void CommandLine::merge(const CommandLine &args)
{
// Skip first argument if it is the module name.
const int firstArg = (args.arg(0)[0] == '-' ? 0 : 1);
for (int i = firstArg; i < args.argc(); ++i)
{
append(args.arg(i));
}
}
void
AbstractTrajectoryAnalysisModuleTestFixture::runTest(const CommandLine &args)
{
TrajectoryAnalysisModule &module = impl_->module();
// Skip first argument if it is the module name.
int firstArg = (args.arg(0)[0] == '-' ? 0 : 1);
for (int i = firstArg; i < args.argc(); ++i)
{
impl_->cmdline_.append(args.arg(i));
}
TestReferenceChecker rootChecker(impl_->data_.rootChecker());
rootChecker.checkString(args.toString(), "CommandLine");
if (!impl_->outputDatasets_.empty())
{
TestReferenceChecker dataChecker(
rootChecker.checkCompound("OutputData", "Data"));
Impl::DatasetNames::const_iterator dataset;
for (dataset = impl_->outputDatasets_.begin();
dataset != impl_->outputDatasets_.end();
++dataset)
{
const char *name = dataset->c_str();
AbstractAnalysisData &dataset = module.datasetFromName(name);
AnalysisDataTestFixture::addReferenceCheckerModule(
dataChecker, name, &dataset);
}
}
TrajectoryAnalysisCommandLineRunner runner(&module);
runner.setPrintCopyright(false);
int rc = 0;
EXPECT_NO_THROW_GMX(rc = runner.run(impl_->cmdline_.argc(), impl_->cmdline_.argv()));
EXPECT_EQ(0, rc);
if (!impl_->outputFiles_.empty())
{
TestReferenceChecker outputChecker(
rootChecker.checkCompound("OutputFiles", "Files"));
Impl::OutputFileList::const_iterator outfile;
for (outfile = impl_->outputFiles_.begin();
outfile != impl_->outputFiles_.end();
++outfile)
{
std::string output = File::readToString(outfile->path);
outputChecker.checkStringBlock(output, outfile->option.c_str());
}
}
}
int Application::main(int argc,char *argv[])
{
// Process command line
cmd=new CommandLine(argc,argv,"");
if(cmd->numArgs()!=2)
throw String("\ndelete-target-gaps <in.maf> <target-name>\n");
String mafFile=cmd->arg(0);
String targetName=cmd->arg(1);
// Setting up alphabet
alphabet=&DnaDashDotAlphabet::global();
gapSymbols.addMember(alphabet->lookup('-'));
gapSymbols.addMember(alphabet->lookup('.'));
gapSymbols.addMember(alphabet->lookup('N'));
alphabetMap=new DropGapMapping(*alphabet,PureDnaAlphabet::global());
// Load the alignments
//int rootID=phylogeny->getRoot()->getID();
alignment=NULL;
ifstream is(mafFile.c_str());
if(!is.good()) throw String("Can't open file ")+mafFile;
while(!is.eof()) {
MultiAlignment *a=new MultiAlignment;
a->loadMAF(is);
if(a->getNumTracks()>0) {
a->toupper();
MultSeqAlignment *m=new MultSeqAlignment(*a,*alphabet,gapSymbols);
int rootID=m->getTrackByName(targetName).getID();
m->deleteTargetGaps(rootID);
if(!alignment) alignment=m;
else {
alignment->append(*m);
delete m;
}
}
delete a;
}
is.close();
// Emit the processed alignment
alignment->printSlice(cout,0,alignment->getLength(),'+',60);
return 0;
}