removed line option

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 731a4101eaff0b6b5712caf15bf7a0ad6feb6e62..a2f79f9b0322670e009cf916c0ce8f05a61c5642 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -36,7 +36,6 @@ SummaryCommand::SummaryCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Estimators.clear();
                
@@ -45,7 +44,7 @@ SummaryCommand::SummaryCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","calc","abund","size"};
+                       string Array[] =  {"label","calc","abund","size"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -63,13 +62,6 @@ SummaryCommand::SummaryCommand(string option){
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter.validFile(parameters, "line", false);                             
-                       if (line == "not found") { line = "";  }
-                       else { 
-                               if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
-                               else { allLines = 1;  }
-                       }
-                       
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
@@ -77,13 +69,10 @@ SummaryCommand::SummaryCommand(string option){
                                else { allLines = 1;  }
                        }
                        
-                       //make sure user did not use both the line and label parameters
-                       if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
-                       //if the user has not specified any line or labels use the ones from read.otu
-                       else if((line == "") && (label == "")) {  
+                       //if the user has not specified any labels use the ones from read.otu
+                       if(label == "") {  
                                allLines = globaldata->allLines; 
                                labels = globaldata->labels; 
-                               lines = globaldata->lines;
                        }
                                
                        calc = validParameter.validFile(parameters, "calc", false);                     
@@ -168,14 +157,14 @@ void SummaryCommand::help(){
        try {
                mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
                mothurOut("The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
-               mothurOut("The summary.single command parameters are label, line, calc, abund.  No parameters are required, but you may not use \n");
-               mothurOut("both the line and label parameters at the same time. The summary.single command should be in the following format: \n");
-               mothurOut("summary.single(label=yourLabel, line=yourLines, calc=yourEstimators).\n");
-               mothurOut("Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
+               mothurOut("The summary.single command parameters are label, calc, abund.  No parameters are required.\n");
+               mothurOut("The summary.single command should be in the following format: \n");
+               mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
+               mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
                validCalculator->printCalc("summary", cout);
                mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
-               mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
+               mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
        }
        catch(exception& e) {
                errorOut(e, "SummaryCommand", "help");
@@ -201,8 +190,6 @@ int SummaryCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               int count = 1;
-               
                //if the users entered no valid calculators don't execute command
                if (sumCalculators.size() == 0) { return 0; }
 
@@ -230,18 +217,15 @@ int SummaryCommand::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 = labels;
-               set<int> userLines = lines;
-               
-               while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
-                       if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){                  
+               while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                       
+                       if(allLines == 1 || labels.count(sabund->getLabel()) == 1){                     
        
                                mothurOut(sabund->getLabel()); mothurOutEndLine();
                                processedLabels.insert(sabund->getLabel());
                                userLabels.erase(sabund->getLabel());
-                               userLines.erase(count);
-
-                               
+                                                               
                                outputFileHandle << sabund->getLabel();
                                for(int i=0;i<sumCalculators.size();i++){
                                        vector<double> data = sumCalculators[i]->getValues(sabund);
@@ -272,7 +256,6 @@ int SummaryCommand::execute(){
                        
                        delete sabund;
                        sabund = input->getSAbundVector();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -288,7 +271,7 @@ int SummaryCommand::execute(){
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                        if (sabund != NULL) {   delete sabund;  }
                        sabund = input->getSAbundVector(lastLabel);