void TTable::Count(TStr CountColName, TStr Col){
if(!ColTypeMap.IsKey(Col)){TExcept::Throw("no such column " + Col);}
TIntV CntCol(NumRows);
switch(GetColType(Col)){
case INT:{
THash<TInt,TIntV> T; // can't really estimate the size of T for constructor hinting
TIntV& Column = IntCols[GetColIdx(Col)];
GroupByIntCol(Col, T, TIntV(0), true);
for(TRowIterator it = BegRI(); it < EndRI(); it++){
CntCol[it.GetRowIdx()] = T.GetDat(Column[it.GetRowIdx()]).Len();
}
break;
}
case FLT:{
THash<TFlt,TIntV> T;
TFltV& Column = FltCols[GetColIdx(Col)];
GroupByFltCol(Col, T, TIntV(0), true);
for(TRowIterator it = BegRI(); it < EndRI(); it++){
CntCol[it.GetRowIdx()] = T.GetDat(Column[it.GetRowIdx()]).Len();
}
break;
}
case STR:{
THash<TStr,TIntV> T;
GroupByStrCol(Col, T, TIntV(0), true);
for(TRowIterator it = BegRI(); it < EndRI(); it++){
CntCol[it.GetRowIdx()] = T.GetDat(GetStrVal(Col, it.GetRowIdx())).Len();
}
}
}
// add count column
IntCols.Add(CntCol);
AddSchemaCol(CountColName, INT);
ColTypeMap.AddDat(CountColName, TPair<TYPE,TInt>(INT, IntCols.Len()-1));
}
void GetParameter(int argc, const char* argv[], Option & opt) {
if (argc <= 2 || argv == NULL)
PrintSynopsis();
else {
PrintOutVersion();
cout << "--INFO-- Input command:";
for (int i = 0; i < argc; i++) {
cout << " " << argv[i];
}
cout << endl;
opt.refFile = argv[1];
cout << "--INFO-- The reference file is " << opt.refFile << endl;
opt.bIndexExist = 0;
string indexsf = ".sdindex";
if (opt.refFile.size() > indexsf.size()
&& opt.refFile.substr(opt.refFile.size() - indexsf.size()) == indexsf) {
opt.bIndexExist = 1;
}
opt.readsFile = argv[2];
cout << "--INFO-- The reads file is " << opt.readsFile << "." << endl;
if (GetIntVal(argc, argv, "-v", opt.mapOpt.nMaxMismatch) == 0)
opt.mapOpt.nMaxMismatch = 2;
if (GetStrVal(argc, argv, "-o", opt.outputFile) == 0) {
string fileName;
GetNameBeforeDot(opt.readsFile, fileName);
opt.outputFile = fileName;
opt.outputFile += ".sam";
}
opt.bSaveIndex = 0;
if (ChkStrExist(argc, argv, "-s")) {
opt.bSaveIndex = 1;
}
if (GetStrVal(argc, argv, "-s", opt.indexFile) == 0
&& opt.bSaveIndex == 1) {
string fileName;
GetNameBeforeDot(opt.refFile, fileName);
opt.indexFile = fileName;
opt.indexFile += indexsf;
}
GetReadLength(opt);
}
}
void GetParameter(int argc, const char* argv[], Option & opt) {
LOG_INFO;
if (argc <= 2 || argv == NULL)
PrintSynopsis();
else {
opt.refFile = argv[1];
cout << "The reference file is " << opt.refFile << endl;
cout << opt.refFile.length() << endl;
cout << opt.refFile.size() << endl;
opt.bIndexExist = 0;
cout << opt.refFile.size() << endl;
cout << opt.refFile.substr(opt.refFile.size() - 6) << endl;
cout << "hah" << endl;
if (opt.refFile.size() > 6
&& opt.refFile.substr(opt.refFile.size() - 6) == ".index") {
opt.bIndexExist = 1;
}
opt.readsFile = argv[2];
cout << "The reads file is " << opt.readsFile << endl;
if (GetIntVal(argc, argv, "-v", opt.mapOpt.nMaxMismatch) == 0)
opt.mapOpt.nMaxMismatch = 2;
if (GetStrVal(argc, argv, "-o", opt.outputFile) == 0) {
string fileName;
GetNameBeforeDot(opt.readsFile, fileName);
opt.outputFile = fileName;
opt.outputFile += ".sam";
}
opt.bSaveIndex = 0;
if (ChkStrExist(argc, argv, "-s")) {
opt.bSaveIndex = 1;
}
if (GetStrVal(argc, argv, "-s", opt.indexFile) == 0
&& opt.bSaveIndex == 1) {
string fileName;
GetNameBeforeDot(opt.refFile, fileName);
opt.indexFile = fileName;
opt.indexFile += ".index";
}
}
}
void TTable::GroupByStrCol(TStr GroupBy, THash<TStr,TIntV>& Grouping, const TIntV& IndexSet, TBool All) const{
if(!ColTypeMap.IsKey(GroupBy)){TExcept::Throw("no such column " + GroupBy);}
if(GetColType(GroupBy) != STR){TExcept::Throw(GroupBy + " values are not of expected type string");}
if(All){
// optimize for the common and most expensive case - itearte over all valid rows
for(TRowIterator it = BegRI(); it < EndRI(); it++){
UpdateGrouping<TStr>(Grouping, it.GetStrAttr(GroupBy), it.GetRowIdx());
}
} else{
// consider only rows in IndexSet
for(TInt i = 0; i < IndexSet.Len(); i++){
if(IsRowValid(IndexSet[i])){
TInt RowIdx = IndexSet[i];
UpdateGrouping<TStr>(Grouping, GetStrVal(GroupBy, RowIdx), RowIdx);
}
}
}
}
void glutInitDisplayString(const char *string)
{
const char *p = string;
int val;
while(*p) {
if(*p == ' ')
p++;
else
if(memcmp(p, "acca", 4) == 0) {
p = GetStrVal(p+4, &AccumSize, 1, 32);
SetAttrib(AccumSize, GLUT_ACCUM);
} else
if(memcmp(p, "acc", 3) == 0) {
p = GetStrVal(p+3, &AccumSize, 1, 32);
SetAttrib(AccumSize, GLUT_ACCUM);
} else
if(memcmp(p, "depth", 5) == 0) {
p = GetStrVal(p+5, &DepthSize, 12, 32);
SetAttrib(DepthSize, GLUT_DEPTH);
} else
if(memcmp(p, "double", 6) == 0) {
val = 1;
p = GetStrVal(p+6, &val, 0, 1);
SetAttrib(val, GLUT_DOUBLE);
} else
if(memcmp(p, "index", 5) == 0) {
val = 1;
p = GetStrVal(p+5, &val, 0, 1);
SetAttrib(val, GLUT_INDEX);
} else
if(memcmp(p, "stencil", 7) == 0) {
p = GetStrVal(p+7, &StencilSize, 0, 1);
SetAttrib(StencilSize, GLUT_STENCIL);
} else
if(memcmp(p, "samples", 7) == 0) {
NumSamples = 1;
p = GetStrVal(p+7, &NumSamples, 0, 16);
SetAttrib(NumSamples, GLUT_MULTISAMPLE);
} else
if(p = strchr(p, ' '))
p++;
else
break;
}
}
