operate_on_mem(void *mem, size_t start, size_t count, memop op) const OVERRIDE { return loaded_data()->operate_on_mem(mem, start, count, op); }
    int cmp_data(size_t start, const AliData& other, size_t ostart, size_t count) const OVERRIDE { return loaded_data()->cmp_data(start, other, ostart, count); }

    UnitPtr unit_left_of(size_t pos) const OVERRIDE { return loaded_data()->unit_left_of(pos); }
    UnitPtr unit_right_of(size_t pos) const OVERRIDE { return loaded_data()->unit_right_of(pos); }

    AliDataPtr create_gap(size_t gapsize, const UnitPair& gapinfo) const OVERRIDE { return loaded_data()->create_gap(gapsize, gapinfo); }
    __ATTR__NORETURN AliDataPtr slice_down(size_t /*start*/, size_t /*count*/) const OVERRIDE {
        GBK_terminate("logic error: slice_down called for explicit LazyAliData");
    }

    void load_data() const; // has to be public to be a friend of EditedTerminal
};

// --------------------------------------------------------------------------------

class EditedTerminal : virtual Noncopyable {
    GBDATA     *gb_data;
    GB_TYPES    type;
    const char *item_name; // name of SAI/species etc
    AliDataPtr  data;
    Deletable   deletable;
    GB_ERROR    error;

    bool has_key(const char *expected_key) const {
        return strcmp(GB_read_key_pntr(gb_data), expected_key) == 0;
    }
    bool has_name(const char *expected_name) const {
        return strcmp(item_name, expected_name) == 0;
    }

    bool is_ref(TerminalType term_type) const {
        return
            type == GB_STRING &&
            ((term_type == IDT_SECSTRUCT && has_key("ref")) ||
             (term_type == IDT_SAI && has_key("_REF")));
    }
    bool is_helix(TerminalType term_type) const {
        return
            type == GB_STRING &&
            term_type == IDT_SAI &&
            (has_name("HELIX") || has_name("HELIX_NR")) &&
            has_key("data");
    }

    bool does_allow_oversize(TerminalType term_type) const { return is_ref(term_type); }
    char get_std_string_gaptype(TerminalType term_type) const {
        bool prefers_dots = is_ref(term_type) || is_helix(term_type);
        return prefers_dots ? '.' : '-';
    }

    AliDataPtr load_data(const SizeAwarable& oversizable, size_t size_, TerminalType term_type) {
        switch(type) {
            case GB_STRING: {
                const char *s = GB_read_char_pntr(gb_data);
                if (!s) error = GB_await_error();
                else {
                    char stdgap             = get_std_string_gaptype(term_type);
                    if (stdgap == '.') data = new SpecificAliData<char>(s, size_, '.', oversizable, deletable);
                    else data               = new SequenceAliData(s, size_, stdgap, '.', oversizable, deletable);
                }
                break;
            }
            case GB_BITS:   {
                const char *b    = GB_read_bits_pntr(gb_data, '-', '+');
                if (!b) error    = GB_await_error();
                else        data = new SpecificAliData<char>(b, size_, '-', oversizable, deletable);
                break;
            }
            case GB_BYTES:  {
                const char *b    = GB_read_bytes_pntr(gb_data);
                if (!b) error    = GB_await_error();
                else        data = new SpecificAliData<char>(b, size_, 0, oversizable, deletable);
                break;
            }
            case GB_INTS:   {
                const GB_UINT4 *ui   = GB_read_ints_pntr(gb_data);
                if (!ui) error       = GB_await_error();
                else            data = new SpecificAliData<GB_UINT4>(ui, size_, 0, oversizable, deletable);
                break;
            }
            case GB_FLOATS: {
                const float *f    = GB_read_floats_pntr(gb_data);
                if (!f) error     = GB_await_error();
                else         data = new SpecificAliData<float>(f, size_, 0.0, oversizable, deletable);
                break;
            }

            default:
                error = GBS_global_string("Unhandled type '%i'", type);
                id_assert(0);
                break;
        }

        id_assert(implicated(!error, size_ == data->elems()));
        return data;
    }

    friend void LazyAliData::load_data() const;

public:
    EditedTerminal(GBDATA *gb_data_, GB_TYPES type_, const char *item_name_, size_t size_, TerminalType term_type, const Alignment& ali, const Deletable& deletable_)
        : gb_data(gb_data_),
          type(type_),
          item_name(item_name_),
          deletable(deletable_),
          error(NULp)
    {
        SizeAwarable oversizable(does_allow_oversize(term_type), ali.get_len());
        data = new LazyAliData(oversizable, size_, term_type, *this);
    }

    GB_ERROR apply(const AliEditCommand& cmd, bool& did_modify) {
        did_modify = false;
        if (!error) {
            AliDataPtr modified_data = cmd.apply(data, error);

            if (!error && modified_data->differs_from(*data)) {
                GB_CSTR modified       = alidata2buffer(*modified_data);
                size_t  modified_elems = modified_data->elems();

                switch (type) {
                    case GB_STRING: {
                        id_assert(strlen(modified) == modified_elems);
                        error = GB_write_string(gb_data, modified);
                        break;
                    }
                    case GB_BITS:   error = GB_write_bits  (gb_data, modified, modified_elems, "-");       break;
                    case GB_BYTES:  error = GB_write_bytes (gb_data, modified, modified_elems);            break;
                    case GB_INTS:   error = GB_write_ints  (gb_data, (GB_UINT4*)modified, modified_elems); break;
                    case GB_FLOATS: error = GB_write_floats(gb_data, (float*)modified, modified_elems);    break;

                    default: id_assert(0); break;
                }

                if (!error) did_modify = true;
            }
        }
        return error;
    }
};

void LazyAliData::load_data() const {
    loaded = terminal.load_data(*this, elems(), term_type);
}

GB_ERROR AliEditor::apply_to_terminal(GBDATA *gb_data, TerminalType term_type, const char *item_name, const Alignment& ali) const {
    GB_TYPES gbtype  = GB_read_type(gb_data);
    GB_ERROR error = NULp;
    if (gbtype >= GB_BITS && gbtype != GB_OBSOLETE) {
        if (shall_edit(gb_data, term_type)) {
            EditedTerminal edited(gb_data, gbtype, item_name, GB_read_count(gb_data), term_type, ali, deletable);

            bool terminal_was_modified;
            error = edited.apply(edit_command(), terminal_was_modified);
            if (terminal_was_modified) {
                progress.subtitle(GBS_global_string("modified: %zu", ++modified_counter));
            }
        }
    }
    progress.inc_and_check_user_abort(error);
    return error;
}

// --------------------------------------------------------------------------------

static size_t countAffectedEntries(GBDATA *Main, const Alignment& ali) {
    AliEntryCounter counter;
    counter.apply_to_alignment(Main, ali);
    return counter.get_entry_count();
}

static GB_ERROR apply_command_to_alignment(const AliEditCommand& cmd, const char *cmd_description, GBDATA *Main, const char *alignment_name, const char *deletable_chars) {
    // applies 'cmd' to one or all alignments
    // (if 'alignment_name' is NULp, all alignments are affected - probably useless case)
    //
    // 'deletable_chars' is either
    // - NULp -> nothing may be deleted
    // - "%" -> anything may be deleted
    // - or a string containing all deletable characters

    Deletable deletable =
        deletable_chars
        ? ( strchr(deletable_chars, '%')
            ? Deletable(Deletable::ANYTHING)
            : Deletable(deletable_chars))
        : Deletable(Deletable::NOTHING);

    GB_ERROR  error      = NULp;
    GBDATA   *gb_presets = GBT_get_presets(Main);

    for (GBDATA *gb_ali = GB_entry(gb_presets, "alignment");
         gb_ali && !error;
         gb_ali = GB_nextEntry(gb_ali))
    {
        GBDATA *gb_name = GB_find_string(gb_ali, "alignment_name", alignment_name, GB_IGNORE_CASE, SEARCH_CHILD);

        if (gb_name) {
            GBDATA    *gb_len = GB_entry(gb_ali, "alignment_len");
            Alignment  ali(GB_read_char_pntr(gb_name), GB_read_int(gb_len));

            size_t resulting_ali_length;
            error = cmd.check_applicable_to(ali, resulting_ali_length);

            if (!error) error = AliEditor(cmd, deletable, cmd_description, countAffectedEntries(Main, ali)).apply_to_alignment(Main, ali);
            if (!error) error = GB_write_int(gb_len, resulting_ali_length);
        }
    }

    free_insDelBuffer();

    if (!error) GB_disable_quicksave(Main, "a lot of sequences changed"); // @@@ only disable if a reasonable amount of sequences has changed!

    return error;
}

static GB_ERROR format_to_alilen(GBDATA *Main, const char *alignment_name) { // @@@ inline
    AliAutoFormatCommand fcmd;
    return apply_command_to_alignment(fcmd, "Formatting alignment", Main, alignment_name, "-.");
}

GB_ERROR ARB_format_alignment(GBDATA *Main, const char *alignment_name) {
    GB_ERROR err = NULp;

    if (strcmp(alignment_name, GENOM_ALIGNMENT) != 0) {         // NEVER EVER format 'ali_genom'
        err           = GBT_check_data(Main, alignment_name);   // detect max. length
        if (!err) err = format_to_alilen(Main, alignment_name); // format sequences in alignment
        if (!err) err = GBT_check_data(Main, alignment_name);   // sets state to "formatted"
    }
    else {
        err = "It's forbidden to format '" GENOM_ALIGNMENT "'!";
    }
    return err;
}

GB_ERROR ARB_insdel_columns(GBDATA *Main, const char *alignment_name, long pos, long count, const char *deletable_chars) {
    /* if count > 0     insert 'count' characters at pos
     * if count < 0     delete pos to pos+|count|
     *
     * Note: deleting is only performed, if found characters in deleted range are listed in 'deletable_chars'
     *       otherwise function returns with an error.
     *       (if 'deletable_chars' contains a '%', any character will be deleted)
     *
     * This affects all species' and SAIs having data in given 'alignment_name' and
     * modifies several data entries found there
     * (see shall_edit() for details which fields are affected).
     */

    GB_ERROR error = NULp;

    if (pos<0) {
        error = GBS_global_string("Illegal sequence position %li", pos);
    }
    else {
        const char *description = NULp;

        SmartPtr<AliEditCommand> idcmd;
        if (count<0) {
            idcmd       = new AliDeleteCommand(pos, -count);
            description = "Deleting columns";
        }
        else {
            idcmd = new AliInsertCommand(pos, count);
            description = "Inserting columns";
        }

        error = apply_command_to_alignment(*idcmd, description, Main, alignment_name, deletable_chars);
    }
    return error;
}

// AISC_MKPT_PROMOTE:class RangeList;
// AISC_MKPT_PROMOTE:enum UseRange { RANGES, SINGLE_COLUMNS };
// AISC_MKPT_PROMOTE:enum InsertWhere { INFRONTOF, BEHIND };

GB_ERROR ARB_delete_columns_using_SAI(GBDATA *Main, const char *alignment_name, const RangeList& ranges, const char *deletable_chars) {
    // Deletes all columns defined by 'ranges'
    // from all members (SAIs, seqs, ..) of alignment named 'alignment_name'.

    GB_ERROR error;
    if (ranges.empty()) {
        error = "Done with deleting nothing :)";
    }
    else {
        AliEditCommand *cmd = new AliAutoFormatCommand; // @@@ use SmartPtr (here and in AliCompositeCommand)
        for (RangeList::reverse_iterator r = ranges.rbegin(); r != ranges.rend(); ++r) {
            cmd = new AliCompositeCommand(cmd, new AliDeleteCommand(r->start(), r->size()));
        }
        error = apply_command_to_alignment(*cmd, "Deleting columns using SAI", Main, alignment_name, deletable_chars);
        delete cmd;
    }
    return error;
}

GB_ERROR ARB_insert_columns_using_SAI(GBDATA *Main, const char *alignment_name, const RangeList& ranges, UseRange units, InsertWhere where, size_t amount) {
    // Insert 'amount' columns into all members of the alignment named 'alignment_name'.
    //
    // If units is
    // - RANGES, each range
    // - SINGLE_COLUMNS, each column of each range
    // is handled as a unit.
    //
    // InsertWhere specifies whether the insertion happens INFRONTOF or BEHIND

    GB_ERROR error;
    if (!amount || ranges.empty()) {
        error = "Done with inserting no gaps :)";
    }
    else {
        AliEditCommand *cmd = new AliAutoFormatCommand; // @@@ use SmartPtr (here and in AliCompositeCommand)
        for (RangeList::reverse_iterator r = ranges.rbegin(); r != ranges.rend(); ++r) {
            switch (units) {
                case RANGES: {
                    int pos = 0;
                    switch (where) {
                        case INFRONTOF: pos = r->start(); break;
                        case BEHIND:    pos = r->end()+1; break;
                    }
                    cmd = new AliCompositeCommand(cmd, new AliInsertCommand(pos, amount));
                    break;
                }
                case SINGLE_COLUMNS: {
                    for (int pos = r->end(); pos >= r->start(); --pos)  {
                        cmd = new AliCompositeCommand(cmd, new AliInsertCommand(where == INFRONTOF ? pos : pos+1, amount));
                    }
                    break;
                }
            }
        }
        error = apply_command_to_alignment(*cmd, "Inserting columns using SAI", Main, alignment_name, NULp);
        delete cmd;
    }
    return error;
}

// --------------------------------------------------------------------------------

#ifdef UNIT_TESTS
#ifndef TEST_UNIT_H
#include <test_unit.h>
#endif
#include <arb_unit_test.h>

#define PLAIN_APPLY_CMD(str,cmd)                                                                                        \
    size_t     str_len = strlen(str);                                                                                   \
    AliDataPtr data    = new SequenceAliData(str, str_len, '-', '.', dontAllowOversize(str_len), Deletable("-."));      \
    GB_ERROR   error   = NULp;                                                                                          \
    AliDataPtr mod     = cmd.apply(data, error)

#define APPLY_CMD(str,cmd)                                                      \
    PLAIN_APPLY_CMD(str, cmd);                                                  \
    TEST_EXPECT_NO_ERROR(error);                                                \
    GB_CSTR    res     = mod->differs_from(*data) ? alidata2buffer(*mod) : NULp

#define DO_FORMAT(str,wanted_len)       \
    AliFormatCommand cmd(wanted_len);   \
    APPLY_CMD(str, cmd)

#define DO_INSERT(str,pos,amount)       \
    AliInsertCommand cmd(pos, amount);  \
    APPLY_CMD(str, cmd)

#define DO_FORMAT_AND_INSERT(str,wanted_len,pos,amount)         \
    AliCompositeCommand cmd(new AliFormatCommand(wanted_len),   \
                            new AliInsertCommand(pos,amount));  \
    APPLY_CMD(str, cmd)

#define DO_DELETE(str,pos,amount)       \
    AliDeleteCommand cmd(pos, amount);  \
    APPLY_CMD(str, cmd)

#define TEST_FORMAT(str,wanted_alilen,expected)         do { DO_FORMAT(str,wanted_alilen); TEST_EXPECT_EQUAL(res, expected);         } while(0)
#define TEST_FORMAT__BROKEN(str,wanted_alilen,expected) do { DO_FORMAT(str,wanted_alilen); TEST_EXPECT_EQUAL__BROKEN(res, expected); } while(0)

#define TEST_INSERT(str,pos,amount,expected)         do { DO_INSERT(str,pos,amount); TEST_EXPECT_EQUAL(res, expected);         } while(0)
#define TEST_INSERT__BROKEN(str,pos,amount,expected) do { DO_INSERT(str,pos,amount); TEST_EXPECT_EQUAL__BROKEN(res, expected); } while(0)

#define TEST_DELETE(str,pos,amount,expected)         do { DO_DELETE(str,pos,amount); TEST_EXPECT_EQUAL(res, expected);         } while(0)
#define TEST_DELETE__BROKEN(str,pos,amount,expected) do { DO_DELETE(str,pos,amount); TEST_EXPECT_EQUAL__BROKEN(res, expected); } while(0)

#define TEST_FORMAT_AND_INSERT(str,wanted_alilen,pos,amount,expected)         do { DO_FORMAT_AND_INSERT(str,wanted_alilen,pos,amount); TEST_EXPECT_EQUAL(res, expected);         } while(0)
#define TEST_FORMAT_AND_INSERT__BROKEN(str,wanted_alilen,pos,amount,expected) do { DO_FORMAT_AND_INSERT(str,wanted_alilen,pos,amount); TEST_EXPECT_EQUAL__BROKEN(res, expected); } while(0)

#define TEST_FORMAT_ERROR(str,wanted_alilen,exp_err) do {        \
        AliFormatCommand cmd(wanted_alilen);                     \
        PLAIN_APPLY_CMD(str, cmd);                               \
        TEST_EXPECT_ERROR_CONTAINS(error, exp_err);              \
    } while(0)

#define TEST_DELETE_ERROR(str,pos,amount,exp_err) do {           \
        AliDeleteCommand cmd(pos, amount);                       \
        PLAIN_APPLY_CMD(str, cmd);                               \
        TEST_EXPECT_ERROR_CONTAINS(error, exp_err);              \
    } while(0)


// --------------------------------------------------------------------------------

void TEST_format_insert_delete() {
    // this test is a bit weird.
    //
    // originally it was used to test the function gbt_insert_delete, which is gone now.
    // now it tests AliFormatCommand, AliInsertCommand, AliDeleteCommand and AliCompositeCommand (but quite implicit).

    const char *UNMODIFIED = NULp;

    TEST_FORMAT("xxx",   5, "xxx..");
    TEST_FORMAT(".x.",   5, ".x...");
    TEST_FORMAT(".x..",  5, ".x...");
    TEST_FORMAT(".x...", 5, UNMODIFIED);

    TEST_FORMAT("xxx--", 3, "xxx");
    TEST_FORMAT("xxx..", 3, "xxx");
    TEST_FORMAT_ERROR("xxxxx", 3, "You tried to delete 'x' at position 3  -> Operation aborted");
    TEST_FORMAT_ERROR("xxx",   0, "You tried to delete 'x' at position 0  -> Operation aborted");

    // insert/delete in the middle
    TEST_INSERT("abcde", 3, 0, UNMODIFIED);
    TEST_INSERT("abcde", 3, 1, "abc-de");
    TEST_INSERT("abcde", 3, 2, "abc--de");

    TEST_DELETE("abcde",   3, 0, UNMODIFIED);
    TEST_DELETE("abc-de",  3, 1, "abcde");
    TEST_DELETE("abc--de", 3, 2, "abcde");
    TEST_DELETE_ERROR("abc-xde", 3, 2, "You tried to delete 'x' at position 4  -> Operation aborted");

    // insert/delete at end
    TEST_INSERT("abcde", 5, 1, "abcde.");
    TEST_INSERT("abcde", 5, 4, "abcde....");

    TEST_DELETE("abcde-",    5, 1, "abcde");
    TEST_DELETE("abcde----", 5, 4, "abcde");

    // insert/delete at start
    TEST_INSERT("abcde", 0, 1, ".abcde");
    TEST_INSERT("abcde", 0, 4, "....abcde");

    TEST_DELETE("-abcde",    0, 1, "abcde");
    TEST_DELETE("----abcde", 0, 4, "abcde");

    // insert behind end
    TEST_FORMAT_AND_INSERT("abcde", 10, 8, 1, "abcde......");
    TEST_FORMAT_AND_INSERT("abcde", 10, 8, 4, "abcde.........");

    // insert/delete all
    TEST_INSERT("",    0, 3, "...");
    TEST_DELETE("---", 0, 3, "");

    free_insDelBuffer();
}

// ------------------------------

static struct arb_unit_test::test_alignment_data TADinsdel[] = {
    { 1, "MtnK1722", "...G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUCACCUCC....." },
    { 1, "MhnFormi", "---A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU....." },
    { 1, "MhnT1916", "...A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU----" },
};

static struct arb_unit_test::test_alignment_data EXTinsdel[] = {
    { 0, "ECOLI",    "---U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCCCACCUGA...." },
    { 0, "HELIX",    ".....[<[.........[..[..[<<.[..].>>]....]..]....].>......]" },
    { 0, "HELIX_NR", ".....1.1.........25.25.34..34.34..34...25.25...1........1" },
};

#define HELIX_REF    ".....x..x........x...x.x....x.x....x...x...x...x.........x"
#define HELIX_STRUCT "VERSION=3\nLOOP={etc.pp\n}\n"

static const char *read_item_entry(GBDATA *gb_item, const char *ali_name, const char *entry_name) {
    const char *result = NULp;
    if (gb_item) {
        GBDATA *gb_ali = GB_find(gb_item, ali_name, SEARCH_CHILD);
        if (gb_ali) {
            GBDATA *gb_entry = GB_entry(gb_ali, entry_name);
            if (gb_entry) {
                result = GB_read_char_pntr(gb_entry);
            }
        }
    }
    if (!result) TEST_EXPECT_NO_ERROR(GB_await_error());
    return result;
}
static char *ints2string(const GB_UINT4 *ints, size_t count) {
    char *str = ARB_alloc<char>(count+1);
    for (size_t c = 0; c<count; ++c) { // IRRELEVANT_LOOP
        str[c] = (ints[c]<10) ? ints[c]+'0' : '?';
    }
    str[count] = 0;
    return str;
}
static GB_UINT4 *string2ints(const char *str, size_t count) {
    GB_UINT4 *ints = ARB_alloc<GB_UINT4>(count);
    for (size_t c = 0; c<count; ++c) { // IRRELEVANT_LOOP
        ints[c] = int(str[c]-'0');
    }
    return ints;
}
static char *floats2string(const float *floats, size_t count) {
    char *str = ARB_alloc<char>(count+1);
    for (size_t c = 0; c<count; ++c) { // IRRELEVANT_LOOP
        str[c] = char(floats[c]*64.0+0.5)+' '+1;
    }
    str[count] = 0;
    return str;
}
static float *string2floats(const char *str, size_t count) {
    float *floats = ARB_alloc<float>(count);
    for (size_t c = 0; c<count; ++c) { // IRRELEVANT_LOOP
        floats[c] = float(str[c]-' '-1)/64.0;
    }
    return floats;
}

static GBDATA *get_ali_entry(GBDATA *gb_item, const char *ali_name, const char *entry_name) {
    GBDATA *gb_entry = NULp;
    if (gb_item) {
        GBDATA *gb_ali = GB_find(gb_item, ali_name, SEARCH_CHILD);
        if (gb_ali) gb_entry = GB_entry(gb_ali, entry_name);
    }
    return gb_entry;
}

static char *read_item_ints_entry_as_string(GBDATA *gb_item, const char *ali_name, const char *entry_name) {
    char   *result   = NULp;
    GBDATA *gb_entry = get_ali_entry(gb_item, ali_name, entry_name);
    if (gb_entry) {
        GB_UINT4 *ints = GB_read_ints(gb_entry);
        result         = ints2string(ints, GB_read_count(gb_entry));
        free(ints);
    }
    if (!result) TEST_EXPECT_NO_ERROR(GB_await_error());
    return result;
}
static char *read_item_floats_entry_as_string(GBDATA *gb_item, const char *ali_name, const char *entry_name) {
    char   *result   = NULp;
    GBDATA *gb_entry = get_ali_entry(gb_item, ali_name, entry_name);
    if (gb_entry) {
        float *floats = GB_read_floats(gb_entry);
        result         = floats2string(floats, GB_read_count(gb_entry));
        free(floats);
    }
    if (!result) TEST_EXPECT_NO_ERROR(GB_await_error());
    return result;
}

#define TEST_ITEM_HAS_ENTRY(find,name,ename,expected)                                   \
    TEST_EXPECT_EQUAL(read_item_entry(find(gb_main, name), ali_name, ename), expected)

#define TEST_ITEM_HAS_INTSENTRY(find,name,ename,expected)                                                               \
    TEST_EXPECT_EQUAL(&*SmartCharPtr(read_item_ints_entry_as_string(find(gb_main, name), ali_name, ename)), expected)

#define TEST_ITEM_HAS_FLOATSENTRY(find,name,ename,expected)                                                             \
    TEST_EXPECT_EQUAL(&*SmartCharPtr(read_item_floats_entry_as_string(find(gb_main, name), ali_name, ename)), expected)

#define TEST_ITEM_HAS_DATA(find,name,expected) TEST_ITEM_HAS_ENTRY(find,name,"data",expected)

#define TEST_SPECIES_HAS_DATA(ad,sd)    TEST_ITEM_HAS_DATA(GBT_find_species,ad.name,sd)
#define TEST_SAI_HAS_DATA(ad,sd)        TEST_ITEM_HAS_DATA(GBT_find_SAI,ad.name,sd)
#define TEST_SAI_HAS_ENTRY(ad,ename,sd) TEST_ITEM_HAS_ENTRY(GBT_find_SAI,ad.name,ename,sd)

#define TEST_SPECIES_HAS_INTS(ad,id)   TEST_ITEM_HAS_INTSENTRY(GBT_find_species,ad.name,"NN",id)
#define TEST_SPECIES_HAS_FLOATS(ad,fd) TEST_ITEM_HAS_FLOATSENTRY(GBT_find_species,ad.name,"FF",fd)

#define TEST_DATA(sd0,sd1,sd2,ed0,ed1,ed2,ref,ints,floats,struct) do {                          \
        TEST_SPECIES_HAS_DATA(TADinsdel[0], sd0);                                               \
        TEST_SPECIES_HAS_DATA(TADinsdel[1], sd1);                                               \
        TEST_SPECIES_HAS_DATA(TADinsdel[2], sd2);                                               \
        TEST_SAI_HAS_DATA(EXTinsdel[0], ed0);                                                   \
        TEST_SAI_HAS_DATA(EXTinsdel[1], ed1);                                                   \
        TEST_SAI_HAS_DATA(EXTinsdel[2], ed2);                                                   \
        TEST_SAI_HAS_ENTRY(EXTinsdel[1], "_REF", ref);                                          \
        GBDATA *gb_ref = GB_search(gb_main, "secedit/structs/ali_mini/struct/ref", GB_FIND);    \
        TEST_EXPECT_EQUAL(GB_read_char_pntr(gb_ref), ref);                                      \
        TEST_SPECIES_HAS_INTS(TADinsdel[0], ints);                                              \
        TEST_SPECIES_HAS_FLOATS(TADinsdel[0], floats);                                          \
        TEST_SAI_HAS_ENTRY(EXTinsdel[1], "_STRUCT", struct);                                    \
    } while(0)

static int get_alignment_aligned(GBDATA *gb_main, const char *aliname) { // former GBT_get_alignment_aligned
    GBDATA *gb_alignment = GBT_get_alignment(gb_main, aliname);
    return gb_alignment ? *GBT_read_int(gb_alignment, "aligned") : -1;
}

#define TEST_ALI_LEN_ALIGNED(len,aligned) do {                                  \
        TEST_EXPECT_EQUAL(GBT_get_alignment_len(gb_main, ali_name), len);       \
        TEST_EXPECT_EQUAL(get_alignment_aligned(gb_main, ali_name), aligned);   \
    } while(0)

static ARB_ERROR add_some_SAIs(GBDATA *gb_main, const char *ali_name) {
    ARB_ERROR      error;
    GB_transaction ta(gb_main);
    TEST_DB_INSERT_SAI(gb_main, error, ali_name, EXTinsdel);

    // add secondary structure to "HELIX"
    GBDATA *gb_helix     = GBT_find_SAI(gb_main, "HELIX");
    if (!gb_helix) error = GB_await_error();
    else {
        GBDATA *gb_struct     = GBT_add_data(gb_helix, ali_name, "_STRUCT", GB_STRING);
        if (!gb_struct) error = GB_await_error();
        else    error         = GB_write_string(gb_struct, HELIX_STRUCT);

        GBDATA *gb_struct_ref     = GBT_add_data(gb_helix, ali_name, "_REF", GB_STRING);
        if (!gb_struct_ref) error = GB_await_error();
        else    error             = GB_write_string(gb_struct_ref, HELIX_REF);
    }

    // add stored secondary structure
    GBDATA *gb_ref     = GB_search(gb_main, "secedit/structs/ali_mini/struct/ref", GB_STRING);
    if (!gb_ref) error = GB_await_error();
    else    error      = GB_write_string(gb_ref, HELIX_REF);

    // create one INTS and one FLOATS entry for first species
    GBDATA *gb_spec = GBT_find_species(gb_main, TADinsdel[0].name);
    {
        GBDATA     *gb_ints   = GBT_add_data(gb_spec, ali_name, "NN", GB_INTS);
        const char *intsAsStr = "9346740960354855652100942568200611650200211394358998513";
        size_t      len       = strlen(intsAsStr);
        GB_UINT4   *ints      = string2ints(intsAsStr, len);
        {
            char *asStr = ints2string(ints, len);
            TEST_EXPECT_EQUAL(intsAsStr, asStr);
            free(asStr);
        }
        error = GB_write_ints(gb_ints, ints, len);
        free(ints);
    }
    {
        GBDATA     *gb_ints     = GBT_add_data(gb_spec, ali_name, "FF", GB_FLOATS);
        const char *floatsAsStr = "ODu8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uCLDoHlWV59DW";
        size_t      len         = strlen(floatsAsStr);
        float      *floats      = string2floats(floatsAsStr, len);
        {
            char *asStr = floats2string(floats, len);
            TEST_EXPECT_EQUAL(floatsAsStr, asStr);
            free(asStr);
        }
        error = GB_write_floats(gb_ints, floats, len);
        free(floats);
    }
    return error;
}

__ATTR__REDUCED_OPTIMIZE__NO_GCSE static void test_insert_delete_DB() {
    GB_shell    shell;
    ARB_ERROR   error;
    const char *ali_name = "ali_mini";
    GBDATA     *gb_main  = TEST_CREATE_DB(error, ali_name, TADinsdel, false);

    arb_suppress_progress noProgress;

    if (!error) error = add_some_SAIs(gb_main, ali_name);
    if (!error) {
        GB_transaction ta(gb_main);

        for (int pass = 1; pass <= 2; ++pass) {
            if (pass == 1) TEST_ALI_LEN_ALIGNED(56, 1);
            if (pass == 2) TEST_ALI_LEN_ALIGNED(57, 0); // was marked as "not aligned"

            TEST_DATA("...G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUCACCUCC.....",
                      "---A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU.....",
                      "...A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU----",
                      "---U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCCCACCUGA....",
                      ".....[<[.........[..[..[<<.[..].>>]....]..]....].>......]",
                      ".....1.1.........25.25.34..34.34..34...25.25...1........1",
                      ".....x..x........x...x.x....x.x....x...x...x...x.........x",
                      "9346740960354855652100942568200611650200211394358998513",  // a INTS entry
                      "ODu8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uCLDoHlWV59DW", // a FLOATS entry
                      HELIX_STRUCT);

            if (pass == 1) TEST_EXPECT_NO_ERROR(GBT_check_data(gb_main, ali_name));
        }

        TEST_EXPECT_NO_ERROR(ARB_format_alignment(gb_main, ali_name));
        TEST_ALI_LEN_ALIGNED(57, 1);
        TEST_DATA("...G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUCACCUCC......",
                  "---A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU.....",
                  "...A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU-----", // @@@ <- should convert '-' to '.'
                  "---U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCCCACCUGA.....",
                  ".....[<[.........[..[..[<<.[..].>>]....]..]....].>......]",
                  ".....1.1.........25.25.34..34.34..34...25.25...1........1",
                  ".....x..x........x...x.x....x.x....x...x...x...x.........x",
                  "934674096035485565210094256820061165020021139435899851300",
                  "ODu8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uCLDoHlWV59DW!",
                  HELIX_STRUCT);

// text-editor column -> alignment column
#define COL(col) ((col)-19)

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(64), 2, "")); // insert in middle
        TEST_ALI_LEN_ALIGNED(59, 1);
        TEST_DATA("...G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC......",
                  "---A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.....",
                  "...A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-----",
                  "---U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.....",
                  ".....[<[.........[..[..[<<.[..].>>]....]..]......].>......]",
                  ".....1.1.........25.25.34..34.34..34...25.25.....1........1",
                  ".....x..x........x...x.x....x.x....x...x...x.....x.........x",
                  "93467409603548556521009425682006116502002113900435899851300",
                  "ODu8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(75), 2, "")); // insert near end
        TEST_ALI_LEN_ALIGNED(61, 1);
        TEST_DATA("...G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC........",
                  "---A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.......",
                  "...A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-------",
                  "---U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.......",
                  ".....[<[.........[..[..[<<.[..].>>]....]..]......].>........]",
                  ".....1.1.........25.25.34..34.34..34...25.25.....1..........1",
                  ".....x..x........x...x.x....x.x....x...x...x.....x...........x",
                  "9346740960354855652100942568200611650200211390043589985100300",
                  "ODu8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(20), 2, "")); // insert near start
        TEST_ALI_LEN_ALIGNED(63, 1);
        TEST_DATA(".....G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC........",
                  "-----A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.......",
                  ".......[<[.........[..[..[<<.[..].>>]....]..]......].>........]",
                  ".......1.1.........25.25.34..34.34..34...25.25.....1..........1",
                  ".......x..x........x...x.x....x.x....x...x...x.....x...........x",
                  "900346740960354855652100942568200611650200211390043589985100300",
                  "O!!Du8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);


        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(26), 2, "")); // insert at left helix start
        TEST_ALI_LEN_ALIGNED(65, 1);
        TEST_DATA(".....G---GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC........",
                  "-----A---CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A---CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U---GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.......",
                  ".........[<[.........[..[..[<<.[..].>>]....]..]......].>........]",
                  ".........1.1.........25.25.34..34.34..34...25.25.....1..........1",
                  ".........x..x........x...x.x....x.x....x...x...x.....x...........x",
                  "90034670040960354855652100942568200611650200211390043589985100300",
                  "O!!Du8E!!Jh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(29), 2, "")); // insert behind left helix start
        TEST_ALI_LEN_ALIGNED(67, 1);
        TEST_DATA(".....G---G--GC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC........",
                  "-----A---C--GA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A---C--GA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U---G--CC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.......",
                  ".........[..<[.........[..[..[<<.[..].>>]....]..]......].>........]",
                  ".........1...1.........25.25.34..34.34..34...25.25.....1..........1",
                  ".........x....x........x...x.x....x.x....x...x...x.....x...........x",
                  "9003467004000960354855652100942568200611650200211390043589985100300",
                  "O!!Du8E!!J!!h60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(32), 2, "")); // insert at left helix end
        TEST_ALI_LEN_ALIGNED(69, 1);
        TEST_DATA(".....G---G--G--C-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.......",
                  ".........[..<..[.........[..[..[<<.[..].>>]....]..]......].>........]",
                  ".........1.....1.........25.25.34..34.34..34...25.25.....1..........1",
                  ".........x......x........x...x.x....x.x....x...x...x.....x...........x",
                  "900346700400000960354855652100942568200611650200211390043589985100300",
                  "O!!Du8E!!J!!h!!60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(35), 2, ""));    // insert behind left helix end
        TEST_ALI_LEN_ALIGNED(71, 1);
        TEST_DATA(".....G---G--G--C---C-G...--A--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-----C--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.....G--G--GAA-CCUG-CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-----G--C--CCU-UAGC-GCGG-UGG--UCC--CACCUGA.......",
                  ".........[..<..[...........[..[..[<<.[..].>>]....]..]......].>........]",
                  ".........1.....1...........25.25.34..34.34..34...25.25.....1..........1",
                  ".........x........x........x...x.x....x.x....x...x...x.....x...........x", // @@@ _REF gets destroyed here! (see #159)
                  //               ^ ^
                  "90034670040000090060354855652100942568200611650200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);


        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(59), 2, "")); // insert at right helix start
        TEST_ALI_LEN_ALIGNED(73, 1);
        TEST_DATA(".....G---G--G--C---C-G...--A--G--GAA-CCU--G-CGGC-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-----C--G--GAA-CCU--G-CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.....G--G--GAA-CCU--G-CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-----G--C--CCU-UAG--C-GCGG-UGG--UCC--CACCUGA.......",
                  ".........[..<..[...........[..[..[<<.[....].>>]....]..]......].>........]",
                  ".........1.....1...........25.25.34..34...34..34...25.25.....1..........1",
                  ".........x........x........x...x.x....x...x....x...x...x.....x...........x",
                  "9003467004000009006035485565210094256820000611650200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYLgxvzrqmeMiMAjB5E!!JxT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(62), 2, ""));       // insert behind right helix start
        TEST_ALI_LEN_ALIGNED(75, 1);
        TEST_DATA(".....G---G--G--C---C-G...--A--G--GAA-CCU--G---CGGC-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-----C--G--GAA-CCU--G---CGGC-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.....G--G--GAA-CCU--G---CGGC-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-----G--C--CCU-UAG--C---GCGG-UGG--UCC--CACCUGA.......",
                  ".........[..<..[...........[..[..[<<.[....]...>>]....]..]......].>........]",
                  ".........1.....1...........25.25.34..34...3..4..34...25.25.....1..........1", // @@@ <- helix nr destroyed
                  //                                         ^^^^
                  ".........x........x........x...x.x....x...x......x...x...x.....x...........x",
                  "900346700400000900603548556521009425682000000611650200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYLgxvzrqmeMiMAjB5E!!J!!xT6JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(67), 2, ""));         // insert at right helix end
        TEST_ALI_LEN_ALIGNED(77, 1);
        TEST_DATA(".....G---G--G--C---C-G...--A--G--GAA-CCU--G---CG--GC-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-----C--G--GAA-CCU--G---CG--GC-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.....G--G--GAA-CCU--G---CG--GC-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-----G--C--CCU-UAG--C---GC--GG-UGG--UCC--CACCUGA.......",
                  ".........[..<..[...........[..[..[<<.[....]...>>..]....]..]......].>........]",
                  ".........1.....1...........25.25.34..34...3..4....34...25.25.....1..........1",
                  ".........x........x........x...x.x....x...x........x...x...x.....x...........x",
                  "90034670040000090060354855652100942568200000061100650200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYLgxvzrqmeMiMAjB5E!!J!!xT6!!JPiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(70), 2, ""));           // insert behind right helix end
        TEST_ALI_LEN_ALIGNED(79, 1);
        TEST_DATA(".....G---G--G--C---C-G...--A--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-----C--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.....G--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-----G--C--CCU-UAG--C---GC--G--G-UGG--UCC--CACCUGA.......",
                  ".........[..<..[...........[..[..[<<.[....]...>>..]......]..]......].>........]",
                  ".........1.....1...........25.25.34..34...3..4....3..4...25.25.....1..........1", // @@@ <- helix nr destroyed
                  ".........x........x........x...x.x....x...x..........x...x...x.....x...........x", // @@@ _REF gets destroyed here! (see #159)
                  "9003467004000009006035485565210094256820000006110060050200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYLgxvzrqmeMiMAjB5E!!J!!xT6!!J!!PiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);



        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(44), 2, ""));           // insert at gap border (between different gap types)
        TEST_ALI_LEN_ALIGNED(81, 1);
        TEST_DATA(".....G---G--G--C---C-G...----A--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCC........", // now prefers '-' here
                  "-----A---C--G--A---U-C-------C--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.......G--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-------G--C--CCU-UAG--C---GC--G--G-UGG--UCC--CACCUGA.......",
                  ".........[..<..[.............[..[..[<<.[....]...>>..]......]..]......].>........]",
                  ".........1.....1.............25.25.34..34...3..4....3..4...25.25.....1..........1",
                  ".........x........x..........x...x.x....x...x..........x...x...x.....x...........x",
                  "900346700400000900603548500565210094256820000006110060050200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYLg!!xvzrqmeMiMAjB5E!!J!!xT6!!J!!PiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);


        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(42), -6, "-.")); // delete gaps
        TEST_ALI_LEN_ALIGNED(75, 1);
        TEST_DATA(".....G---G--G--C---C-G.A--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-C--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.G--G--GAA-CCU--G---CG--G--C-UGG--AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-G--C--CCU-UAG--C---GC--G--G-UGG--UCC--CACCUGA.......",
                  ".........[..<..[.......[..[..[<<.[....]...>>..]......]..]......].>........]",
                  ".........1.....1.......25.25.34..34...3..4....3..4...25.25.....1..........1",
                  ".........x........x....x...x.x....x...x..........x...x...x.....x...........x",
                  "900346700400000900603545210094256820000006110060050200211390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYzrqmeMiMAjB5E!!J!!xT6!!J!!PiCvQrq4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(74), -1, "-.")); // delete gap inside helix destroying helix nrs
        TEST_ALI_LEN_ALIGNED(74, 1);
        TEST_DATA(".....G---G--G--C---C-G.A--G--GAA-CCU--G---CG--G--C-UGG-AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-C--G--GAA-CCU--G---CG--G--C-UGG-AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.G--G--GAA-CCU--G---CG--G--C-UGG-AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-G--C--CCU-UAG--C---GC--G--G-UGG-UCC--CACCUGA.......",
                  ".........[..<..[.......[..[..[<<.[....]...>>..]......].]......].>........]",
                  ".........1.....1.......25.25.34..34...3..4....3..4...2525.....1..........1", // @@@ helix nr destroyed ('25.25' -> '2525')
                  ".........x........x....x...x.x....x...x..........x...x..x.....x...........x",
                  "90034670040000090060354521009425682000000611006005020021390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYzrqmeMiMAjB5E!!J!!xT6!!J!!PiCvQr4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);


        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(47), -1, "-.")); // delete gap between helices destroying helix nrs
        TEST_ALI_LEN_ALIGNED(73, 1);
        TEST_DATA(".....G---G--G--C---C-G.A--G-GAA-CCU--G---CG--G--C-UGG-AUC--ACCUCC........",
                  "-----A---C--G--A---U-C-C--G-GAA-CCU--G---CG--G--C-UGG-AUC--ACCUCCU.......",
                  ".....A---C--G--A---A-C.G--G-GAA-CCU--G---CG--G--C-UGG-AUC--ACCUCCU-------",
                  "-----U---G--C--C---U-G-G--C-CCU-UAG--C---GC--G--G-UGG-UCC--CACCUGA.......",
                  ".........[..<..[.......[..[.[<<.[....]...>>..]......].]......].>........]",
                  ".........1.....1.......25.2534..34...3..4....3..4...2525.....1..........1", // @@@ helix nr destroyed ('25.34' -> '2534')
                  ".........x........x....x...xx....x...x..........x...x..x.....x...........x",
                  "9003467004000009006035452100425682000000611006005020021390043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYzrqmeiMAjB5E!!J!!xT6!!J!!PiCvQr4uC!!LDoHlWV59!!DW!",
                  HELIX_STRUCT);


        TEST_EXPECT_NO_ERROR(ARB_insdel_columns(gb_main, ali_name, COL(72), -5, "%")); // delete anything
        TEST_ALI_LEN_ALIGNED(68, 1);
        TEST_DATA(".....G---G--G--C---C-G.A--G-GAA-CCU--G---CG--G--C-UGG-ACCUCC........",
                  "-----A---C--G--A---U-C-C--G-GAA-CCU--G---CG--G--C-UGG-ACCUCCU.......",
                  ".....A---C--G--A---A-C.G--G-GAA-CCU--G---CG--G--C-UGG-ACCUCCU-------",
                  "-----U---G--C--C---U-G-G--C-CCU-UAG--C---GC--G--G-UGG-CACCUGA.......",
                  ".........[..<..[.......[..[.[<<.[....]...>>..]......]...].>........]",
                  ".........1.....1.......25.2534..34...3..4....3..4...2...1..........1",
                  ".........x........x....x...xx....x...x..........x...x...x...........x",
                  "90034670040000090060354521004256820000006110060050200043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYzrqmeiMAjB5E!!J!!xT6!!J!!PiCvQ!LDoHlWV59!!DW!",
                  HELIX_STRUCT);

    }

    if (!error) {
        {
            GB_transaction ta(gb_main);
            TEST_EXPECT_EQUAL(ARB_insdel_columns(gb_main, ali_name, COL(35), -3, "-."), // illegal delete
                              "SAI 'HELIX': You tried to delete 'x' at position 18  -> Operation aborted");
            ta.close("xxx");
        }
        {
            GB_transaction ta(gb_main);
            TEST_EXPECT_EQUAL(ARB_insdel_columns(gb_main, ali_name, COL(57), -3, "-."), // illegal delete
                              "SAI 'HELIX_NR': You tried to delete '4' at position 40  -> Operation aborted");
            ta.close("xxx");
        }
        {
            GB_transaction ta(gb_main);
            TEST_EXPECT_EQUAL(ARB_insdel_columns(gb_main, ali_name, 4711, 3, "-."), // illegal insert
                              "Can't insert at position 4711 (exceeds length 68 of alignment 'ali_mini')");
            ta.close("xxx");
        }
        {
            GB_transaction ta(gb_main);
            TEST_EXPECT_EQUAL(ARB_insdel_columns(gb_main, ali_name, 66, -3, "-."), // illegal delete
                              "Can't delete positions 66-68 (exceeds max. position 67 of alignment 'ali_mini')");
            ta.close("xxx");
        }
        {
            GB_transaction ta(gb_main);
            TEST_EXPECT_EQUAL(ARB_insdel_columns(gb_main, ali_name, -1, 3, "-."), // illegal insert
                              "Illegal sequence position -1");
            ta.close("xxx");
        }
    }
    if (!error) {
        GB_transaction ta(gb_main);
        TEST_DATA(".....G---G--G--C---C-G.A--G-GAA-CCU--G---CG--G--C-UGG-ACCUCC........",
                  "-----A---C--G--A---U-C-C--G-GAA-CCU--G---CG--G--C-UGG-ACCUCCU.......",
                  ".....A---C--G--A---A-C.G--G-GAA-CCU--G---CG--G--C-UGG-ACCUCCU-------",
                  "-----U---G--C--C---U-G-G--C-CCU-UAG--C---GC--G--G-UGG-CACCUGA.......",
                  ".........[..<..[.......[..[.[<<.[....]...>>..]......]...].>........]",
                  ".........1.....1.......25.2534..34...3..4....3..4...2...1..........1",
                  ".........x........x....x...xx....x...x..........x...x...x...........x",
                  "90034670040000090060354521004256820000006110060050200043589985100300",
                  "O!!Du8E!!J!!h!!6!!0e1XYzrqmeiMAjB5E!!J!!xT6!!J!!PiCvQ!LDoHlWV59!!DW!",
                  HELIX_STRUCT);
    }

    GB_close(gb_main);
    TEST_EXPECT_NO_ERROR(error.deliver());
}
void TEST_insert_delete_DB() {
    test_insert_delete_DB(); // wrap test code in subroutine (otherwise nm 2.24 fails to provide source-location, even if TEST_PUBLISH is used)
}

__ATTR__REDUCED_OPTIMIZE void TEST_insert_delete_DB_using_SAI() {
    GB_shell    shell;
    ARB_ERROR   error;
    const char *ali_name = "ali_mini";
    GBDATA     *gb_main  = TEST_CREATE_DB(error, ali_name, TADinsdel, false);

    arb_suppress_progress noProgress;

    if (!error) error = add_some_SAIs(gb_main, ali_name);
    if (!error) {
        GB_transaction ta(gb_main);

        // test here is just a duplicate from TEST_insert_delete_DB() - just here to show the data
        TEST_EXPECT_NO_ERROR(ARB_format_alignment(gb_main, ali_name));
        int alilen_exp = 57;
        TEST_ALI_LEN_ALIGNED(alilen_exp, 1);
        TEST_DATA("...G-GGC-C-G...--A--G--GAA-CCUG-CGGC-UGG--AUCACCUCC......",
                  "---A-CGA-U-C-----C--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU.....",
                  "...A-CGA-A-C.....G--G--GAA-CCUG-CGGC-UGG--AUCACCUCCU-----",
                  "---U-GCC-U-G-----G--C--CCU-UAGC-GCGG-UGG--UCCCACCUGA.....",
                  ".....[<[.........[..[..[<<.[..].>>]....]..]....].>......]",
                  ".....1.1.........25.25.34..34.34..34...25.25...1........1",
                  ".....x..x........x...x.x....x.x....x...x...x...x.........x",
                  "934674096035485565210094256820061165020021139435899851300",
                  "ODu8EJh60e1XYLgxvzrqmeMiMAjB5EJxT6JPiCvQrq4uCLDoHlWV59DW!",
                  HELIX_STRUCT);

        RangeList delRanges  = build_RangeList_from_string(
            /* */ "xxx-------x-x-xxx---------x---------x---------------xxxx-",
            "x", false);
        TEST_EXPECT_NO_ERROR(ARB_delete_columns_using_SAI(gb_main, ali_name, delRanges, ".-"));
        alilen_exp -= 14;
        TEST_ALI_LEN_ALIGNED(alilen_exp, 1);
        TEST_DATA("G-GGC-CG.A--G--GAACCUG-CGGCUGG--AUCACCUCC..",
                  "A-CGA-UC-C--G--GAACCUG-CGGCUGG--AUCACCUCCU.",
                  "A-CGA-AC.G--G--GAACCUG-CGGCUGG--AUCACCUCCU-",
                  "U-GCC-UG-G--C--CCUUAGC-GCGGUGG--UCCCACCUGA.",
                  "..[<[....[..[..[<<[..].>>]...]..]....].>..]",
                  "..1.1....25.25.34.34.34..34..25.25...1....1",
                  "..x..x...x...x.x...x.x....x..x...x...x.....x",
                  "6740960585210094258200611652002113943589980",
                  "8EJh60eXLzrqmeMiMAB5EJxT6JPCvQrq4uCLDoHlWV!",
                  HELIX_STRUCT);

        // insert INFRONTOF each range
        RangeList insRanges = build_RangeList_from_string(
            /* */ "---xx---xxxxxxxx---------xxxx--------------",
            "x", false);
        TEST_EXPECT_NO_ERROR(ARB_insert_columns_using_SAI(gb_main, ali_name, insRanges, RANGES, INFRONTOF, 2));
        alilen_exp += 3*2;
        TEST_ALI_LEN_ALIGNED(alilen_exp, 1);
        TEST_DATA("G-G--GC-CG...A--G--GAACCUG-CG--GCUGG--AUCACCUCC..",
                  "A-C--GA-UC---C--G--GAACCUG-CG--GCUGG--AUCACCUCCU.",
                  "A-C--GA-AC...G--G--GAACCUG-CG--GCUGG--AUCACCUCCU-",
                  "U-G--CC-UG---G--C--CCUUAGC-GC--GGUGG--UCCCACCUGA.",
                  "..[..<[......[..[..[<<[..].>>..]...]..]....].>..]",
                  "..1...1......25.25.34.34.34....34..25.25...1....1",
                  "..x....x.....x...x.x...x.x......x..x...x...x.....x",
                  "6740009605008521009425820061100652002113943589980",
                  "8EJ!!h60eX!!LzrqmeMiMAB5EJxT6!!JPCvQrq4uCLDoHlWV!",
                  HELIX_STRUCT);

        // insert BEHIND each range
        insRanges = build_RangeList_from_string(
            /* */ "-----------xx-x------------xxxxxx---------------x",
            "x", false);
        TEST_EXPECT_NO_ERROR(ARB_insert_columns_using_SAI(gb_main, ali_name, insRanges, RANGES, BEHIND, 4));
        alilen_exp += 4*4;
        TEST_ALI_LEN_ALIGNED(alilen_exp, 1);
        TEST_DATA("G-G--GC-CG.......A------G--GAACCUG-CG--GC----UGG--AUCACCUCC......",
                  "A-C--GA-UC-------C------G--GAACCUG-CG--GC----UGG--AUCACCUCCU.....",
                  "A-C--GA-AC.......G------G--GAACCUG-CG--GC----UGG--AUCACCUCCU-----",
                  "U-G--CC-UG-------G------C--CCUUAGC-GC--GG----UGG--UCCCACCUGA.....",
                  "..[..<[..........[......[..[<<[..].>>..].......]..]....].>..]....",
                  "..1...1..........25.....25.34.34.34....34......25.25...1....1....",
                  "..x....x.........x.......x.x...x.x......x......x...x...x.........x", // @@@ ref gets destroyed here
                  "67400096050080000520000100942582006110065000020021139435899800000",
                  "8EJ!!h60eX!!L!!!!zr!!!!qmeMiMAB5EJxT6!!JP!!!!CvQrq4uCLDoHlWV!!!!!",
                  HELIX_STRUCT);

        // insert INFRONTOF each column
        insRanges = build_RangeList_from_string(
            /* */ "x----xx--------------------------------------xxx----xxxx--------x",
            "x", false);
        TEST_EXPECT_NO_ERROR(ARB_insert_columns_using_SAI(gb_main, ali_name, insRanges, SINGLE_COLUMNS, INFRONTOF, 1));
        alilen_exp += 11*1;
        TEST_ALI_LEN_ALIGNED(alilen_exp, 1);
        TEST_DATA(".G-G---G-C-CG.......A------G--GAACCUG-CG--GC-----U-G-G--AU-C-A-C-CUCC.......",
                  ".A-C---G-A-UC-------C------G--GAACCUG-CG--GC-----U-G-G--AU-C-A-C-CUCCU......",
                  ".A-C---G-A-AC.......G------G--GAACCUG-CG--GC-----U-G-G--AU-C-A-C-CUCCU------",
                  ".U-G---C-C-UG-------G------C--CCUUAGC-GC--GG-----U-G-G--UC-C-C-A-CCUGA......",
                  "...[...<.[..........[......[..[<<[..].>>..]..........]..]........].>..].....",
                  "...1.....1..........25.....25.34.34.34....34.........25.25.......1....1.....",
                  "...x......x.........x.......x.x...x.x......x.........x...x.......x..........x",
                  "0674000009605008000052000010094258200611006500000200002113090403058998000000",
                  "!8EJ!!!h!60eX!!L!!!!zr!!!!qmeMiMAB5EJxT6!!JP!!!!!C!v!Qrq4u!C!L!D!oHlWV!!!!!!",
                  HELIX_STRUCT);

        // insert BEHIND each column
        insRanges   = build_RangeList_from_string(
            /* */ "------------------------------xxxxxxx----------------------------xxxxxx-----",
            "x", false);
        TEST_EXPECT_NO_ERROR(ARB_insert_columns_using_SAI(gb_main, ali_name, insRanges, SINGLE_COLUMNS, BEHIND, 2));
        alilen_exp += 13*2;
        TEST_ALI_LEN_ALIGNED(alilen_exp, 1);
        TEST_DATA(".G-G---G-C-CG.......A------G--G--A--A--C--C--U--G---CG--GC-----U-G-G--AU-C-A-C-C--U--C--C.............",
                  ".A-C---G-A-UC-------C------G--G--A--A--C--C--U--G---CG--GC-----U-G-G--AU-C-A-C-C--U--C--C--U..........",
                  ".A-C---G-A-AC.......G------G--G--A--A--C--C--U--G---CG--GC-----U-G-G--AU-C-A-C-C--U--C--C--U----------",
                  ".U-G---C-C-UG-------G------C--C--C--U--U--A--G--C---GC--GG-----U-G-G--UC-C-C-A-C--C--U--G--A..........",
                  "...[...<.[..........[......[..[..<..<..[........]...>>..]..........]..]........].....>........].......",
                  "...1.....1..........25.....25.3..4.....3..4.....3..4....34.........25.25.......1..............1.......",  // @@@ helix nrs destroyed
                  "...x......x.........x.......x.x...........x.....x........x.........x...x.......x......................x", // @@@ ref destroyed further
                  "067400000960500800005200001009400200500800200000000611006500000200002113090403050080090090080000000000",
                  "!8EJ!!!h!60eX!!L!!!!zr!!!!qmeMi!!M!!A!!B!!5!!E!!J!!xT6!!JP!!!!!C!v!Qrq4u!C!L!D!o!!H!!l!!W!!V!!!!!!!!!!",
                  HELIX_STRUCT);
    }

    GB_close(gb_main);
    TEST_EXPECT_NO_ERROR(error.deliver());
}
TEST_PUBLISH(TEST_insert_delete_DB_using_SAI);

#endif // UNIT_TESTS