vector<string> setParameters();
string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
int screenNameGroupFile(set<string>);
int screenGroupFile(set<string>);
+ int screenCountFile(set<string>);
int screenAlignReport(set<string>);
int screenQual(set<string>);
int screenTaxonomy(set<string>);
#endif
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+ string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile;
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
vector<string> outputNames;
vector<string> optimize;
in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
}
- pDataArray->count = pDataArray->end;
+
for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+ pDataArray->count++;
+
if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
Sequence current(in); pDataArray->m->gobble(in);
in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
}
- pDataArray->count = pDataArray->end;
for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+ pDataArray->count++;
+
if (pDataArray->m->control_pressed) { in.close(); badAccnosFile.close(); goodFile.close(); pDataArray->count = 1; return 1; }
Sequence currSeq(in); pDataArray->m->gobble(in);