modified read.otu and shared command

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 4857a3482737a2b305b5a9ad381e228328289c19..26ba2211906fa025e3807aedf8c13ef3d913e413 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -20,6 +20,25 @@ SharedCommand::SharedCommand(){
                filename = getRootName(filename);
                filename = filename + "shared";
                openOutputFile(filename, out);
+               
+               groupMap = globaldata->gGroupmap;
+               
+               //fill filehandles with neccessary ofstreams
+               int i;
+               ofstream* temp;
+               for (i=0; i<groupMap->getNumGroups(); i++) {
+                       temp = new ofstream;
+                       filehandles[groupMap->namesOfGroups[i]] = temp;
+               }
+               
+               //set fileroot
+               fileroot = getRootName(globaldata->getListFile());
+               
+               //clears file before we start to write to it below
+               for (int i=0; i<groupMap->getNumGroups(); i++) {
+                       remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+               }
+
        }
        catch(exception& e) {
                errorOut(e, "SharedCommand", "SharedCommand");
@@ -31,7 +50,6 @@ SharedCommand::SharedCommand(){
 int SharedCommand::execute(){
        try {
                
-               mothurOut("creating sharedfile..."); mothurOutEndLine();
                //lookup.clear();
                int count = 1;
                string errorOff = "no error";
@@ -55,7 +73,10 @@ int SharedCommand::execute(){
                        
 
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+                                       
                                        lookup = SharedList->getSharedRAbundVector();
+                                       mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+                                       
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                                
@@ -69,6 +90,8 @@ int SharedCommand::execute(){
                                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+                                       
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                                        
@@ -100,6 +123,8 @@ int SharedCommand::execute(){
                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                        lookup = SharedList->getSharedRAbundVector();
+                       mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+                       
                        printSharedData(lookup); //prints info to the .shared file
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                        delete SharedList;
@@ -110,7 +135,11 @@ int SharedCommand::execute(){
                
                out.close();
                
-               mothurOut("complete."); mothurOutEndLine();
+               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+                       delete it3->second;
+               }
+
+               
                return 0;
        }
        catch(exception& e) {
@@ -126,6 +155,11 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                for (int i = 0; i < thislookup.size(); i++) {
                        out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
                        thislookup[i]->print(out);
+                       
+                       openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+                       (*filehandles[thislookup[i]->getGroup()]) << thislookup[i]->getLabel()  << '\t' << thislookup[i]->getGroup()  << '\t';
+                       thislookup[i]->print(*(filehandles[thislookup[i]->getGroup()]));
+                       (*(filehandles[thislookup[i]->getGroup()])).close();
                }
  
        }