removed line option

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 8cbb9d4a06ed2c3d578821520968f47630f6c0ce..80a44297b48bfde50c633edfe7354e2f3e0cb115 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -16,7 +16,6 @@ GetSAbundCommand::GetSAbundCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                
                //allow user to run help
@@ -24,7 +23,7 @@ GetSAbundCommand::GetSAbundCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label"};
+                       string Array[] =  {"label"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -42,13 +41,6 @@ GetSAbundCommand::GetSAbundCommand(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 { 
@@ -56,13 +48,10 @@ GetSAbundCommand::GetSAbundCommand(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;
                        }
                                
                        if (abort == false) {
@@ -82,13 +71,13 @@ GetSAbundCommand::GetSAbundCommand(string option){
 void GetSAbundCommand::help(){
        try {
                mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
-               mothurOut("The get.sabund command parameters are line and label.  No parameters are required, and you may not use line and label at the same time.\n");
-               mothurOut("The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
-               mothurOut("The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels).\n");
-               mothurOut("Example get.sabund(line=1-3-5).\n");
-               mothurOut("The default value for line and label are all lines in your inputfile.\n");
-               mothurOut("The get.sabund command outputs a .sabund file containing the lines you selected.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
+               mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
+               mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
+               mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
+               mothurOut("Example get.sabund().\n");
+               mothurOut("The default value for label is all labels in your inputfile.\n");
+               mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
        }
        catch(exception& e) {
                errorOut(e, "GetSAbundCommand", "help");
@@ -108,8 +97,6 @@ int GetSAbundCommand::execute(){
                
                if (abort == true) { return 0; }
        
-               int count = 1;
-               
                //using order vector so you don't have to distinguish between the list and rabund files
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
@@ -121,12 +108,10 @@ int GetSAbundCommand::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((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
+                       if(allLines == 1 || labels.count(order->getLabel()) == 1){
                                        mothurOut(order->getLabel());  mothurOutEndLine();
                                        sabund = new SAbundVector();
                                        *sabund = (order->getSAbundVector());
@@ -135,7 +120,6 @@ int GetSAbundCommand::execute(){
 
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
-                                       userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -157,7 +141,6 @@ int GetSAbundCommand::execute(){
                        
                        delete order;           
                        order = (input->getOrderVector());
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -173,7 +156,7 @@ int GetSAbundCommand::execute(){
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                        if (order != NULL) {    delete order;   }
                        order = (input->getOrderVector(lastLabel));