fixed bug with normalize.shared, printed out numbins twice. fixed bug with summary...

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index d68d00ac6258e0ac10346ce5b67b7d10a2de7495..1e0e8dbc552a872df3fe591d15ea378db3316959 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -506,52 +506,64 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                
                //open each groups summary file
                string newLabel = "";
-               ifstream* temp;
-               map<string, ifstream*> filehandles;
+               map<string, vector<string> > files;
                for (int i=0; i<outputNames.size(); i++) {
-                       temp = new ifstream;
-                       filehandles[outputNames[i]] = temp;
-                       m->openInputFile(outputNames[i], *(temp));
+                       vector<string> thisFilesLines;
+                       
+                       ifstream temp;
+                       m->openInputFile(outputNames[i], temp);
                        
                        //read through first line - labels
                        string tempLabel;
                        if (i == 0) { //we want to save the labels to output below
                                for (int j = 0; j < numCols+1; j++) {  
-                                       *(temp) >> tempLabel; 
+                                       temp >> tempLabel; 
                                        
                                        if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
                                        }else{  newLabel += tempLabel + '\t';   }
                                }
-                       }else{  for (int j = 0; j < numCols+1; j++) {  *(temp) >> tempLabel;  }  }
+                       }else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
+                       
+                       m->gobble(temp);
+                       
+                       //for each label
+                       for (int k = 0; k < numLines; k++) {
+                               
+                               string thisLine = "";
+                               string tempLabel;
+                                       
+                               for (int j = 0; j < numCols+1; j++) {  
+                                       temp >> tempLabel; 
+                                               
+                                       //save for later
+                                       if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
+                                       else{  thisLine += tempLabel + "\t";    }
+                               }
+                                       
+                               thisLine += "\n";
+                               
+                               thisFilesLines.push_back(thisLine);
+                                       
+                               m->gobble(temp);
+                       }
+                               
+                       files[outputNames[i]] = thisFilesLines;
                        
-                       m->gobble(*(temp));
+                       temp.close();
                }
                
                //output label line to new file
                out << newLabel << endl;
                
                //for each label
-               for (int i = 0; i < numLines; i++) {
+               for (int k = 0; k < numLines; k++) {
                
                        //grab summary data for each group
                        for (int i=0; i<outputNames.size(); i++) {
-                               string tempLabel;
-                               
-                               for (int j = 0; j < numCols+1; j++) {  
-                                       *(filehandles[outputNames[i]]) >> tempLabel; 
-                                       
-                                       //print to combined file
-                                       if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t';    }
-                                       else{  out << tempLabel << '\t';        }
-                               }
-                               
-                               out << endl;
-                               m->gobble(*(filehandles[outputNames[i]]));
+                               out << files[outputNames[i]][k];
                        }
                }       
                
-               //close each groups summary file
-               for (int i=0; i<outputNames.size(); i++) {  (*(filehandles[outputNames[i]])).close();  remove(outputNames[i].c_str());  }
                outputNames.clear();
                
                out.close();