added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index fd2671750afa59b42fb3015c182df778b8871583..9c45afe95277b5c7106e3f87f64e60e53b9bf321 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -149,10 +149,10 @@ MGClusterCommand::MGClusterCommand(string option) {
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
                        precisionLength = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "0.70"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -162,10 +162,10 @@ MGClusterCommand::MGClusterCommand(string option) {
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 
                        temp = validParameter.validFile(parameters, "length", false);                   if (temp == "not found") { temp = "5"; }
-                       convert(temp, length); 
+                       m->mothurConvert(temp, length); 
                        
                        temp = validParameter.validFile(parameters, "penalty", false);                  if (temp == "not found") { temp = "0.10"; }
-                       convert(temp, penalty); 
+                       m->mothurConvert(temp, penalty); 
                        
                        temp = validParameter.validFile(parameters, "min", false);                              if (temp == "not found") { temp = "true"; }
                        minWanted = m->isTrue(temp); 
@@ -230,11 +230,13 @@ int MGClusterCommand::execute(){
                
                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());
+                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                        outputTypes.clear();
                        return 0; 
                }
                
+               double saveCutoff = cutoff;
+               
                if (!hclusterWanted) {
                        //get distmatrix and overlap
                        SparseMatrix* distMatrix = read->getDistMatrix();
@@ -251,7 +253,7 @@ int MGClusterCommand::execute(){
                        
                        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());
+                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -263,7 +265,7 @@ int MGClusterCommand::execute(){
                                
                                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());
+                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                        outputTypes.clear();
                                        return 0; 
                                }
@@ -286,7 +288,7 @@ int MGClusterCommand::execute(){
                                                
                                                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());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                                        outputTypes.clear();
                                                        return 0; 
                                                }
@@ -317,7 +319,7 @@ int MGClusterCommand::execute(){
                                        
                                        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());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                                        outputTypes.clear();
                                                        return 0; 
                                        }
@@ -347,7 +349,7 @@ int MGClusterCommand::execute(){
                        
                        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());
+                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -364,7 +366,7 @@ int MGClusterCommand::execute(){
                        
                        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());
+                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -373,11 +375,16 @@ int MGClusterCommand::execute(){
                
                                seqs = hcluster->getSeqs();
                                
+                               //to account for cutoff change in average neighbor
+                               if (seqs.size() != 0) {
+                                       if (seqs[0].dist > cutoff) { break; }
+                               }
+                               
                                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());
+                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                       m->mothurRemove(distFile);
+                                       m->mothurRemove(overlapFile);
                                        outputTypes.clear();
                                        return 0; 
                                }
@@ -386,13 +393,13 @@ int MGClusterCommand::execute(){
                                        
                                        if (seqs[i].seq1 != seqs[i].seq2) {
                
-                                               hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+                                               cutoff = 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());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       m->mothurRemove(distFile);
+                                                       m->mothurRemove(overlapFile);
                                                        outputTypes.clear();
                                                        return 0; 
                                                }
@@ -414,9 +421,9 @@ int MGClusterCommand::execute(){
                                                                
                                                                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());
+                                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                                       m->mothurRemove(distFile);
+                                                                       m->mothurRemove(overlapFile);
                                                                        outputTypes.clear();
                                                                        return 0; 
                                                                }
@@ -450,9 +457,9 @@ int MGClusterCommand::execute(){
                                        
                                        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());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       m->mothurRemove(distFile);
+                                                       m->mothurRemove(overlapFile);
                                                        outputTypes.clear();
                                                        return 0; 
                                        }
@@ -467,8 +474,8 @@ int MGClusterCommand::execute(){
                        }
                        
                        delete hcluster;
-                       remove(distFile.c_str());
-                       remove(overlapFile.c_str());
+                       m->mothurRemove(distFile);
+                       m->mothurRemove(overlapFile);
                }
                
                delete list; 
@@ -479,7 +486,7 @@ int MGClusterCommand::execute(){
        
                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());
+                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                        outputTypes.clear();
                        return 0; 
                }
@@ -491,6 +498,13 @@ int MGClusterCommand::execute(){
                m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
                m->mothurOutEndLine();
                
+               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");
@@ -644,12 +658,12 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
        try {
                //sort distFile
                string sortedDistFile = m->sortFile(unsortedDist, outputDir);
-               remove(unsortedDist.c_str());  //delete unsorted file
+               m->mothurRemove(unsortedDist);  //delete unsorted file
                distFile = sortedDistFile;
                
                //sort overlap file
                string sortedOverlapFile = m->sortFile(unsortedOverlap, outputDir);
-               remove(unsortedOverlap.c_str());  //delete unsorted file
+               m->mothurRemove(unsortedOverlap);  //delete unsorted file
                overlapFile = sortedOverlapFile;
        }
        catch(exception& e) {