fixed bug in rarefaction.single creating the groups file. working on cooccurrence...

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index dabcef486ee7541c183fc594f10da9a9f6624561..82ff7faef0d8886d21fc6b642f34c88c1b143ea1 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -474,7 +474,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                
                //find different types of files
                map<string, map<string, string> > typesFiles;
-        map<string, string> temp; 
                for (int i = 0; i < outputNames.size(); i++) {
                        string extension = m->getExtension(outputNames[i]);
                        
@@ -485,9 +484,15 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                        string newLine = labels.substr(0, labels.find_first_of('\t'));
                        
                        newLine += "\tGroup" + labels.substr(labels.find_first_of('\t'));
-                       
-            temp[outputNames[i]] = file2Group[i];
-                       typesFiles[extension] = temp;
+            
+            map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
+            if (itfind != typesFiles.end()) {
+                (itfind->second)[outputNames[i]] = file2Group[i];
+            }else {
+                map<string, string> temp;  
+                temp[outputNames[i]] = file2Group[i];
+                typesFiles[extension] = temp;
+            }
                        
                        string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
                        
@@ -507,7 +512,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                        string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
                        m->openOutputFileAppend(combineFileName, out);
                        newFileNames.push_back(combineFileName);
-                       
                        map<string, string> thisTypesFiles = it->second;
                
                        //open each type summary file
@@ -518,7 +522,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                 
                 string thisfilename = itFileNameGroup->first;
                 string group = itFileNameGroup->second;
-                
+               
                                ifstream temp;
                                m->openInputFile(thisfilename, temp);
                                
@@ -541,7 +545,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                                        count++;
                                                                        
                                        thisFilesLines.push_back(thisLine);
-                                       
                                        m->gobble(temp);
                                }
                                
@@ -562,7 +565,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                                for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
                     
                                        string thisfilename = itFileNameGroup->first;
-                    
                                        map<int, int>::iterator itLine = lineToNumber.find(k);
                                        if (itLine != lineToNumber.end()) {
                                                string output = toString(itLine->second);