added list parameter to get.seqs and remove.seqs and added readline library for inter...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 0dcdfc0143b12ae0c827086465a16bfb486dc66b..c827207f76529ebf79e8008deea7f245498a40b6 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -20,6 +20,7 @@ SharedCommand::SharedCommand(){
                filename = getRootName(filename);
                filename = filename + "shared";
                openOutputFile(filename, out);
+               pickedGroups = false;
                
                groupMap = globaldata->gGroupmap;
                
@@ -28,6 +29,7 @@ SharedCommand::SharedCommand(){
                        groups = groupMap->namesOfGroups;
                }else{ //they have specified groups
                        groups = globaldata->Groups;
+                       pickedGroups = true;
                }
                
                //fill filehandles with neccessary ofstreams
@@ -114,12 +116,15 @@ int SharedCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = globaldata->labels;    
-               
+       
                while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
-                       
+               
                        if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       if (pickedGroups) { //check for otus with no seqs in them
+                                               eliminateZeroOTUS(lookup);
+                                       }
                                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                        
                                        printSharedData(lookup); //prints info to the .shared file
@@ -136,6 +141,9 @@ int SharedCommand::execute(){
                                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       if (pickedGroups) { //check for otus with no seqs in them
+                                               eliminateZeroOTUS(lookup);
+                                       }
                                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                        
                                        printSharedData(lookup); //prints info to the .shared file
@@ -170,6 +178,9 @@ int SharedCommand::execute(){
                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                        lookup = SharedList->getSharedRAbundVector();
+                       if (pickedGroups) { //check for otus with no seqs in them
+                               eliminateZeroOTUS(lookup);
+                       }
                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                        
                        printSharedData(lookup); //prints info to the .shared file
@@ -216,6 +227,46 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
        }
 }
 //**********************************************************************************************************************
+void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+       try {
+               
+               vector<SharedRAbundVector*> newLookup;
+               for (int i = 0; i < thislookup.size(); i++) {
+                       SharedRAbundVector* temp = new SharedRAbundVector();
+                       temp->setLabel(thislookup[i]->getLabel());
+                       temp->setGroup(thislookup[i]->getGroup());
+                       newLookup.push_back(temp);
+               }
+               
+               //for each bin
+               for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+               
+                       //look at each sharedRabund and make sure they are not all zero
+                       bool allZero = true;
+                       for (int j = 0; j < thislookup.size(); j++) {
+                               if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
+                       }
+                       
+                       //if they are not all zero add this bin
+                       if (!allZero) {
+                               for (int j = 0; j < thislookup.size(); j++) {
+                                       newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+                               }
+                       }
+                       //else{  cout << "bin # " << i << " is all zeros" << endl;  }
+               }
+       
+               for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
+               thislookup = newLookup;
+       
+ 
+       }
+       catch(exception& e) {
+               errorOut(e, "SharedCommand", "eliminateZeroOTUS");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 void SharedCommand::createMisMatchFile() {
        try {
                ofstream outMisMatch;