removed line option

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 9b4935f5ec076ddc870ed7716b0588184e13dee4..6ccbf35d9affe9d0ab345018ba2165fe80d37dd8 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -27,7 +27,6 @@ MatrixOutputCommand::MatrixOutputCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Groups.clear();
                Estimators.clear();
@@ -37,7 +36,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","calc","groups"};
+                       string Array[] =  {"label","calc","groups"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -58,13 +57,6 @@ MatrixOutputCommand::MatrixOutputCommand(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 @@ MatrixOutputCommand::MatrixOutputCommand(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);                 
@@ -141,11 +130,11 @@ MatrixOutputCommand::MatrixOutputCommand(string option){
 void MatrixOutputCommand::help(){
        try {
                mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
-               mothurOut("The dist.shared command parameters are groups, calc, line and label.  The calc parameter is required, and you may not use line and label at the same time.\n");
+               mothurOut("The dist.shared command parameters are groups, calc and label.  No parameters are required.\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 distance matrices created for, and are also separated by dashes.\n");
-               mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels).\n");
-               mothurOut("Example dist.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund).\n");
+               mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
+               mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+               mothurOut("Example dist.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 and thetayc.\n");
                validCalculator->printCalc("matrix", cout);
@@ -175,9 +164,7 @@ int MatrixOutputCommand::execute(){
        try {
                
                if (abort == true) {    return 0;       }
-       
-               int count = 1;  
-                               
+                       
                //if the users entered no valid calculators don't execute command
                if (matrixCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine();  return 0; }
 
@@ -192,22 +179,20 @@ int MatrixOutputCommand::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;
-                               
+                                       
                if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups.  I cannot run the command."); mothurOutEndLine(); return 0;}
                
                numGroups = lookup.size();
                                
                //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)) {
@@ -222,13 +207,11 @@ int MatrixOutputCommand::execute(){
                                userLabels.erase(lookup[0]->getLabel());
                        }
 
-                        
                        lastLabel = lookup[0]->getLabel();                      
                        
                        //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
@@ -244,7 +227,7 @@ int MatrixOutputCommand::execute(){
                        }
                }
                
-               //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);