outFile << setprecision(4);
if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
-
+ int countSmall = 0;
+ int countAll = 0;
for(int i=startLine;i<endLine;i++){
if(output == "lt") {
string name = alignDB.get(i).getName();
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
-
+ //cout << seqI.getName() << '\t' << seqJ.getName() << endl;
+ //cout << alignment->getSeqAAln() << endl << alignment->getSeqBAln() << endl;
+
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
-
+
+ //cout << "dist = " << dist << endl;
+
if(dist <= cutoff){
+ if (dist < 0.01) { countSmall++; }
+ countAll++;
+
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
if (output == "lt") { outFile << dist << '\t'; }
}
m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-
+ cout << "num less than 0.01 = " << countSmall << " of " << countAll << endl;
outFile.close();
delete alignment;
delete distCalculator;