removed line option

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index e4e4c48d98e06014ee7a243fa6e43672445b0c5d..08ae6b607a13e3406aa4fe42d8a1f5025a41bbc0 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -15,7 +15,6 @@ BinSeqCommand::BinSeqCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                
                //allow user to run help
@@ -23,7 +22,7 @@ BinSeqCommand::BinSeqCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"fasta","line","label","name", "group"};
+                       string AlignArray[] =  {"fasta","label","name", "group"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -51,12 +50,6 @@ BinSeqCommand::BinSeqCommand(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 = ""; }
@@ -65,13 +58,10 @@ BinSeqCommand::BinSeqCommand(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);
@@ -103,11 +93,11 @@ BinSeqCommand::BinSeqCommand(string option){
 void BinSeqCommand::help(){
        try {
                mothurOut("The bin.seqs command can only be executed after a successful read.otu command of a listfile.\n");
-               mothurOut("The bin.seqs command parameters are fasta, name, line, label and group.  The fasta parameter is 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 bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels).\n");
-               mothurOut("Example bin.seqs(fasta=amazon.fasta, 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 bin.seqs command parameters are fasta, name, label and group.  The fasta parameter is required.\n");
+               mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
+               mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
+               mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n");
+               mothurOut("The default value for label is all lines in your inputfile.\n");
                mothurOut("The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n");
                mothurOut("If you provide a groupfile, then it also appends the sequences group to the name.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
@@ -137,7 +127,6 @@ int BinSeqCommand::execute(){
        try {
                if (abort == true) {    return 0;       }
        
-               int count = 1;
                int error = 0;
                
                //read fastafile
@@ -163,19 +152,17 @@ int BinSeqCommand::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){
                                
                                error = process(list);  
                                if (error == 1) { return 0; }   
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
-                               userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -187,14 +174,12 @@ int BinSeqCommand::execute(){
                                                                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
-                               
                        }
                        
                        lastLabel = list->getLabel();                   
                        
                        delete list;
                        list = input->getListVector();
-                       count++;
                }
                
                
@@ -211,7 +196,7 @@ int BinSeqCommand::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);