int RemoveGroupsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
groupMap->readMap();
//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
vector<string> namesGroups = groupMap->getNamesOfGroups();
vector<string> checkedGroups;
for (int i = 0; i < Groups.size(); i++) {
if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
else { m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
}
if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
else {
Groups = checkedGroups;
m->setGroups(Groups);
}
//fill names with names of sequences that are from the groups we want to remove
fillNames();
delete groupMap;
}else if (countfile != ""){
if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
CountTable ct;
ct.readTable(countfile, true, false);
if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
vector<string> gNamesOfGroups = ct.getNamesOfGroups();
SharedUtil util;
util.setGroups(Groups, gNamesOfGroups);
vector<string> namesOfSeqs = ct.getNamesOfSeqs();
sort(Groups.begin(), Groups.end());
for (int i = 0; i < namesOfSeqs.size(); i++) {
vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
names.insert(namesOfSeqs[i]);
}
}
}
if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
if (countfile != "") { readCount(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (sharedfile != "") { readShared(); }
if (designfile != "") { readDesign(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
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();
//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); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
itTypes = outputTypes.find("design");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "execute");
exit(1);
}
}
void ModelsimGenerator::parseFiles( QSharedPointer<Component> component, const QString& viewName ) {
Q_ASSERT_X(component, "ModelsimGenerator::parseFiles",
"Null component-pointer given as parameter");
// inform user that component is being processed
emit noticeMessage(tr("Processing view %1 of component %2:%3:%4:%5").arg(
viewName).arg(
component->getVlnv()->getVendor()).arg(
component->getVlnv()->getLibrary()).arg(
component->getVlnv()->getName()).arg(
component->getVlnv()->getVersion()));
// pointer to the named view under given component
View* view = component->findView(viewName);
// if view was not found
if (!view) {
// if component does not contain any views
if (component->viewCount() == 0) {
emit noticeMessage(tr("Component %1 didn't contain any views, "
"adding all found RTL-files from component file sets.").arg(
component->getVlnv()->getName()));
parseBlindFileSet(component);
viewName_ = viewName;
return;
}
// component did contain views but not the specified view
else {
emit errorMessage(tr("View %1 not found within component %2").arg(
viewName).arg(component->getVlnv()->getName()));
return;
}
}
// if the view was found but was not hierarchical
if (view && !view->isHierarchical()) {
// ask which file sets are included in the view
QStringList fileSets = view->getFileSetRefs();
// parse the file sets from the component and add them to the list of files
parseFileSets(component, fileSets);
}
// view was found and was hierarchical
else if (view && view->isHierarchical()) {
VLNV designVLNV;
QSharedPointer<Design> design;
VLNV desConfVLNV;
QSharedPointer<DesignConfiguration> designConf;
VLNV vlnv = view->getHierarchyRef();
// if the specified vlnv is not found within library
if (!handler_->contains(vlnv)) {
emit errorMessage(tr("Hierarchy reference %1:%2:%3:%4 referenced "
"within view %5 in component %6 was not found in the library."
" Stopping generation.").arg(
vlnv.getVendor()).arg(
vlnv.getLibrary()).arg(
vlnv.getName()).arg(
vlnv.getVersion()).arg(
viewName).arg(
component->getVlnv()->getName()));
return;
}
// get the real type of the referenced document
vlnv.setType(handler_->getDocumentType(vlnv));
// if component contained reference to a design configuration
if (vlnv.getType() == VLNV::DESIGNCONFIGURATION) {
// parse the design configuration
desConfVLNV = vlnv;
QSharedPointer<LibraryComponent> libComp = handler_->getModel(desConfVLNV);
designConf = libComp.staticCast<DesignConfiguration>();
// find the referenced design
designVLNV = designConf->getDesignRef();
}
// if component contained direct reference to a design
else if (vlnv.getType() == VLNV::DESIGN) {
designVLNV = vlnv;
}
// if item was some other type
else {
emit errorMessage(tr("Item %1:%2:%3:%4 was not neither design or "
"design configuration, stopping generation.").arg(
vlnv.getVendor()).arg(
vlnv.getLibrary()).arg(
vlnv.getName()).arg(
vlnv.getVersion()));
return;
}
// if design does not exist
if (!handler_->contains(designVLNV)) {
emit errorMessage(tr("Design %1:%2:%3:%4 referenced within "
"design configuration %5 was not found within library. "
"Stopping generation.").arg(
designVLNV.getVendor()).arg(
designVLNV.getLibrary()).arg(
designVLNV.getName()).arg(
designVLNV.getVersion()).arg(
desConfVLNV.getName()));
return;
}
// parse the design
QSharedPointer<LibraryComponent> libComp = handler_->getModel(designVLNV);
design = libComp.staticCast<Design>();
// read the design and it's component instances
readDesign(design, designConf);
// if this view contains a reference to a view that contains component's
// top level implementation
QString topLevelView = view->getTopLevelView();
if (!topLevelView.isEmpty()) {
parseFiles(component, topLevelView);
}
}
viewName_ = viewName;
sourceXml_ = handler_->getPath(*component->getVlnv());
}