PWIZ_API_DECL size_t ProteinList::find(const string& id) const
{
for (size_t index = 0, end = size(); index < end; ++index)
if (protein(index, false)->id == id)
return index;
return size();
}
PWIZ_API_DECL IndexList ProteinList::findKeyword(const string& keyword, bool caseSensitive /*= true*/) const
{
IndexList indexList;
if (caseSensitive)
{
for (size_t index = 0, end = size(); index < end; ++index)
if (protein(index, false)->description.find(keyword) != string::npos)
indexList.push_back(index);
}
else
{
string lcKeyword = keyword;
for (size_t index = 0, end = size(); index < end; ++index)
{
string lcDescription = protein(index, false)->description;
bal::to_lower(lcDescription);
if (lcDescription.find(lcKeyword) != string::npos)
indexList.push_back(index);
}
}
return indexList;
}
// printStartQuery - prints the hit
void SpectraSTTxtSearchOutput::printHit(string query, unsigned int hitRank, SpectraSTLibEntry* entry, SpectraSTSimScores& simScores) {
if (!entry) {
(*m_fout).width(4);
(*m_fout) << "0";
(*m_fout).width(MAX_NAME_LEN);
(*m_fout) << left << "NO_MATCH";
(*m_fout) << endl;
return;
}
if (hitRank > 1) {
(*m_fout).width(MAX_NAME_LEN);
(*m_fout) << left << "--";
}
(*m_fout).width(4);
(*m_fout) << left << hitRank;
stringstream peptidess;
peptidess << entry->getName();
(*m_fout).width(MAX_NAME_LEN);
(*m_fout) << left << peptidess.str();
simScores.printFixedWidth((*m_fout));
(*m_fout).width(10);
(*m_fout) << left << entry->getStatus();
(*m_fout).width(10);
string inst("");
if (entry->getOneComment("Inst", inst)) {
(*m_fout) << left << inst;
} else {
(*m_fout) << left << "Unk";
}
(*m_fout).width(6);
string spectrumType("");
if (entry->getOneComment("Spec", spectrumType)) {
(*m_fout) << left << spectrumType.substr(0, spectrumType.length() < 3 ? spectrumType.length() : 3);
} else {
(*m_fout) << left << "Unk";
}
(*m_fout).width(20);
(*m_fout) << left << entry->getLibFileOffset();
string protein("");
stringstream proteinss;
string sample("");
string::size_type pos = 0;
if (entry->getOneComment("Protein", protein)) {
if (protein.find('/') != string::npos) {
int proteinCount = atoi(nextToken(protein, 0, pos, "/\t\r\n").c_str());
proteinss << proteinCount << ':';
bool isFirstProtein = true;
while (pos < protein.length()) {
if (!isFirstProtein) proteinss << ';';
proteinss << nextToken(protein, pos, pos, "/\t\r\n", "/");
isFirstProtein = false;
}
} else {
proteinss << '1' << ':' << protein;
}
} else if (entry->getOneComment("Sample", sample)) {
// if no protein field is given, use the sample field. (this is useful for unidentified spectra)
if (sample.find('/') != string::npos) {
int sampleCount = atoi(nextToken(sample, 0, pos, "/\t\r\n").c_str());
proteinss << sampleCount << ':';
bool isFirstSample = true;
while (pos < sample.length()) {
if (!isFirstSample) proteinss << ';';
proteinss << nextToken(sample, pos, pos, "/\t\r\n", "/");
isFirstSample = false;
}
}
} else {
proteinss << '0';
}
(*m_fout) << proteinss.str();
(*m_fout) << endl;
}
