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#include "distcdataset.h"
#include "getdistscommand.h"
#include "listseqscommand.h"
#include "getseqscommand.h"
/***********************************************************************/
DistCDataSet::DistCDataSet() {
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
columnFile = "/Users/sarahwestcott/Desktop/mothur/TestMothur/TestFiles/stability.MISeq_SOP.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.dist";
countFile = "/Users/sarahwestcott/Desktop/mothur/TestMothur/TestFiles/stability.count_table";
}
/***********************************************************************/
vector<string> DistCDataSet::getFiles(int numSeqs) {
vector<string> newFiles;
if (numSeqs > 2055) { m->mothurOut("[ERROR]: too many seqs requested in DistCDataSet::getFiles\n"); }
else {
string inputString = "count=" + countFile;
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: list.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* listCommand = new ListSeqsCommand(inputString);
listCommand->execute();
map<string, vector<string> > filenames = listCommand->getOutputFiles();
delete listCommand;
current->setMothurCalling(false);
string accnosfile = filenames["accnos"][0];
m->mothurOut("/******************************************/\n");
ifstream in;
util.openInputFile(accnosfile, in);
ofstream out;
util.openOutputFile("temp.accnos", out);
int count = 0; string name;
while(!in.eof()) {
if (m->getControl_pressed()) { break; }
in >> name; util.gobble(in);
out << name << endl;
count++;
if (count >= numSeqs) { break; }
}
in.close();
out.close();
util.mothurRemove(accnosfile);
inputString = "count=" + countFile + ", accnos=temp.accnos";
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* getCommand = new GetSeqsCommand(inputString);
getCommand->execute();
filenames = getCommand->getOutputFiles();
delete getCommand;
current->setMothurCalling(false);
string newCountfile = filenames["count"][0];
m->mothurOut("/******************************************/\n");
inputString = "column=" + columnFile + ", accnos=temp.accnos";
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.dists(" + inputString + ")\n");
current->setMothurCalling(true);
Command* getDCommand = new GetDistsCommand(inputString);
getDCommand->execute();
filenames = getDCommand->getOutputFiles();
delete getDCommand;
current->setMothurCalling(false);
string newColumnfile = filenames["column"][0];
m->mothurOut("/******************************************/\n");
newFiles.push_back(newColumnfile); newFiles.push_back(newCountfile);
}
return newFiles;
}
/***********************************************************************/
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