added smart distance feature and optimized all commands using line by line processing

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index c29d5499808e13bd9246098f50706337b3f9e592..b4de07b082fb0274c02ba71793c0e3023d192a35 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -36,26 +36,70 @@ SharedCommand::SharedCommand(){
 int SharedCommand::execute(){
        try {
                globaldata = GlobalData::getInstance();
+               int count = 1;
+               string errorOff = "no error";
                        
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
                input = globaldata->ginput;
                SharedList = globaldata->gSharedList;
+               SharedListVector* lastList = SharedList;
+               
+               //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;
                
                shared = new Shared();
-               int i = 0;
-               while(SharedList != NULL){
                
-                       if(globaldata->allLines == 1 || globaldata->lines.count(i+1) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+               while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                       
+                                               
+                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
                        
-                               shared->getSharedVectors(i, SharedList); //fills sharedGroups with new info and updates sharedVector
-                               printSharedData(); //prints info to the .shared file
+                                       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());
                        }
                        
+                       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
-                       i++;
                }
+               
+               //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
+               }
+               
+               delete lastList;
+               delete shared;
+               
                return 0;
        }
        catch(exception& e) {
@@ -93,6 +137,7 @@ void SharedCommand::printSharedData() {
 SharedCommand::~SharedCommand(){
        //delete list;
        delete read;
+       
 }
 
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