1.12.0

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 182e78dc31502fb6c9a75e1703c8f17ffe4ba0fb..9a1ac215388e09e6477fffa034e0542c38c208b1 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -166,13 +166,6 @@ int MGClusterCommand::execute(){
                
                list = new ListVector(nameMap->getListVector());
                RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
-for (int i = 0; i < list->getNumBins(); i++) {
-string bin = list->get(i);
-if(bin == "") {
-cout << "bin " << i << " is blank."<< endl;
-}
-}
-cout << "after outputting blank bins." << endl;
                
                if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; return 0; }
                
@@ -215,7 +208,7 @@ cout << "after outputting blank bins." << endl;
                                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; 
                        }
-       int count = 0;          
+               
                        //cluster using cluster classes
                        while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
                                
@@ -234,16 +227,13 @@ cout << "after outputting blank bins." << endl;
                                }else{
                                        rndDist = roundDist(dist, precision); 
                                }
-cout << "here " << count << '\t' << dist << endl;
                                
                                if(previousDist <= 0.0000 && dist != previousDist){
                                        oldList.setLabel("unique");
                                        printData(&oldList);
-                                       Seq2Bin = cluster->getSeqtoBin();
                                }
                                else if(rndDist != rndPreviousDist){
                                        if (merge) {
-                                               Seq2Bin = cluster->getSeqtoBin();
                                                ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
                                                
                                                if (m->control_pressed) { 
@@ -260,22 +250,20 @@ cout << "here " << count << '\t' << dist << endl;
                                                printData(&oldList);
                                        }
                                }
-       //cout << "after merge " << count << '\t' << dist << endl;      
-       count++;                
+       
                                previousDist = dist;
                                rndPreviousDist = rndDist;
                                oldList = *list;
+                               Seq2Bin = cluster->getSeqtoBin();
                                oldSeq2Bin = Seq2Bin;
                        }
                        
                        if(previousDist <= 0.0000){
                                oldList.setLabel("unique");
                                printData(&oldList);
-                               Seq2Bin = cluster->getSeqtoBin();
                        }
                        else if(rndPreviousDist<cutoff){
                                if (merge) {
-                                       Seq2Bin = cluster->getSeqtoBin();
                                        ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
                                        
                                        if (m->control_pressed) { 
@@ -365,11 +353,9 @@ cout << "here " << count << '\t' << dist << endl;
                                                if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
                                                        oldList.setLabel("unique");
                                                        printData(&oldList);
-                                                       Seq2Bin = hcluster->getSeqtoBin();
                                                }
                                                else if((rndDist != rndPreviousDist)){
                                                        if (merge) {
-                                                               Seq2Bin = hcluster->getSeqtoBin();
                                                                ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
                                                                
                                                                if (m->control_pressed) { 
@@ -392,6 +378,7 @@ cout << "here " << count << '\t' << dist << endl;
                                                previousDist = seqs[i].dist;
                                                rndPreviousDist = rndDist;
                                                oldList = *list;
+                                               Seq2Bin = cluster->getSeqtoBin();
                                                oldSeq2Bin = Seq2Bin;
                                        }
                                }
@@ -404,7 +391,6 @@ cout << "here " << count << '\t' << dist << endl;
                        }
                        else if(rndPreviousDist<cutoff){
                                if (merge) {
-                                       Seq2Bin = hcluster->getSeqtoBin();
                                        ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
                                        
                                        if (m->control_pressed) { 
@@ -485,16 +471,6 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
        try {
                //create new listvector so you don't overwrite the clustering
                ListVector* newList = new ListVector(oldList);
-for (int i = 0; i < newList->getNumBins(); i++) {
-string bin = newList->get(i);
-if(bin == "") {
-cout << "bin " << i << " is blank."<< endl;
-for (map<string, int>::iterator itBin = binInfo.begin(); itBin != binInfo.end(); itBin++) {
-       if (itBin->second == i) { cout << itBin->first << " maps to an empty bin." << endl; }
-}
-}
-}
-cout << "after outputting blank bins." << endl;                
 
                bool done = false;
                ifstream inOverlap;
@@ -524,13 +500,16 @@ cout << "after outputting blank bins." << endl;
                                        float overlapDistance;
                                        inOverlap >> firstName >> secondName >> overlapDistance; gobble(inOverlap);
                                        
-                                       map<string,int>::iterator itA = nameMap->find(firstName);
-                                       map<string,int>::iterator itB = nameMap->find(secondName);
-                                       if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);  }
-                                       if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
+                                       //commented out because we check this in readblast already
+                                       //map<string,int>::iterator itA = nameMap->find(firstName);
+                                       //map<string,int>::iterator itB = nameMap->find(secondName);
+                                       //if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);  }
+                                       //if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
                                        
-                                       overlapNode.seq1 = itA->second;
-                                       overlapNode.seq2 = itB->second;
+                                       //overlapNode.seq1 = itA->second;
+                                       //overlapNode.seq2 = itB->second;
+                                       overlapNode.seq1 = nameMap->get(firstName);
+                                       overlapNode.seq2 = nameMap->get(secondName);
                                        overlapNode.dist = overlapDistance;
                                }else { inOverlap.close(); break; }
                        } 
@@ -541,22 +520,24 @@ cout << "after outputting blank bins." << endl;
                                string name2 = nameMap->get(overlapNode.seq2);
                        
                                //use binInfo to find out if they are already in the same bin
-                               map<string, int>::iterator itBin1 = binInfo.find(name1);
-                               map<string, int>::iterator itBin2 = binInfo.find(name2);
+                               //map<string, int>::iterator itBin1 = binInfo.find(name1);
+                               //map<string, int>::iterator itBin2 = binInfo.find(name2);
                                
-                               if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
-                               if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
-cout << overlapNode.dist << '\t' << dist << endl;
-                               int binKeep = itBin1->second;
-                               int binRemove = itBin2->second;
+                               //if(itBin1 == binInfo.end()){  cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1);  }
+                               //if(itBin2 == binInfo.end()){  cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1);  }
+
+                               //int binKeep = itBin1->second;
+                               //int binRemove = itBin2->second;
+                               
+                               int binKeep = binInfo[name1];
+                               int binRemove = binInfo[name2];
                        
                                //if not merge bins and update binInfo
                                if(binKeep != binRemove) {
-       cout << "bin keep = " << binKeep << " bin remove = " << binRemove << endl;              
+               
                                        //save names in old bin
                                        string names = newList->get(binRemove);
-                       cout << names << endl << endl << endl;  
-                       cout << newList->get(binKeep) << endl << endl << endl;  
+               
                                        //merge bins into name1s bin
                                        newList->set(binKeep, newList->get(binRemove)+','+newList->get(binKeep));
                                        newList->set(binRemove, "");