ps_node.cxx

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// =============================================================== //
//                                                                 //
//   File      : ps_node.cxx                                       //
//   Purpose   :                                                   //
//                                                                 //
//   Coded by Wolfram Foerster in October 2002                     //
//   Institute of Microbiology (Technical University Munich)       //
//   http://www.arb-home.de/                                       //
//                                                                 //
// =============================================================== //

#include "ps_node.hxx"

using namespace std;

//
// *** disk output ASCII ***
//
bool PS_Node::saveASCII(PS_FileBuffer* _fb, char *buffer) {   // buffer MUST be at least 100 chars long
    unsigned int size;
    int          count;
    //
    // write num
    //
    count = sprintf(buffer, "N[%i", num);
    _fb->put(buffer, count);
    //
    // write probes
    //
    size = countProbes();
    if (size) {
        count = sprintf(buffer, " P{%u", size);
        _fb->put(buffer, count);
        for (PS_ProbeSetCIter i=probes->begin(); i!=probes->end(); ++i) {
            count = sprintf(buffer, " (%i_%i_%i)", (*i)->quality, (*i)->length, (*i)->GC_content);
            _fb->put(buffer, count);
        }
        _fb->put_char('}');
    }
    //
    // write children
    //
    size  = children.size();
    if (size) {
        count = sprintf(buffer, " C<%u", size);
        _fb->put(buffer, count);
        for (PS_NodeMapIterator i=children.begin(); i!=children.end(); ++i) {
            _fb->put_char('\n');
            if (num == -1) _fb->put_char('+');
            i->second->saveASCII(_fb, buffer);
        }
        _fb->put_char('>');
    }

    _fb->put_char(']');
    return true; // success
}


//
// *** disk output ***
//
bool PS_Node::save(PS_FileBuffer* _fb) {
    unsigned int size;
    //
    // write num
    //
    _fb->put_int(num);
    //
    // write probes
    //
    size = countProbes();
    _fb->put_uint(size);
    if (size) {
        PS_Probe p;
        for (PS_ProbeSetCIter i=probes->begin(); i!=probes->end(); ++i) {
            p = **i;
            _fb->put(&p, sizeof(PS_Probe));
        }
    }
    //
    // write children
    //
    size = children.size();
    _fb->put_uint(size);
    for (PS_NodeMapIterator i=children.begin(); i!=children.end(); ++i) {
        i->second->save(_fb);
    }
    return true; // success
}


//
// *** disk input ***
//
bool PS_Node::load(PS_FileBuffer* _fb) {
    unsigned int size;
    //
    // read num
    //
    _fb->get_int(num);
    //
    // read probes
    //
    _fb->get_uint(size);
    if (size) {               // does node have probes ?
        probes = new PS_ProbeSet;                                 // make new probeset
        for (unsigned int i=0; i<size; ++i) {
            PS_Probe *p = new PS_Probe;
            _fb->get(p, sizeof(PS_Probe));                        // read new probe
            PS_ProbePtr new_probe(p);                             // make new probe-smartpointer
            probes->insert(new_probe);                            // append new probe to probeset
        }
    }
    else {
        probes = NULp;                                            // unset probeset
    }
    //
    // read children
    //
    _fb->get_uint(size);
    if (num == -1) {
        for (unsigned int i=0; i<size; ++i) {
            PS_NodePtr new_child(new PS_Node(-1));                // make new child
            new_child->load(_fb);                                 // read new child
            children[new_child->getNum()] = new_child;            // insert new child to childmap
            if (i % 200 == 0) printf("loaded 1st level #%i (%i)\n", i+1, new_child->getNum());
        }
    }
    else {
        for (unsigned int i=0; i<size; ++i) {
            PS_NodePtr new_child(new PS_Node(-1));                // make new child
            new_child->load(_fb);                                 // read new child
            children[new_child->getNum()] = new_child;            // insert new child to childmap
        }
    }
    return true; // success
}


//
// *** disk input appending ***
//
bool PS_Node::append(PS_FileBuffer* _fb) {
    unsigned int size;
    //
    // read num if root
    //
    if (num == -1) {
        _fb->get_int(num);
    }
    //
    // read probes
    //
    _fb->get_uint(size);
    if (size) {               // does node have probes ?
        if (!probes) probes = new PS_ProbeSet;                    // make new probeset
        for (unsigned int i=0; i<size; ++i) {
            PS_Probe *p = new PS_Probe;
            _fb->get(p, sizeof(PS_Probe));                        // read new probe
            PS_ProbePtr new_probe(p);                             // make new probe-smartpointer
            probes->insert(new_probe);                            // append new probe to probeset
        }
    }
    //
    // read children
    //
    _fb->get_uint(size);
    for (unsigned int i=0; i<size; ++i) {
        //
        // read num of child
        //
        SpeciesID childNum;
        _fb->get_int(childNum);
        if ((num == -1) && (i % 200 == 0)) printf("appended 1st level #%i (%i)\n", i+1, childNum);
        //
        // test if child already exists
        //
        PS_NodeMapIterator it = children.find(childNum);
        if (it != children.end()) {
            it->second->append(_fb);                             // 'update' child
        }
        else {
            PS_NodePtr newChild(new PS_Node(childNum));          // make new child
            newChild->append(_fb);                               // read new child
            children[childNum] = newChild;                       // insert new child to childmap
        }
    }
    return true; // success
}


//
// disk read with callback
// children are stored as child[0] one after the other
//
bool PS_Node::read(PS_FileBuffer* _fb, PS_Callback *_call_destination) {
    unsigned int size;
    //
    // read num if root
    //
    if (num == -1) {
        _fb->get_int(num);
    }
    //
    // read probes
    //
    _fb->get_uint(size);
    if (size) {               // does node have probes ?
        if (!probes) probes = new PS_ProbeSet;                    // make new probeset
        for (unsigned int i=0; i<size; ++i) {
            PS_Probe *p = new PS_Probe;
            _fb->get(p, sizeof(PS_Probe));                        // read new probe
            PS_ProbePtr new_probe(p);                             // make new probe-smartpointer
            probes->insert(new_probe);                            // append new probe to probeset
        }
    }
    //
    // callback
    //
    _call_destination->callback(this);
    //
    // read children
    //
    _fb->get_uint(size);
    for (unsigned int i=0; i<size; ++i) {
        //
        // read num of child
        //
        SpeciesID childNum;
        _fb->get_int(childNum);
        if ((num == -1) && (i % 200 == 0)) printf("read 1st level #%i (%i)\n", i+1, childNum);
        //
        // read children
        //
        PS_NodePtr child(new PS_Node(childNum));                // make child
        children[0] = child;                                    // store child as Number Zero
        child->read(_fb, _call_destination);                    // read child
        children.erase(0);                                      // remove previous child
    }
    return true; // success
}