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

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index b649582758636370f812a51cf182ce7813bc3e02..e7fda2e5dedcd8052b3c610931964377e356a7af 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -115,7 +115,8 @@ SummaryCommand::~SummaryCommand(){
 
 int SummaryCommand::execute(){
        try {
-       
+               int count = 1;
+               
                //if the users entered no valid calculators don't execute command
                if (sumCalculators.size() == 0) { return 0; }
 
@@ -125,7 +126,11 @@ int SummaryCommand::execute(){
        
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
-
+               
+               sabund = globaldata->sabund;
+               SAbundVector* lastSAbund = sabund;
+               input = globaldata->ginput;
+               
                for(int i=0;i<sumCalculators.size();i++){
                        if(sumCalculators[i]->getCols() == 1){
                                outputFileHandle << '\t' << sumCalculators[i]->getName();
@@ -136,14 +141,18 @@ int SummaryCommand::execute(){
                }
                outputFileHandle << endl;
                
-               sabund = globaldata->sabund;
-               input = globaldata->ginput;
-               int count = 1;
-               while(sabund != NULL){
+               //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((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                       
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){                      
        
                                cout << sabund->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(sabund->getLabel());
+                               userLabels.erase(sabund->getLabel());
+
                                
                                outputFileHandle << sabund->getLabel();
                                for(int i=0;i<sumCalculators.size();i++){
@@ -151,13 +160,57 @@ int SummaryCommand::execute(){
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
                                }
-                               
                                outputFileHandle << endl;
                        }
+                       
+                       if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
+
+                               cout << lastSAbund->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(lastSAbund->getLabel());
+                               userLabels.erase(lastSAbund->getLabel());
+                               
+                               outputFileHandle << lastSAbund->getLabel();
+                               for(int i=0;i<sumCalculators.size();i++){
+                                       vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+                                       outputFileHandle << '\t';
+                                       sumCalculators[i]->print(outputFileHandle);
+                               }
+                               outputFileHandle << endl;
+                       }               
+
+                       if (count != 1) { delete lastSAbund; }
+                       lastSAbund = sabund;                    
+
                        sabund = input->getSAbundVector();
                        count++;
                }
-       
+               
+               //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(lastSAbund->getLabel()) != 1) {
+                               cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+                               needToRun = true;
+                       }else {
+                               cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+                       }
+               }
+               
+               //run last line if you need to
+               if (needToRun == true)  {
+                       cout << lastSAbund->getLabel() << '\t' << count << endl;
+                       outputFileHandle << lastSAbund->getLabel();
+                       for(int i=0;i<sumCalculators.size();i++){
+                               vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+                               outputFileHandle << '\t';
+                               sumCalculators[i]->print(outputFileHandle);
+                       }
+                       outputFileHandle << endl;
+               }
+               
+               delete lastSAbund;
                return 0;
        }
        catch(exception& e) {