void createTestFeatureMapSimVector_(FeatureMapSimVector& feature_maps)
{
feature_maps.clear();
// first feature map TVQMENQFVAFVDK,ACHKKKKHHACAC,AAAAHTKLRTTIPPEFG,RYCNHKTUIKL
FeatureMapSim fm1,fm2;
ProteinHit prothit1,prothit2,prothit3,prothit4,prothit5,prothit6;
// create first map
prothit1.setSequence("AAAAAAAKHHHHHHHHHHH");
prothit1.setMetaValue("description", "test sequence 1");
prothit1.setAccession("ACC1");
prothit1.setMetaValue("intensity", 200.0);
prothit2.setSequence("CNHAAAAAAAAA");
prothit2.setMetaValue("description", "test sequence 2");
prothit2.setAccession("ACC2");
prothit2.setMetaValue("intensity", 100.0);
prothit3.setSequence("LDCELR");
prothit3.setMetaValue("description", "test sequence 3");
prothit3.setAccession("ACC3");
prothit3.setMetaValue("intensity", 100.0);
ProteinIdentification protIdent1;
protIdent1.insertHit(prothit1);
protIdent1.insertHit(prothit2);
protIdent1.insertHit(prothit3);
vector<ProteinIdentification> protIdents_vec1;
protIdents_vec1.push_back(protIdent1);
fm1.setProteinIdentifications(protIdents_vec1);
// create labeled map
prothit4.setSequence("AAAAAAAKHHHHHHHHHHH"); // same as protein 1 from first map
prothit4.setMetaValue("description", "test sequence 4");
prothit4.setAccession("ACC4");
prothit4.setMetaValue("intensity", 50.0);
prothit5.setSequence("CNHAAAAAAAAA");
prothit5.setMetaValue("description", "test sequence 5");
prothit5.setAccession("ACC5");
prothit5.setMetaValue("intensity", 100.0);
prothit6.setSequence("CNHAADDAAAAA");
prothit6.setMetaValue("description", "test sequence 6");
prothit6.setAccession("ACC6");
prothit6.setMetaValue("intensity", 120.0);
ProteinIdentification protIdent2;
protIdent2.insertHit(prothit4);
protIdent2.insertHit(prothit5);
protIdent2.insertHit(prothit6);
vector<ProteinIdentification> protIdents_vec2;
protIdents_vec2.push_back(protIdent2);
fm2.setProteinIdentifications(protIdents_vec2);
feature_maps.push_back(fm1);
feature_maps.push_back(fm2);
}
void digestFeaturesMapSimVector_(FeatureMapSimVector& feature_maps)
{
// digest here
DigestSimulation digest_sim;
Param p;
p.setValue("model", "naive");
p.setValue("model_naive:missed_cleavages", 0);
digest_sim.setParameters(p);
std::cout << digest_sim.getParameters() << std::endl;
for(FeatureMapSimVector::iterator iter = feature_maps.begin() ; iter != feature_maps.end() ; ++iter)
{
digest_sim.digest((*iter));
}
}
FeatureMapSim BaseLabeler::mergeProteinIdentificationsMaps_(const FeatureMapSimVector & maps)
{
// we do not have any features yet (or at least we ignore them), so simply iterate over the protein
// identifications
std::map<String, ProteinHit> prot_hits;
Size channel_index = 1;
for (FeatureMapSimVector::const_iterator maps_iterator = maps.begin(); maps_iterator != maps.end(); ++maps_iterator)
{
if (maps_iterator->getProteinIdentifications().size() == 0)
continue;
for (std::vector<ProteinHit>::const_iterator protein_hit = (*maps_iterator).getProteinIdentifications()[0].getHits().begin();
protein_hit != (*maps_iterator).getProteinIdentifications()[0].getHits().end();
++protein_hit)
{
if (prot_hits.count((*protein_hit).getSequence())) // we already know this protein -- sum up abundances
{
SimIntensityType new_intensity = prot_hits[(*protein_hit).getSequence()].getMetaValue("intensity");
// remember channel intensity
prot_hits[(*protein_hit).getSequence()].setMetaValue("intensity_" + String(channel_index), new_intensity);
new_intensity += static_cast<SimIntensityType>((*protein_hit).getMetaValue("intensity"));
prot_hits[(*protein_hit).getSequence()].setMetaValue("intensity", new_intensity);
}
else // new protein hit .. remember
{
ProteinHit protHit(*protein_hit);
protHit.setMetaValue("intensity_" + String(channel_index), protHit.getMetaValue("intensity"));
prot_hits.insert(std::pair<String, ProteinHit>((*protein_hit).getSequence(), protHit));
}
}
++channel_index;
}
FeatureMapSim final_map;
ProteinIdentification protIdent;
for (std::map<String, ProteinHit>::iterator prot_hit_iter = prot_hits.begin(); prot_hit_iter != prot_hits.end(); ++prot_hit_iter)
{
protIdent.insertHit(prot_hit_iter->second);
}
std::vector<ProteinIdentification> protIdents;
protIdents.push_back(protIdent);
final_map.setProteinIdentifications(protIdents);
return final_map;
}
FeatureMapSim fm1,fm2,fm3;
FeatureMapSimVector fm_vec;
fm_vec.push_back(fm1);
TEST_EXCEPTION_WITH_MESSAGE(Exception::IllegalArgument, labeler.setUpHook(fm_vec), "1 channel(s) given. 18O Labeling only works with 2 channels. Please provide two FASTA files!")
fm_vec.push_back(fm2);
labeler.setUpHook(fm_vec);
fm_vec.push_back(fm3);
TEST_EXCEPTION_WITH_MESSAGE(Exception::IllegalArgument, labeler.setUpHook(fm_vec), "3 channel(s) given. 18O Labeling only works with 2 channels. Please provide two FASTA files!")
}
END_SECTION
START_SECTION((void postDigestHook(FeatureMapSimVector &)))
{
FeatureMapSimVector feature_maps;
createTestFeatureMapSimVector_(feature_maps);
digestFeaturesMapSimVector_(feature_maps);
// maps are digested by now
O18Labeler labeler;
labeler.postDigestHook(feature_maps);
TEST_EQUAL(feature_maps.size(), 1)
ABORT_IF(feature_maps.size() != 1)
TEST_EQUAL(feature_maps[0].size(), 6)
ABORT_IF(feature_maps[0].size() != 6)
TEST_EQUAL(feature_maps[0][0].getIntensity(), 50)
TEST_EQUAL(feature_maps[0][0].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAAAAK(Label:18O(2))")
