added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index d98f5c69926f795cb75510853184197676647ab9..47136938a19e6c5d4b8dd2b8110849249ac50b06 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -182,14 +182,14 @@ HClusterCommand::HClusterCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0)); 
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -260,7 +260,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                return 0;  
                        }
                        
@@ -276,7 +276,7 @@ int HClusterCommand::execute(){
                        sabundFile.close();
                        rabundFile.close();
                        listFile.close();
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                        return 0;  
                }
 
@@ -306,35 +306,41 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                return 0;  
                }
 
+               float saveCutoff = cutoff;
                
                while (seqs.size() != 0){
                
                        seqs = cluster->getSeqs();
                        
+                       //to account for cutoff change in average neighbor
+                       if (seqs.size() != 0) {
+                               if (seqs[0].dist > cutoff) { break; }
+                       }
+                       
                        if (m->control_pressed) {  
                                delete cluster;
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                return 0;  
                        }
 
                        for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
                                
                                if (seqs[i].seq1 != seqs[i].seq2) {
-                                       cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+                                       cutoff = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
                                        
                                        if (m->control_pressed) {  
                                                delete cluster;
                                                sabundFile.close();
                                                rabundFile.close();
                                                listFile.close();
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                                return 0;  
                                        }
 
@@ -367,7 +373,7 @@ int HClusterCommand::execute(){
                        sabundFile.close();
                        rabundFile.close();
                        listFile.close();
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                        return 0;  
                }
                                        
@@ -384,10 +390,18 @@ int HClusterCommand::execute(){
                delete cluster;
                
                if (m->control_pressed) {  
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                        return 0;  
                }
                
+               
+               if (saveCutoff != cutoff) { 
+                       if (hard)       {  saveCutoff = m->ceilDist(saveCutoff, precision);     }
+                       else            {       saveCutoff = m->roundDist(saveCutoff, precision);  }
+                       
+                       m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
+               }
+               
                //set list file as new current listfile
                string current = "";
                itTypes = outputTypes.find("list");