string extension = toString(i) + ".temp";
// Allocate memory for thread data.
- pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
+ pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, i);
pDataArray.push_back(tempDist);
processIDS.push_back(i);
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();
alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
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 (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
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'; }
if (output == "lt") { outFile << endl; }
if(i % 100 == 0){
- m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
- m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << "num less than 0.01 = " << countSmall << " of " << countAll << endl;
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+
outFile.close();
delete alignment;
delete distCalculator;
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- outFile << dist << '\t';
+ outFile << dist << '\t';
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outFile << endl;
if(i % 100 == 0){
- m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
- m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete alignment;
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
+
+ if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
if(dist <= cutoff){
outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
+
+ if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
outputString += toString(dist) + "\t";
}
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- outputString += toString(dist) + "\t";
+ outputString += toString(dist) + "\t";
+
+ if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outputString += "\n";