void ToolsConfigWidget::readConfig()
{
readGroup("Tool Menu", &m_toolsmenuEntries);
readGroup("File Context", &m_filecontextEntries);
readGroup("Dir Context", &m_dircontextEntries);
updateListBoxes();
}
static void
activateCB_pushButton11(
Widget wgt,
XtPointer cd,
XtPointer cb)
{
_UxCgroupNamesForm *UxSaveCtx,
*UxContext;
Widget UxWidget = wgt;
XtPointer UxClientData = cd;
XtPointer UxCallbackArg = cb;
UxSaveCtx = UxGroupNamesFormContext;
UxGroupNamesFormContext = UxContext =
(_UxCgroupNamesForm *) UxGetContext(UxWidget);
{
DMAN_GROUPNAMES g;
CONDITION cond;
cond = readGroup(&g);
if (cond != 1) {
COND_DumpConditions();
return;
}
cond = DMAN_Delete(&dmanHandle, (DMAN_GENERICRECORD *) & g);
if (cond != DMAN_NORMAL)
COND_DumpConditions();
loadGroupGroupList();
loadGroupTitleList(g.GroupName);
}
UxGroupNamesFormContext = UxSaveCtx;
}
/**
* Add a new group definition to the ELSTABLE. Returns 0 if OK, -1 if parsing FORMULA
* fails. Assumes the syntax of grpname is correct.
*/
QString KMolCalc::defineGroup (const QString& grpname, const QString& formula) {
ElementList* els = new ElementList(grpname);
QString error = readGroup(formula, els);
if (error != "OK")
return error;
if (els->contains(grpname))
return QString("Can't define a group recursively!\n");
elstable->replace(grpname, els);
return QString("OK");
}
int ListSeqsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
//read functions fill names vector
if (fastafile != "") { inputFileName = fastafile; readFasta(); }
else if (fastqfile != "") { inputFileName = fastqfile; readFastq(); }
else if (namefile != "") { inputFileName = namefile; readName(); }
else if (groupfile != "") { inputFileName = groupfile; readGroup(); }
else if (alignfile != "") { inputFileName = alignfile; readAlign(); }
else if (listfile != "") { inputFileName = listfile; readList(); }
else if (taxfile != "") { inputFileName = taxfile; readTax(); }
else if (countfile != "") { inputFileName = countfile; readCount(); }
if (m->getControl_pressed()) { outputTypes.clear(); return 0; }
//sort in alphabetical order
sort(names.begin(), names.end());
if (outputDir == "") { outputDir += util.hasPath(inputFileName); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(inputFileName));
string outputFileName = getOutputFileName("accnos", variables);
util.printAccnos(outputFileName, names);
outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFileName); return 0; }
current->setAccnosFile(outputFileName);
m->mothurOut("\nOutput File Names: \n");
m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
//set accnos file as new current accnosfile
string currentName = "";
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setAccnosFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ListSeqsCommand", "execute");
exit(1);
}
}
int main(int argc, const char * argv[]) {
Tgroup contestants;
int size = readGroup(&contestants);
int winner_index = findLeast_time(contestants, size);
calc_timeLag(&contestants, size, winner_index);
printf("\nThe winner is:\n\n");
printWinners(contestants, size, winner_index);
printf("\nThe result list:\n\n");
printLoosers(contestants, size, winner_index);
printf("\n\n"); return 0;
}
void SearchGroup::read(SearchXmlCachingReader& reader)
{
reset();
m_label->setGroupOperator(reader.groupOperator());
m_label->setDefaultFieldOperator(reader.defaultFieldOperator());
startReadingGroups(reader);
while (!reader.atEnd())
{
reader.readNext();
if (reader.isEndElement())
{
break;
}
// subgroup
if (reader.isGroupElement())
{
readGroup(reader);
}
if (reader.isFieldElement())
{
QString name = reader.fieldName();
SearchField* field = 0;
SearchFieldGroup* fieldGroup = 0;
foreach(fieldGroup, m_fieldGroups)
{
if ((field = fieldGroup->fieldForName(name)))
{
break;
}
}
if (field)
{
field->read(reader);
fieldGroup->markField(field);
fieldGroup->setFieldsVisible(true);
}
else
{
qCWarning(DIGIKAM_GENERAL_LOG) << "Unhandled search field in XML with field name" << name;
reader.readToEndOfElement();
}
}
}
void SVGReader::readSVG(void)
{
Q_ASSERT(mXml.isStartElement() && mXml.name() == "svg");
while (mXml.readNextStartElement()) {
if (mXml.name() == "g") {
readGroup();
}
else if (mXml.name() == "desc" && mXml.attributes().value("version").toString().toDouble() > 0.4) {
readDesc();
}
else {
mXml.skipCurrentElement();
}
}
}
bool JsonFileReader::read(const std::string &fileDir)
{
QFile loadFile(QString::fromUtf8(fileDir.c_str()));
if (!loadFile.open(QIODevice::ReadOnly)) {
return false;
}
QByteArray saveData = loadFile.readAll();
QJsonDocument loadDoc(QJsonDocument::fromJson(saveData));
QJsonObject jsonObj = loadDoc.object();
QJsonArray canvasShapes = jsonObj["CanvasShapes"].toArray();
readGroup(m_mainGroup, canvasShapes);
return true;
}
MeshData* LoadObj::readObjFile(std::string pObj)
{
bool first = true;
fstream f(pObj.c_str());
string tmp;
if(f)
{
while(f.eof() != true)
{
f >> tmp;
if(tmp == "v")
readVertices(f);
if(tmp == "vt")
readTexC(f);
if(tmp == "vn")
readNormal(f);
if(tmp == "f")
readFaces(f);
if(tmp == "mtllib")
readMtl(f);
if(tmp == "g")
readGroup(f);
if(f.eof())
break;
}
}
MeshData* data = new MeshData();
data->position = position;
data->textureCoordinate = textureCoordinate;
data->normal = normal;
data->vertices = vertices;
data->indices = indices;
reset();
return data;
}
void ContactsReader::readQNS(void)
{
Q_ASSERT(isStartElement() && name() == "qns");
while (!atEnd())
{
readNext();
if (isEndElement())
break;
if (isStartElement())
{
if (name() == "Group")
readGroup(0);
else if (name() == "Contact")
readContact(0);
else if (name() == "BlockedContact")
readBlocked();
else
readUnknownElement();
}
}
}
int GetSeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
names = m->readAccnos(accnosfile);
if (m->control_pressed) { return 0; }
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");
}
}
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (fastqfile != "") { readFastq(); }
if (groupfile != "") { readGroup(); }
if (countfile != "") { readCount(); }
if (alignfile != "") { readAlign(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (qualfile != "") { readQual(); }
if (accnosfile2 != "") { compareAccnos(); }
if (m->debug) { runSanityCheck(); }
if (m->control_pressed) { outputTypes.clear(); 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("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(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, "GetSeqsCommand", "execute");
exit(1);
}
}
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);
}
}
bool WRL1BASE::ReadNode( WRLPROC& proc, WRL1NODE* aParent, WRL1NODE** aNode )
{
// This function reads a node and stores a pointer to it in aNode.
// A value 'true' is returned if a node is successfully read or,
// if the node is not supported, successfully discarded. Callers
// must always check the value of aNode when the function returns
// 'true' since it will be NULL if the node type is not supported.
if( NULL != aNode )
*aNode = NULL;
if( NULL == aParent )
{
#ifdef DEBUG_VRML1
do {
std::ostringstream ostr;
ostr << __FILE__ << ": " << __FUNCTION__ << ": " << __LINE__ << "\n";
ostr << " * [BUG] invalid parent pointer (NULL)";
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
} while( 0 );
#endif
return false;
}
std::string glob;
WRL1NODES ntype;
if( !proc.ReadName( glob ) )
{
#if defined( DEBUG_VRML1 ) && ( DEBUG_VRML1 > 1 )
if( !proc.eof() )
{
std::ostringstream ostr;
ostr << __FILE__ << ": " << __FUNCTION__ << ": " << __LINE__ << "\n";
ostr << proc.GetError();
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
}
#endif
return false;
}
// Process node name:
// the names encountered at this point should be one of the
// built-in node names or one of:
// DEF, USE
if( !glob.compare( "USE" ) )
{
if( !implementUse( proc, aParent, aNode ) )
{
#if defined( DEBUG_VRML1 ) && ( DEBUG_VRML1 > 1 )
do {
std::ostringstream ostr;
ostr << __FILE__ << ": " << __FUNCTION__ << ": " << __LINE__ << "\n";
ostr << proc.GetError();
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
} while( 0 );
#endif
return false;
}
return true;
}
if( !glob.compare( "DEF" ) )
{
if( !implementDef( proc, aParent, aNode ) )
{
#if defined( DEBUG_VRML1 ) && ( DEBUG_VRML1 > 1 )
do {
std::ostringstream ostr;
ostr << __FILE__ << ": " << __FUNCTION__ << ": " << __LINE__ << "\n";
ostr << proc.GetError();
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
} while( 0 );
#endif
return false;
}
return true;
}
ntype = getNodeTypeID( glob );
size_t line = 0;
size_t column = 0;
proc.GetFilePosData( line, column );
#if defined( DEBUG_VRML1 ) && ( DEBUG_VRML1 > 2 )
do {
std::ostringstream ostr;
ostr << " * [INFO] Processing node '" << glob << "' ID: " << ntype;
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
} while( 0 );
#endif
switch( ntype )
{
case WRL1_GROUP:
if( !readGroup( proc, aParent, aNode ) )
return false;
break;
case WRL1_SEPARATOR:
if( !readSeparator( proc, aParent, aNode ) )
return false;
break;
case WRL1_SWITCH:
if( !readSwitch( proc, aParent, aNode ) )
return false;
break;
case WRL1_MATERIAL:
if( !readMaterial( proc, aParent, aNode ) )
return false;
break;
case WRL1_MATERIALBINDING:
if( !readMatBinding( proc, aParent, aNode ) )
return false;
break;
case WRL1_COORDINATE3:
if( !readCoords( proc, aParent, aNode ) )
return false;
break;
case WRL1_INDEXEDFACESET:
if( !readFaceSet( proc, aParent, aNode ) )
return false;
break;
case WRL1_TRANSFORM:
case WRL1_TRANSLATION:
case WRL1_ROTATION:
case WRL1_SCALE:
if( !readTransform( proc, aParent, aNode ) )
return false;
break;
case WRL1_SHAPEHINTS:
if( !readShapeHints( proc, aParent, aNode ) )
return false;
break;
//
// items not implemented or for optional future implementation:
//
default:
proc.GetFilePosData( line, column );
if( !proc.DiscardNode() )
{
#if defined( DEBUG_VRML1 ) && ( DEBUG_VRML1 > 1 )
do {
std::ostringstream ostr;
ostr << proc.GetError() << "\n";
ostr << __FILE__ << ": " << __FUNCTION__ << ": " << __LINE__ << "\n";
ostr << " * [INFO] could not discard node at line " << line;
ostr << ", column " << column;
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
} while( 0 );
#endif
return false;
}
#if defined( DEBUG_VRML1 ) && ( DEBUG_VRML1 > 1 )
else
{
std::ostringstream ostr;
ostr << " * [INFO] discarded node '" << glob << "' at line ";
ostr << line << ", col " << column << " (currently unsupported)";
wxLogTrace( MASK_VRML, "%s\n", ostr.str().c_str() );
}
#endif
break;
}
return true;
}
void inline testID3() {
ID3Group id3G;
char inputFilePath[] = "./data/DecisionTree/buyComputer1.txt";
readGroup(id3G, inputFilePath);
}
