list = new ListVector(nameMap->getListVector());
RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+ if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; return 0; }
+
start = time(NULL);
oldList = *list;
openOutputFile(fileroot+ tag + ".rabund", rabundFile);
openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+ if (m->control_pressed) {
+ delete nameMap; delete read; delete list; delete rabund;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
if (!hclusterWanted) {
//get distmatrix and overlap
SparseMatrix* distMatrix = read->getDistMatrix();
else if(method == "average"){ cluster = new AverageLinkage(rabund, list, distMatrix, cutoff, method); }
cluster->setMapWanted(true);
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
//cluster using cluster classes
while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
cluster->update(cutoff);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
float dist = distMatrix->getSmallDist();
float rndDist = roundDist(dist, precision);
if (merge) {
map<string, int> seq2Bin = cluster->getSeqtoBin();
ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
if (merge) {
map<string, int> seq2Bin = cluster->getSeqtoBin();
ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
//sort the distance and overlap files
sortHclusterFiles(distFile, overlapFile);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
//create cluster
hcluster = new HCluster(rabund, list, method, distFile, nameMap, cutoff);
vector<seqDist> seqs; seqs.resize(1); // to start loop
//ifstream inHcluster;
//openInputFile(distFile, inHcluster);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
while (seqs.size() != 0){
seqs = hcluster->getSeqs();
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
+
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
if (seqs[i].seq1 != seqs[i].seq2) {
hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
float rndDist = roundDist(seqs[i].dist, precision);
if (merge) {
map<string, int> seq2Bin = hcluster->getSeqtoBin();
ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
if (merge) {
map<string, int> seq2Bin = hcluster->getSeqtoBin();
ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
globaldata->setListFile(fileroot+ tag + ".list");
globaldata->setFormat("list");
+ if (m->control_pressed) {
+ delete nameMap;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ globaldata->setListFile("");
+ globaldata->setFormat("");
+ return 0;
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();
}else { if (overlapMatrix.size() == 0) { done = true; } }
while (!done) {
+ if (m->control_pressed) {
+ if (hclusterWanted) { inOverlap.close(); }
+ return newList;
+ }
//get next overlap
seqDist overlapNode;
void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
try {
//sort distFile
- string sortedDistFile = sortFile(unsortedDist);
+ string sortedDistFile = sortFile(unsortedDist, outputDir);
remove(unsortedDist.c_str()); //delete unsorted file
distFile = sortedDistFile;
//sort overlap file
- string sortedOverlapFile = sortFile(unsortedOverlap);
+ string sortedOverlapFile = sortFile(unsortedOverlap, outputDir);
remove(unsortedOverlap.c_str()); //delete unsorted file
overlapFile = sortedOverlapFile;
}