source: tags/arb_5.2/PROBE_SET/ps_node.cxx

#include "ps_node.hxx"
#include <unistd.h>

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 = (probes == 0) ? 0 : probes->size();
    if (size) {
        count = sprintf( buffer, " P{%i", 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<%i", 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( '>' );
    }
    //
    // return true to signal success
    //
    _fb->put_char( ']' );
    return true;
}


//
// *** disk output ***
//
bool PS_Node::save( PS_FileBuffer* _fb ) {
    unsigned int size;
    //
    // write num
    //
    _fb->put_int( num );
    //
    // write probes
    //
    size = (probes == 0) ? 0 : probes->size();
    _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 to signal success
    //
    return true;
}


//
// *** 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 = 0;                                               // 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 to signal success
    return true;
}


//
// *** 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 to signal success
    return true;
}


//
// 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 to signal success
    //
    return true;
}