removed line option

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 27f701ffd20da0ea1d83a011b575a5d9fb5ea956..d25c46adde9b46ce3044a115d1c816dd552ac146 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -27,7 +27,6 @@ TreeGroupCommand::TreeGroupCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Groups.clear();
                Estimators.clear();
@@ -37,7 +36,7 @@ TreeGroupCommand::TreeGroupCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
+                       string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -78,13 +77,6 @@ TreeGroupCommand::TreeGroupCommand(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 { 
@@ -92,13 +84,10 @@ TreeGroupCommand::TreeGroupCommand(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);                 
@@ -172,13 +161,13 @@ void TreeGroupCommand::help(){
        try {
                mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
                mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
-               mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision, line and label.  You may not use line and label at the same time.\n");
+               mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision 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 group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
                mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used.  If you use a column file the name filename is required. \n");
                mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
-               mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels).\n");
-               mothurOut("Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund).\n");
+               mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+               mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
                mothurOut("The default value for groups is all the groups in your groupfile.\n");
                mothurOut("The default value for calc is jclass-thetayc.\n");
                mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
@@ -427,7 +416,6 @@ void TreeGroupCommand::makeSimsDist() {
 /***********************************************************/
 void TreeGroupCommand::makeSimsShared() {
        try {
-               int count = 1;  
        
                //clear globaldatas old tree names if any
                globaldata->Treenames.clear();
@@ -442,18 +430,16 @@ void TreeGroupCommand::makeSimsShared() {
                
                set<string> processedLabels;
                set<string> userLabels = labels;
-               set<int> userLines = lines;
-
+               
                //as long as you are not at the end of the file or done wih the lines you want
-               while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                
-                       if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){                       
+                       if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                process(lookup);
                                
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
-                               userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -472,7 +458,6 @@ void TreeGroupCommand::makeSimsShared() {
                        //get next line to process
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        lookup = input->getSharedRAbundVectors();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -488,7 +473,7 @@ void TreeGroupCommand::makeSimsShared() {
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                        for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {             delete lookup[i]; }             } 
                        lookup = input->getSharedRAbundVectors(lastLabel);