removed line option

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 0c6c53c0652df0786b885966919f3ce15a2f5197..0f758c15a0eafc98d620d2fb37980be6f221a767 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -27,7 +27,6 @@ BootSharedCommand::BootSharedCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Groups.clear();
                Estimators.clear();
@@ -37,7 +36,7 @@ BootSharedCommand::BootSharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","calc","groups","iters"};
+                       string Array[] =  {"label","calc","groups","iters"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -58,13 +57,6 @@ BootSharedCommand::BootSharedCommand(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 { 
@@ -72,13 +64,10 @@ BootSharedCommand::BootSharedCommand(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;
                        }
                                
                        groups = validParameter.validFile(parameters, "groups", false);                 
@@ -158,11 +147,11 @@ BootSharedCommand::BootSharedCommand(string option){
 void BootSharedCommand::help(){
        try {
                mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n");
-               mothurOut("The bootstrap.shared command parameters are groups, calc, iters, line and label.  You may not use line and label at the same time.\n");
+               mothurOut("The bootstrap.shared command parameters are groups, calc, iters and label.\n");
                mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
-               mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
-               mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters).\n");
-               mothurOut("Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100).\n");
+               mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n");
+               mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n");
+               mothurOut("Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n");
                mothurOut("The default value for groups is all the groups in your groupfile.\n");
                mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n");
        }
@@ -191,7 +180,6 @@ int BootSharedCommand::execute(){
        
                if (abort == true) {    return 0;       }
        
-               int count = 1;
                util = new SharedUtil();        
        
                //read first line
@@ -207,7 +195,6 @@ int BootSharedCommand::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;
                                
                //set users groups
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
@@ -224,19 +211,18 @@ int BootSharedCommand::execute(){
                tmap->makeSim(globaldata->gGroupmap);
                globaldata->gTreemap = tmap;
                        
-               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();
                                process(order);
                                
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
-                               userLines.erase(count);
                        }
                        
-                       //you have a label the user want that is smaller than this line and the last line has not already been processed
+                       //you have a label the user want that is smaller than this label and the last label has not already been processed
                        if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                
                                delete order;
@@ -254,7 +240,6 @@ int BootSharedCommand::execute(){
                        //get next line to process
                        delete order;
                        order = input->getSharedOrderVector();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -280,8 +265,6 @@ int BootSharedCommand::execute(){
 
                }
                
-               
-               
                //reset groups parameter
                globaldata->Groups.clear();