ps_node.hxx

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#ifndef PS_NODE_HXX
#define PS_NODE_HXX

#ifndef SMARTPTR_H
#include <smartptr.h>
#endif
#ifndef PS_DEFS_HXX
#include "ps_defs.hxx"
#endif
#ifndef PS_FILEBUFFER_HXX
#include "ps_filebuffer.hxx"
#endif

using namespace std;

struct PS_Probe {
    short int          quality;             // negative quality <=> matches inverse path
    unsigned short int length;
    unsigned short int GC_content;
};

typedef SmartPtr<PS_Probe> PS_ProbePtr;

inline void PS_printProbe(const PS_Probe *p) {
    printf("%+i_%u_%u", p->quality, p->length, p->GC_content);
}

inline void PS_printProbe(const PS_ProbePtr& p) {
    printf("%+i_%u_%u", p->quality, p->length, p->GC_content);
}

struct lt_probe {
    bool operator()(const PS_ProbePtr& p1, const PS_ProbePtr& p2) const {
        if (abs(p1->quality) == abs(p2->quality)) {
            if (p1->length == p2->length) {
                return p1->GC_content < p2->GC_content; // equal quality & length => sort by GC-content
            }
            else {
                return p1->length < p2->length;         // equal quality => sort by length
            }
        }
        else {
            return p1->quality < p2->quality;       // sort by quality
        }
    }
};


typedef set<PS_ProbePtr, lt_probe>   PS_ProbeSet;
typedef PS_ProbeSet*                PS_ProbeSetPtr;
typedef PS_ProbeSet::iterator       PS_ProbeSetIter;
typedef PS_ProbeSet::const_iterator PS_ProbeSetCIter;
class PS_Node;
typedef SmartPtr<PS_Node>         PS_NodePtr;
typedef map<SpeciesID, PS_NodePtr> PS_NodeMap;
typedef PS_NodeMap::iterator         PS_NodeMapIterator;
typedef PS_NodeMap::reverse_iterator PS_NodeMapRIterator;
typedef PS_NodeMap::const_iterator         PS_NodeMapConstIterator;
typedef PS_NodeMap::const_reverse_iterator PS_NodeMapConstRIterator;

class PS_Node : virtual Noncopyable {
    SpeciesID      num;
    PS_NodeMap     children;
    PS_ProbeSetPtr probes;

public:

    //
    // *** num ***
    //
    void      setNum(SpeciesID id) { num = id; }
    SpeciesID getNum() const         { return num; }

    //
    // *** children ***
    //
    bool addChild(PS_NodePtr& _child) {
        PS_NodeMapIterator it = children.find(_child->getNum());
        if (it == children.end()) {
            children[_child->getNum()] = _child;
            return true;
        }
        else {
            printf("child[#%u] already exists\n", _child->getNum());
            return false;
        }
    }

    PS_NodePtr assertChild(SpeciesID _id) {
        PS_NodeMapIterator it = children.find(_id);
        if (it == children.end()) {
            PS_NodePtr new_child(new PS_Node(_id));
            children[_id] = new_child;
            return new_child;
        }
        else {
            return it->second;
        }
    }

    pair<bool, PS_NodePtr> getChild(SpeciesID id) {
        PS_NodeMapIterator it = children.find(id);
        return pair<bool, PS_NodePtr>(it!=children.end(), it->second);
    }

    pair<bool, const PS_NodePtr> getChild(SpeciesID id) const {
        PS_NodeMapConstIterator it = children.find(id);
        return pair<bool, const PS_NodePtr>(it!=children.end(), it->second);
    }

    size_t countChildren() const { return children.size(); }
    bool   hasChildren()   const { return !children.empty(); }

    PS_NodeMapIterator       getChildrenBegin()        { return children.begin(); }
    PS_NodeMapRIterator      getChildrenRBegin()       { return children.rbegin(); }
    PS_NodeMapConstIterator  getChildrenBegin()  const { return children.begin(); }
    PS_NodeMapConstRIterator getChildrenRBegin() const { return children.rbegin(); }
    PS_NodeMapIterator       getChildrenEnd()          { return children.end(); }
    PS_NodeMapRIterator      getChildrenREnd()         { return children.rend(); }
    PS_NodeMapConstIterator  getChildrenEnd()    const { return children.end(); }
    PS_NodeMapConstRIterator getChildrenREnd()   const { return children.rend(); }

    //
    // *** probes ***
    //
    bool addProbe(const PS_ProbePtr& probe) {
        if (!probes) {
            probes = new PS_ProbeSet;
            probes->insert(probe);
            return true;
        }
        else {
            pair<PS_ProbeSetCIter, bool> p = probes->insert(probe);
            return p.second;
        }
    }

    void addProbes(PS_ProbeSetCIter _begin, PS_ProbeSetCIter _end) {
        if (_begin == _end) return;
        if (!probes) probes = new PS_ProbeSet;
        for (PS_ProbeSetCIter probe = _begin; probe != _end; ++probe) {
            probes->insert(*probe);
        }
    }

    void addProbesInverted(PS_ProbeSetCIter _begin, PS_ProbeSetCIter _end) {
        if (_begin == _end) return;
        if (!probes) probes = new PS_ProbeSet;
        for (PS_ProbeSetCIter probe = _begin; probe != _end; ++probe) {
            PS_ProbePtr new_probe(new PS_Probe);
            new_probe->length     = (*probe)->length;
            new_probe->quality    = -((*probe)->quality);
            new_probe->GC_content = (*probe)->GC_content;
            probes->insert(new_probe);
        }
    }

    size_t countProbes() const { return probes ? probes->size() : 0; }
    bool   hasProbes()   const { return probes; }
    bool   hasPositiveProbes() const {
        if (!probes) return false;
        for (PS_ProbeSetCIter i=probes->begin(); i!=probes->end(); ++i) {
            if ((*i)->quality >= 0) return true;
        }
        return false;
    }

    bool   hasInverseProbes() const {
        if (!probes) return false;
        for (PS_ProbeSetCIter i=probes->begin(); i!=probes->end(); ++i) {
            if ((*i)->quality < 0) return true;
        }
        return false;
    }

    PS_ProbeSetCIter getProbesBegin() const {
        ps_assert(probes);
        return probes->begin();
    }
    PS_ProbeSetCIter getProbesEnd() const {
        ps_assert(probes);
        return probes->end();
    }

    void   removeProbe(PS_ProbeSetCIter it) {
        ps_assert(probes);
        probes->erase(it);
    }
    void   removeProbes() {
        if (probes) {
            delete probes;
            probes = NULp;
        }
    }

    //
    // *** output **
    //
    void print() {
        printf("\nN[%d] P[ ", num);
        if (probes) {
            for (PS_ProbeSetCIter i=probes->begin(); i!=probes->end(); ++i) {
                PS_printProbe(*i);
                fputc(' ', stdout);
            }
        }
        printf("] C[");
        for (PS_NodeMapIterator i=children.begin(); i!=children.end(); ++i) {
            i->second->print();
        }
        fputc(']', stdout);
    }

    void printOnlyMe() const {
        printf("N[%d] P[ ", num);
        if (probes) {
            for (PS_ProbeSetCIter i=probes->begin(); i!=probes->end(); ++i) {
                PS_printProbe(*i);
                fputc(' ', stdout);
            }
        }
        printf("] C[ %zu ]", children.size());
    }

    //
    // *** disk i/o ***
    //
    bool save(PS_FileBuffer *_fb);
    bool saveASCII(PS_FileBuffer *_fb, char *buffer);
    bool load(PS_FileBuffer *_fb);
    bool append(PS_FileBuffer *_fb);      // load from file and append to node
    bool read(PS_FileBuffer *_fb, PS_Callback *_call_destination);        // parse file and callback after probes read

    //
    // *** constructors ***
    //
    PS_Node(SpeciesID id) { num = id; probes = NULp; }

    //
    // *** destructor ***
    //
    ~PS_Node() {
        if (probes) delete probes;
        children.clear();
    }
};

#else
#error ps_node.hxx included twice
#endif