vector<string> setParameters();
string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
vector<string> outputNames;
vector<string> optimize;
map<string, int> nameMap;
- int readNames();
int getSummary(vector<unsigned long long>&);
int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
int count;
MothurOut* m;
string goodFName, badAccnosFName, filename;
- set<string>* badSeqNames;
+ set<string> badSeqNames;
sumScreenData(){}
- sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf, set<string>* bn) {
+ sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf) {
startPos = s;
endPos = e;
minLength = minl;
m = mout;
start = st;
end = en;
- badSeqNames = bn;
count = 0;
}
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MySumThreadFunction(LPVOID lpParam){
sumData* pDataArray;
}
else{
badAccnosFile << currSeq.getName() << endl;
- pDataArray->badSeqNames->insert(currSeq.getName());
+ pDataArray->badSeqNames.insert(currSeq.getName());
}
}