added ordergroup parameter to read.otu

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 91bb8e19604d3d9446016c4b9eaf82f566172c0a..195996e50d41ff81953f5715704964398b9715e9 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -71,6 +71,9 @@ int SharedCommand::execute(){
                string errorOff = "no error";
                //errorOff = "";
                
+               //if user provided an order file containing the order the shared file should be in read it
+               if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+               
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
@@ -280,18 +283,46 @@ int SharedCommand::execute(){
 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
        try {
                
-               sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
-               
-               //initialize bin values
-               for (int i = 0; i < thislookup.size(); i++) {
-//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() <<  endl;
-                       out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
-                       thislookup[i]->print(out);
+               if (order.size() == 0) { //user has not specified an order so do aplabetically
+                       sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+                       
+                       //initialize bin values
+                       for (int i = 0; i < thislookup.size(); i++) {
+                               out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+                               thislookup[i]->print(out);
+                               
+                               RAbundVector rav = thislookup[i]->getRAbundVector();
+                               openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+                               rav.print(*(filehandles[thislookup[i]->getGroup()]));
+                               (*(filehandles[thislookup[i]->getGroup()])).close();
+                       }
+               }else{
+                       //create a map from groupName to each sharedrabund
+                       map<string, SharedRAbundVector*> myMap;
+                       map<string, SharedRAbundVector*>::iterator myIt;
+                       
+                       for (int i = 0; i < thislookup.size(); i++) {
+                               myMap[thislookup[i]->getGroup()] = thislookup[i];
+                       }
+                       
                        
-                       RAbundVector rav = thislookup[i]->getRAbundVector();
-                       openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
-                       rav.print(*(filehandles[thislookup[i]->getGroup()]));
-                       (*(filehandles[thislookup[i]->getGroup()])).close();
+                       //loop through ordered list and print the rabund
+                       for (int i = 0; i < order.size(); i++) {
+                               myIt = myMap.find(order[i]);
+                               
+                               if(myIt != myMap.end()) { //we found it
+                                       out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
+                                       (myIt->second)->print(out);
+                               
+                                       RAbundVector rav = (myIt->second)->getRAbundVector();
+                                       openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+                                       rav.print(*(filehandles[(myIt->second)->getGroup()]));
+                                       (*(filehandles[(myIt->second)->getGroup()])).close();
+                               }else{
+                                       m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
+                               }
+                       }
+               
                }
  
        }
@@ -458,7 +489,32 @@ SharedCommand::~SharedCommand(){
        
        
 }
-
+//**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+       try {
+               //remove old names
+               order.clear();
+               
+               ifstream in;
+               openInputFile(globaldata->getOrderGroupFile(), in);
+               string thisGroup;
+               
+               while(!in.eof()){
+                       in >> thisGroup; gobble(in);
+                                               
+                       order.push_back(thisGroup);
+                       
+                       if (m->control_pressed) { order.clear(); break; }
+               }
+               in.close();             
+               
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedCommand", "readOrderFile");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {