removed line option

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 441e82438b54c33891d4e80e54cbf38410ca6a87..07486191e886c72d5d2aafd1db781bad96411874 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -15,7 +15,6 @@ GetOTURepCommand::GetOTURepCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                
                //allow user to run help
@@ -23,7 +22,7 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        help(); abort = true;
                } else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","list","line","label","name", "group"};
+                       string Array[] =  {"fasta","list","label","name", "group"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -53,13 +52,6 @@ GetOTURepCommand::GetOTURepCommand(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 { 
@@ -67,13 +59,10 @@ GetOTURepCommand::GetOTURepCommand(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;
                        }
                        
                        namesfile = validParameter.validFile(parameters, "name", true);
@@ -136,11 +125,11 @@ GetOTURepCommand::GetOTURepCommand(string option){
 void GetOTURepCommand::help(){
        try {
                mothurOut("The get.oturep command can only be executed after a successful read.dist command.\n");
-               mothurOut("The get.oturep command parameters are list, fasta, name, group, line and label.  The fasta and list 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 a output files created for, and are separated by dashes.\n");
-               mothurOut("The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels).\n");
-               mothurOut("Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, line=1-3-5, name=amazon.names).\n");
-               mothurOut("The default value for line and label are all lines in your inputfile.\n");
+               mothurOut("The get.oturep command parameters are list, fasta, name, group and label.  The fasta and list parameters are required.\n");
+               mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
+               mothurOut("The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
+               mothurOut("Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, name=amazon.names).\n");
+               mothurOut("The default value for label is all labels in your inputfile.\n");
                mothurOut("The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin.\n");
                mothurOut("If you provide a groupfile, then it also appends the names of the groups present in that bin.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
@@ -171,7 +160,6 @@ int GetOTURepCommand::execute(){
        
                if (abort == true) { return 0; }
 
-               int count = 1;
                int error;
                
                //read fastafile
@@ -198,19 +186,16 @@ int GetOTURepCommand::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() + "\t" + toString(list->size())); mothurOutEndLine();
                                        error = process(list);
                                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                                        
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
-                                       userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -228,7 +213,6 @@ int GetOTURepCommand::execute(){
                        
                        delete list;
                        list = input->getListVector();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -243,7 +227,7 @@ int GetOTURepCommand::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);
@@ -332,7 +316,7 @@ string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, i
                        group = group.substr(0, group.length()-1);
                }
 
-               // if only 1 sequence in bin or processing the "unique" line, then 
+               // if only 1 sequence in bin or processing the "unique" label, then 
                // the first sequence of the OTU is the representative one
                if ((names.size() == 1) || (list->getLabel() == "unique")) {
                        return names[0];