source: tags/ms_r16q3/CONSENSUS_TREE/CT_part.hxx

// ============================================================= //
//                                                               //
//   File      : CT_part.hxx                                     //
//   Purpose   :                                                 //
//                                                               //
//   Institute of Microbiology (Technical University Munich)     //
//   http://www.arb-home.de/                                     //
//                                                               //
// ============================================================= //

#ifndef CT_PART_HXX
#define CT_PART_HXX

#ifndef ARBTOOLS_H
#include <arbtools.h>
#endif
#ifndef ARBDB_BASE_H
#include <arbdb_base.h>
#endif
#ifndef CT_DEF_HXX
#include "CT_def.hxx"
#endif
#ifndef ARB_ASSERT_H
#include <arb_assert.h>
#endif
#ifndef ARB_MEM_H
#include <arb_mem.h>
#endif


typedef unsigned int PELEM;
class PART;

#if defined(ASSERTION_USED)
inline bool is_similar(double d1, double d2, double eps) {
    double diff = d1-d2;
    if (diff<0) diff = -diff;
    return diff<eps;
}
#endif

class PartitionSize {
    PELEM cutmask;  // this mask is used to zero unused bits from the last long (in PART::p)
    int   longs;    // number of longs per part
    int   bits;     // number of bits per part ( = overall number of species)
    
    mutable size_t id;      // unique id (depending on part creation order, which depends on the added trees)

public:
    PartitionSize(int len);

    int get_longs() const { return longs; }
    int get_bits() const { return bits; }
    size_t get_unique_id() const { id++; return id; }
    PELEM get_cutmask() const { return cutmask; }

    PART *create_root() const;
    PELEM *alloc_mem() const { return ARB_calloc<PELEM>(get_longs()); }
};

class PART {
    const PartitionSize *info;

    PELEM   *p;
    GBT_LEN  len;    // length between two nodes (weighted by weight)
    double   weight; // sum of weights
    size_t   id;
    int      members;

    PART(const PART& other)
        : info(other.info),
          p(info->alloc_mem()),
          len(other.len),
          weight(other.weight),
          id(info->get_unique_id()),
          members(other.members)
    {
        int longs = get_longs();
        for (int i = 0; i<longs; ++i) {
            p[i] = other.p[i];
        }
        arb_assert(is_valid());
    }
    DECLARE_ASSIGNMENT_OPERATOR(PART);

    int count_members() const;

    void set_weight(double pc) {
        double lenScale  = pc/weight;
        weight           = pc;
        len             *= lenScale;
    }

    static int byte_pos(int pos) { return pos / sizeof(PELEM) / 8; }
    static PELEM bit_mask(int pos) { return 1 << (pos % (sizeof(PELEM)*8)); }

public:

    PART(const PartitionSize* size_info, double weight_)
        : info(size_info),
          p(info->alloc_mem()),
          len(0),
          weight(weight_),
          id(info->get_unique_id()),
          members(0)
    {
        arb_assert(is_valid());
    }
    ~PART() {
        free(p);
    }

    PART *clone() const { return new PART(*this); }

    int get_longs() const { return info->get_longs(); }
    int get_maxsize() const { return info->get_bits(); }
    PELEM get_cutmask() const { return info->get_cutmask(); }

    bool is_valid() const {
        PELEM last = p[get_longs()-1];

        bool only_valid_bits    = (last&get_cutmask()) == last;
        bool valid_member_count = members >= 0 && members <= get_maxsize();
        bool valid_weight       = weight >= 0.0;

        return only_valid_bits && valid_member_count && valid_weight;
    }

    void setbit(int pos) {
        /*! set the bit at position 'pos'
         */
        arb_assert(is_valid());

        int   idx = byte_pos(pos);
        PELEM bit = bit_mask(pos);

        if (!(p[idx]&bit)) {
            p[idx] |= bit;
            members++;
        }

        arb_assert(is_valid());
    }
    bool bit_is_set(int pos) const {
        /*! return true if the bit at the position 'pos' is set
         */
        arb_assert(is_valid());

        int   idx = byte_pos(pos);
        PELEM bit = bit_mask(pos);

        return p[idx] & bit;
    }

    void set_len(GBT_LEN length) {
        arb_assert(is_valid());
        len = length*weight;
    }
    GBT_LEN get_len() const {
        if (weight == 0.0) {
            // if weight is 0.0 = > branch never occurred!
            return 1.0; // return worst distance between these nodes (which are disjunct trees)
        }
        return len/weight;
    }

    double get_weight() const { return weight; }

    void addWeightAndLength(const PART *other) {
        weight += other->weight;
        len    += other->len;
    }

    void takeMean(double overall_weight) {
        set_weight(get_weight() / overall_weight);
        arb_assert(is_valid());
        arb_assert(weight <= 1.0);
    }

    void set_faked_weight(double w) { set_weight(w); }

    void invert();
    void invertInSuperset(const PART *superset);

    bool is_standardized() const;
    void standardize();

    void add_members_from(const PART *source);

    bool is_subset_of(const PART *other) const {
        int longs = get_longs();
        for (int i=0; i<longs; i++) {
            if ((p[i] & other->p[i]) != p[i]) {
                return false;
            }
        }
        return true;
    }
    bool is_real_son_of(const PART *father) const { return is_subset_of(father) && differs(father); }

    bool overlaps_with(const PART *other) const;
    bool disjunct_from(const PART *other) const { return !overlaps_with(other); }

    bool equals(const PART *other) const;
    bool differs(const PART *other) const { return !equals(other); }

    int index() const;
    unsigned key() const;

    int get_members() const { return members; }
    int get_nonmembers() const { return get_maxsize() - get_members(); }

    bool is_leaf_edge() const { int size = members; return size == 1 || size == (get_maxsize()-1); }
    int distance_to_tree_center() const { return abs(get_maxsize()/2 - members); }

    int insertionOrder_cmp(const PART *other) const;
    int topological_cmp(const PART *other) const;

#if defined(NTREE_DEBUG_FUNCTIONS)
    void print() const;
    static void start_pretty_printing(const class CharPtrArray& names_);
    static void stop_pretty_printing();
#endif
};

#else
#error CT_part.hxx included twice
#endif // CT_PART_HXX