Commit ac2e56d3 authored by Carsten Kemena's avatar Carsten Kemena

started alignment output

parent e99789e7
......@@ -58,6 +58,15 @@ struct RadsOptions
};*/
struct RadsQueryResult
{
BSDL::DomainArrangement<BSDL::Domain> queryDA;
std::string alnString1;
std::string alnString2;
};
struct RadsHit
{
std::string targetName;
......
......@@ -57,7 +57,7 @@ int
main(int argc, char *argv[])
{
std::string version(std::string(STR(MAJOR_VERSION)) + "." + std::string(STR(MINOR_VERSION)) + "." + std::string(STR(PATCH_VERSION)) );
fs::path queryDomainFile, querySeqFile, outFile, domainDB;
fs::path queryDomainFile, querySeqFile, outFile, domainDB, alignmentFile;
fs::path prefix;
vector<std::string> q, domains;
......@@ -67,6 +67,7 @@ main(int argc, char *argv[])
("help,h", "Produces this help message")
("db,d", po::value<fs::path>(&prefix)->required(), "The database prefix")
("out,o", po::value<fs::path>(&outFile)->value_name("FILE"), "The output file")
("alignments,a", po::value<fs::path>(&alignmentFile)->value_name("FILE"), "File to write the alignments into")
("threads,n", po::value<unsigned short>(&nThreads)->default_value(1), "The number of threads to use")
;
......@@ -143,7 +144,6 @@ main(int argc, char *argv[])
domainDB = settings["pfam_db"];
}
BioSeqDataLib::DSM simMat;
try
{
......@@ -231,6 +231,7 @@ main(int argc, char *argv[])
buf << "# -------------------------------------------------------------------\n";
buf.setf(ios::fixed, ios::floatfield);
buf.precision(2);
for (auto &result : results)
{
const auto &hit = result.second;
......
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