#include "chimera.h"
//***************************************************************************************************************
-//this is a vertical filter
+//this is a vertical soft filter
void Chimera::createFilter(vector<Sequence*> seqs) {
try {
}
}
+ //zero out spot where all sequences have blanks
//zero out spot where all sequences have blanks
int numColRemoved = 0;
for(int i = 0;i < seqs[0]->getAligned().length(); i++){
else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) { filterString[i] = '0'; numColRemoved++; }
//cout << "a = " << a[i] << " t = " << t[i] << " g = " << g[i] << " c = " << c[i] << endl;
}
+
//cout << "filter = " << filterString << endl;
mothurOut("Filter removed " + toString(numColRemoved) + " columns."); mothurOutEndLine();
ifstream in;
openInputFile(file, in);
vector<Sequence*> container;
+ int count = 0;
+ int length = 0;
+ unaligned = false;
//read in seqs and store in vector
while(!in.eof()){
- Sequence* current = new Sequence(in);
- container.push_back(current);
- gobble(in);
+ Sequence* current = new Sequence(in); gobble(in);
+
+ if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
+ else if (length != current->getAligned().length()) { //seqs are unaligned
+ unaligned = true;
+ }
+
+ if (current->getName() != "") { container.push_back(current); }
}
in.close();
openInputFile(quanfile, in);
vector< vector<float> > quan;
+ vector <float> temp; temp.resize(6, 0);
+
+ //to fill 0
+ quan.push_back(temp);
int num; float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
- vector <float> temp;
+ temp.clear();
temp.push_back(ten);
temp.push_back(twentyfive);