fixed multiple bugs for 1.4 release

[mothur.git] / getgroupcommand.cpp

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 3fc67d11612bccfdced922b1a8276b90cfc5b023..4d439592127e53ff8b61fc465ef5e27db238e49e 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -13,8 +13,13 @@
 GetgroupCommand::GetgroupCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               groupMap = globaldata->gGroupmap;
-               outputFile = globaldata->inputFileName + ".bootGroups";
+               
+               //open shared file
+               sharedfile = globaldata->getSharedFile();
+               openInputFile(sharedfile, in);
+               
+               //open output file
+               outputFile = getRootName(globaldata->inputFileName) + "bootGroups";
                openOutputFile(outputFile, out);
        }
        catch(exception& e) {
@@ -37,11 +42,42 @@ GetgroupCommand::~GetgroupCommand(){
 
 int GetgroupCommand::execute(){
        try {
-               vector<string> groupNames = groupMap->namesOfGroups;    
-               for(int i = 0; i < groupNames.size(); i++) {
-                       cout << groupNames[i] << "\n";
-                       out << groupNames[i] << "\t" << groupNames[i] << "\n";
+               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
+               cout << groupN << endl;
+               out << groupN << '\t' << groupN << endl;        
+                       
+               //get rest of line
+               for(int i=0;i<num;i++){
+                       in >> inputData;
+               }
+               
+               if (in.eof() != true) { in >> nextLabel; }
+               
+               //read the rest of the groups info in
+               while ((nextLabel == holdLabel) && (in.eof() != true)) {
+                       in >> groupN >> num;
+                       count++;
+                       
+                       //output next group
+                       cout << groupN << endl;
+                       out << groupN << '\t' << groupN << endl;                                
+                       
+                       //fill vector.  
+                       for(int i=0;i<num;i++){
+                               in >> inputData;
+                       }
+                       
+                       if (in.eof() != true) { in >> nextLabel; }
                }
+               
                out.close();
                return 0;       
        }