fixing minor bugs

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 0cc1e22f2d9067fb7fcad21b6cff5c456f5e7049..dd900643a741d576d1595c1a9c346d6b6c334361 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -36,21 +36,80 @@ SharedCommand::SharedCommand(){
 int SharedCommand::execute(){
        try {
                globaldata = GlobalData::getInstance();
+               //lookup.clear();
+               int count = 1;
+               string errorOff = "no error";
                        
                //read in listfile
-               read = new ReadPhilFile(globaldata->inputFileName);     
+               read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
+
                input = globaldata->ginput;
                SharedList = globaldata->gSharedList;
+               SharedListVector* lastList = SharedList;
+               //lookup = SharedList->getSharedRAbundVector();
+               //vector<SharedRAbundVector*> lastLookup = lookup;
+               
+               //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;
+               set<int> userLines = globaldata->lines;
                
                shared = new Shared();
-               int i = 0;
-               while(SharedList != NULL){
-                       shared->getSharedVectors(i, SharedList); //fills sharedGroups with new info and updates sharedVector
+               
+               while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+                       
+
+                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+                                       
+                                       shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
+                                       printSharedData(); //prints info to the .shared file
+                               
+                                       processedLabels.insert(SharedList->getLabel());
+                                       userLabels.erase(SharedList->getLabel());
+                                       userLines.erase(count);
+                       }
+                       
+                       if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+                                       shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
+                                       printSharedData(); //prints info to the .shared file
+
+                                       processedLabels.insert(lastList->getLabel());
+                                       userLabels.erase(lastList->getLabel());
+                       }
+                       
+                       if (count != 1) { delete lastList; }
+                       lastList = SharedList;                  
                        SharedList = input->getSharedListVector(); //get new list vector to process
+                       
+                       //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
+                       //lastLookup = lookup; 
+                       //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
+               }
+               
+               //output error messages about any remaining user labels
+               set<string>::iterator it;
+               bool needToRun = false;
+               for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+                       //cout << "Your file does not include the label "<< *it; 
+                       if (processedLabels.count(lastList->getLabel()) != 1) {
+                               //cout << ". I will use " << lastList->getLabel() << "." << endl;
+                               needToRun = true;
+                       }else {
+                               //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+                       }
+               }
+               
+               //run last line if you need to
+               if (needToRun == true)  {
+                       shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
                        printSharedData(); //prints info to the .shared file
-                       i++;
                }
+               
+               delete lastList;
+               delete shared;
+               out.close();
+               
                return 0;
        }
        catch(exception& e) {
@@ -66,6 +125,12 @@ int SharedCommand::execute(){
 //**********************************************************************************************************************
 void SharedCommand::printSharedData() {
        try {
+       
+               ///for (int i = 0; i < thislookup.size(); i++) {
+               //      out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+//cout << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;                      
+               //      thislookup[i]->print(out);
+       //      }
                //prints out horizontally
                for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
                        out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
@@ -88,6 +153,7 @@ void SharedCommand::printSharedData() {
 SharedCommand::~SharedCommand(){
        //delete list;
        delete read;
+       
 }
 
 //**********************************************************************************************************************