DispatchStatus
demo::MyHello::___testSeq(ServerRequest& __inS)
{
InputStream& __is = __inS.incoming();
OutputStream& __os = __inS.outgoing();
::demo::MyStruct cd;
cd.__read(__is);
Long lvalue;
Long __ret = testSeq(cd, lvalue);
__inS.initReply ();
__os.write_long(lvalue);
__os.write_long(__ret);
return DispatchOK;
}
/** perform a single line test */
void doTest(int x0, int y0, int x1, int y1) {
int min_visits = std::min(std::abs(x0 - x1), std::abs(y0 - y1));
cout << "\nTesting line from " << x0 << ", " << y0 << " to " << x1 << ", " << y1 << "...\n";
vector<CoOrd> results;
Visitor visitor(results);
line(x0, y0, x1, y1, visitor);
OutputCoOrd outputter;
for_each(results.begin(), results.end(), outputter);
TestSequence testSeq(*results.begin());
for_each(results.begin() + 1, results.end(), testSeq);
CPPUNIT_ASSERT(results.size() >= min_visits);
CPPUNIT_ASSERT(results.front().first == x0 && results.front().second == y0);
CPPUNIT_ASSERT(results.back().first == x1 && results.back().second == y1);
}
int main(int argc, char *argv[]) {
int A[ASIZE];
for (int i=0; i<ASIZE; i++) A[i] = rand()%10000;
testSeq(A,ASIZE);
return 0;
}
int FilterSeqsCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ifstream inFASTA;
m->openInputFile(fastafileNames[0], inFASTA);
Sequence testSeq(inFASTA);
alignmentLength = testSeq.getAlignLength();
inFASTA.close();
////////////create filter/////////////////
m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
filter = createFilter();
m->mothurOutEndLine(); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); return 0; }
ofstream outFilter;
//prevent giantic file name
map<string, string> variables;
variables["[filename]"] = outputDir + filterFileName + ".";
if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
string filterFile = getOutputFileName("filter", variables);
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
outFilter.close();
outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
////////////run filter/////////////////
m->mothurOut("Running Filter... "); m->mothurOutEndLine();
filterSequences();
m->mothurOutEndLine(); m->mothurOutEndLine();
int filteredLength = 0;
for(int i=0;i<alignmentLength;i++){
if(filter[i] == '1'){ filteredLength++; }
}
if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "execute");
exit(1);
}
}
sequence_set_t SVS_method(const unique_ptr<DFSM>& fsm, int extraStates) {
RETURN_IF_UNREDUCED(fsm, "FSMtesting::SVS_method", sequence_set_t());
if (extraStates < 0) return sequence_set_t();
auto stateCover = getStateCover(fsm);
auto traversalSet = getTraversalSet(fsm, extraStates);
traversalSet.emplace(sequence_in_t());
auto VSet = getVerifyingSet(fsm);
auto SCSets = getStatesCharacterizingSets(fsm, getStatePairsShortestSeparatingSequences, true, reduceSCSet_LS_SL);
for (int i = 0; i < SCSets.size(); i++) {
if (!VSet[i].empty()) {
SCSets[i].clear();
SCSets[i].emplace(move(VSet[i]));
}
}
bool startWithStout = (SCSets[0].begin()->front() == STOUT_INPUT);
if (fsm->isOutputState()) {
extraStates *= 2; // STOUT_INPUT follows each input in traversalSet
}
FSMlib::PrefixSet pset;
for (const auto& trSeq : stateCover) {
for (const auto& extSeq : traversalSet) {
sequence_in_t transferSeq(trSeq);
transferSeq.insert(transferSeq.end(), extSeq.begin(), extSeq.end());
state_t state = fsm->getEndPathState(0, transferSeq);
if (state == WRONG_STATE) continue;
for (const auto& SCSet : SCSets) {// i.e. VSet
for (const auto& cSeq : SCSet) {// usually only one seq = SVS
sequence_in_t testSeq(transferSeq);
if (startWithStout) {
testSeq.push_front(STOUT_INPUT);
testSeq.pop_back();// the last STOUT_INPUT (it will be at the beginning of appended cSeq)
}
testSeq.insert(testSeq.end(), cSeq.begin(), cSeq.end());
pset.insert(move(testSeq));
}
}
if (extSeq.size() == extraStates) {// check outcoming transitions
//state_t state = getIdx(states, fsm->getEndPathState(0, transferSeq));
for (input_t input = 0; input < fsm->getNumberOfInputs(); input++) {
// usually only one seq = SVS is sufficient for transition verification
//printf("%d-%d ", fsm->getNextState(state, input), SCSets[fsm->getNextState(state, input)].size());
state_t nextState = fsm->getNextState(state, input);
if (nextState == NULL_STATE) continue;
for (const auto& cSeq : SCSets[nextState]) {
sequence_in_t testSeq(transferSeq);
testSeq.push_back(input);
if (startWithStout) {
testSeq.push_front(STOUT_INPUT);
}
else if (fsm->isOutputState()) {
testSeq.push_back(STOUT_INPUT);
}
testSeq.insert(testSeq.end(), cSeq.begin(), cSeq.end());
pset.insert(move(testSeq));
}
}
}
}
}
return pset.getMaximalSequences();
}