try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+ //CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if (countfile != "" && namefile != "") { m->mothurOut("Cannot have both a name file and count file. Please use one or the other."); m->mothurOutEndLine(); abort = true; }
if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
list = new ListVector(nameMap->getListVector());
RAbundVector* rabund = NULL;
- if(large) {
- map<string, int> nameMapCounts = m->readNames(namefile);
- createRabund(nameMapCounts);
+ if(countfile != "") {
+ //map<string, int> nameMapCounts = m->readNames(namefile);
+ CountTable ct = new CountTable();
+ ct.readTable(countfile);
+ createRabund(ct, list);
rabund = &rav;
}else {
rabund = new RAbundVector(list->getRAbundVector());
//**********************************************************************************************************************
-void MGClusterCommand::createRabund(map<string, int> nameMapCounts){
+void MGClusterCommand::createRabund(CountTable ct, ListVector list){
try {
- //RAbundVector rav;
- map<string,int>::iterator it;
- //it = nameMapCounts.begin();
- //for(int i = 0; i < list->getNumBins(); i++) { rav.push_back((*it).second); it++; }
- for ( it=nameMapCounts.begin(); it!=nameMapCounts.end(); it++ ) { rav.push_back( it->second ); }
+ //vector<string> names = ct.getNamesOfSeqs();
+
+ //for ( int i; i < ct.getNumGroups(); i++ ) { rav.push_back( ct.getNumSeqs(names[i]) ); }
//return rav;
+
+ for(int i = 0; i < list->getNumBins(); i++) {
+ vector<string> binNames;
+ string bin = list->get(i);
+ m->splitAtComma(bin, binNames);
+ int total = 0;
+ for (int j = 0; j < binNames.size(); j++) {
+ total += ct->getNumSeqs(binNames[j]);
+ }
+ rav.push_back(total);
+ }
+
+
}
catch(exception& e) {
m->errorOut(e, "MGClusterCommand", "createRabund");
#include "hcluster.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
+#include "counttable.h"
/**********************************************************************/
vector<seqDist> overlapMatrix;
vector<string> outputNames;
- string blastfile, method, namefile, overlapFile, distFile, outputDir;
+ string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
ofstream sabundFile, rabundFile, listFile;
double cutoff;
float penalty;
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);
- void createRabund(map<string, int>);
+ void createRabund(CountTable);
};