removed line option

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index dd4fdd58178a0ce13467d5f45a00a105a8954fca..04b1b0badcf7dfc009296ac145aa49da50a3de50 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -16,7 +16,6 @@ GetRAbundCommand::GetRAbundCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                
                //allow user to run help
@@ -24,7 +23,7 @@ GetRAbundCommand::GetRAbundCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","sorted"};
+                       string Array[] =  {"label","sorted"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -47,13 +46,6 @@ GetRAbundCommand::GetRAbundCommand(string option){
                        temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
                        sorted = isTrue(temp);
                        
-                       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 { 
@@ -61,13 +53,10 @@ GetRAbundCommand::GetRAbundCommand(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) {
@@ -87,14 +76,14 @@ GetRAbundCommand::GetRAbundCommand(string option){
 void GetRAbundCommand::help(){
        try {
                mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
-               mothurOut("The get.rabund command parameters are line, label and sorted.  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 .rabund file, and are separated by dashes.\n");
+               mothurOut("The get.rabund command parameters are label and sorted.  No parameters are required.\n");
+               mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
                mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
-               mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels, sorted=yourSorted).\n");
-               mothurOut("Example get.rabund(line=1-3-5, sorted=F).\n");
-               mothurOut("The default value for line and label are all lines in your inputfile.\n");
+               mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
+               mothurOut("Example get.rabund(sorted=F).\n");
+               mothurOut("The default value for label is all labels in your inputfile.\n");
                mothurOut("The get.rabund command outputs a .rabund 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("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
        }
        catch(exception& e) {
                errorOut(e, "GetRAbundCommand", "help");
@@ -115,8 +104,6 @@ int GetRAbundCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               int count = 1;
-               
                //read first line
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
@@ -128,12 +115,10 @@ int GetRAbundCommand::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((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
+                       if(allLines == 1 || labels.count(list->getLabel()) == 1){
                                        mothurOut(list->getLabel()); mothurOutEndLine();
                                        rabund = new RAbundVector();                            
                                        *rabund = (list->getRAbundVector());
@@ -145,7 +130,6 @@ int GetRAbundCommand::execute(){
                                                                                                                        
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
-                                       userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -169,7 +153,6 @@ int GetRAbundCommand::execute(){
                        
                        delete list;
                        list = input->getListVector();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -185,7 +168,7 @@ int GetRAbundCommand::execute(){
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                        if (list != NULL) {     delete list;    }
                        list = input->getListVector(lastLabel);