metastats in progress

[mothur.git] / getgroupcommand.cpp

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 194e8e16b1e388bdb8d01ac372fbc884cbc92e43..8dae3f30092d0ae94e8b709119e933252f946f4a 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "getgroupcommand.h"
+#include "inputdata.h"
 
 //**********************************************************************************************************************
 vector<string> GetgroupCommand::setParameters(){       
@@ -121,55 +122,20 @@ int GetgroupCommand::execute(){
        try {
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
-               
-               //open shared file
-               m->openInputFile(sharedfile, in);
                        
                //open output file
                outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
                m->openOutputFile(outputFile, out);
-                       
-               int num, inputData, count;
-               count = 0;  
-               string holdLabel, nextLabel, groupN, label;
-               
-               //read in first row since you know there is at least 1 group.
-               in >> label >> groupN >> num;
-               holdLabel = label;
-               
-               //output first group
-               m->mothurOut(groupN); m->mothurOutEndLine();
-               out << groupN << '\t' << groupN << endl;        
-                       
-               //get rest of line
-               for(int i=0;i<num;i++){
-                       in >> inputData;
-               }
                
-               if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); m->mothurRemove(outputFile);   return 0; }
-
-               if (in.eof() != true) { in >> nextLabel; }
+               InputData input(sharedfile, "sharedfile");
+               vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
                
-               //read the rest of the groups info in
-               while ((nextLabel == holdLabel) && (in.eof() != true)) {
-                       if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); m->mothurRemove(outputFile);   return 0; }
-                       
-                       in >> groupN >> num;
-                       count++;
-                       
-                       //output next group
-                       m->mothurOut(groupN); m->mothurOutEndLine();
-                       out << groupN << '\t' << groupN << endl;                                
-                       
-                       //fill vector.  
-                       for(int i=0;i<num;i++){
-                               in >> inputData;
-                       }
-                       
-                       if (in.eof() != true) { in >> nextLabel; }
+               for (int i = 0; i < lookup.size(); i++) {
+                       out << lookup[i]->getGroup() << '\t' << lookup[i]->getGroup() << endl;
+                       m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
+                       delete lookup[i];
                }
                
-               in.close();
                out.close();
                
                if (m->control_pressed) {  m->mothurRemove(outputFile);   return 0; }