/* Copyright (C) 2005 Christoph Helma <helma@in-silico.de>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
#include "lazmolvect.h"
#ifndef F_DB_H
#define F_DB_H
using namespace std;
//! compounds with features
template <class MolType, class FeatureType, class ActivityType>
class FeatMolVect: public MolVect<MolType,FeatureType,ActivityType> {
public:
typedef FeatMol < MolType, FeatureType, ActivityType > * MolRef ;
typedef Feature<FeatureType> * FeatRef;
private:
map<const string, FeatRef> feature_map; // lookup features by name
vector<FeatRef> features;
Out * out;
public:
FeatMolVect< MolType, FeatureType, ActivityType >(char * feat_file, char * structure_file, Out * out);
~FeatMolVect() {
for (unsigned int i=0; i<features.size(); i++) {
delete features[i];
}
}
//! read features from a file
void read_features(char * feat_file);
void add_feature(MolRef s, string name);
void copy_level(vector<Feature<FeatureType> *> * level, MolRef test_comp);
vector<FeatRef> * get_features() { return(&features); };
};
// read a feature file
template <class MolType, class FeatureType, class ActivityType>
FeatMolVect<MolType, FeatureType, ActivityType>::FeatMolVect(char * feat_file, char * structure_file, Out * out): MolVect< MolType, FeatureType, ActivityType >(structure_file,out), out(out) {
ifstream input;
input.open(feat_file);
if (!input) {
*out << "Cannot open " << feat_file << endl;
out->print_err();
exit(1);
}
string line;
string tmp_field;
int line_nr =1;
FeatRef feat_ptr;
*out << "Reading features from " << feat_file << endl;
out->print_err();
while (getline(input, line)) {
istringstream iss(line);
int i =0;
while(getline(iss, tmp_field, '\t') && i < 2) { // split at tab and read exactly 2 fields
remove_dos_cr(&tmp_field);
if (i==0) { // SMARTS
feat_ptr = new Feature<FeatureType>(tmp_field); // initialize Feature with smarts
feature_map[tmp_field] = feat_ptr;
features.push_back(feat_ptr);
}
else { // MATCHES
size_t startpos = 0, endpos = 0;
vector<string> tokens;
for (;;) {
startpos = tmp_field.find_first_not_of(" \t\n",startpos);
endpos = tmp_field.find_first_of(" \t\n",startpos);
if (endpos < tmp_field.size() && startpos <= tmp_field.size())
tokens.push_back(tmp_field.substr(startpos,endpos-startpos));
else
break;
startpos = endpos + 1;
}
for (unsigned int i = 0 ; i < tokens.size() ; i++ ) {
if ( tokens[i] == "[" )
continue;
else if ( tokens[i] == "]" )
break;
int comp_nr = atoi(tokens[i].c_str());
feat_ptr->add_match(comp_nr); // comp_nr is line number
this->get_compound(comp_nr)->add_feature(feat_ptr);
}
}
i++;
}
line_nr++;
}
input.close();
};
template <class MolType, class FeatureType, class ActivityType>
void FeatMolVect<MolType, FeatureType, ActivityType>::add_feature(MolRef s, string name) {
typename map<const string, FeatRef>::iterator pos;
pos = feature_map.find(name);
if (pos != feature_map.end())
s->add_feature(pos->second);
};
template <class MolType, class FeatureType, class ActivityType>
void FeatMolVect<MolType, FeatureType, ActivityType>::copy_level(vector<Feature<FeatureType> *> * level, MolRef test_comp) {
typename vector<Feature<FeatureType> *>::iterator frag;
typename map<const string, Feature<FeatureType> *>::iterator pos;
string name;
for (frag = level->begin(); frag != level->end(); frag++) {
name = (*frag)->get_name();
if ((*frag)->nr_matches() == 0) {
test_comp->add_unknown(name);
delete *frag; // free memory
*frag = NULL;
level->erase(frag);
frag--; // set the iterator back to avoid skipping the next compound
}
else // search in the feature_map
this->add_feature(test_comp,name);
}
};
#endif // F_DB_H
