removed line option

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 697bc5340d66d54f9bdfcd8505bd8927a7e0ac57..18faa2d699333bade9ce3f492b52a1dbe2eb10a2 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -41,7 +41,6 @@ CollectSharedCommand::CollectSharedCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Estimators.clear();
                Groups.clear();
@@ -51,7 +50,7 @@ CollectSharedCommand::CollectSharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"freq","line","label","calc","groups"};
+                       string Array[] =  {"freq","label","calc","groups"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -72,14 +71,7 @@ CollectSharedCommand::CollectSharedCommand(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;  }
-                       }
-                       
+                       // ...at some point should added some additional type checking..
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
@@ -87,13 +79,10 @@ CollectSharedCommand::CollectSharedCommand(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;
                        }
                                
                        calc = validParameter.validFile(parameters, "calc", false);                     
@@ -184,14 +173,14 @@ CollectSharedCommand::CollectSharedCommand(string option){
 void CollectSharedCommand::help(){
        try {
                mothurOut("The collect.shared command can only be executed after a successful read.otu command.\n");
-               mothurOut("The collect.shared command parameters are label, line, freq, calc and groups.  No parameters are required, but you may not use \n");
-               mothurOut("both the line and label parameters at the same time. The collect.shared command should be in the following format: \n");
-               mothurOut("collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n");
-               mothurOut("Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+               mothurOut("The collect.shared command parameters are label, freq, calc and groups.  No parameters are required \n");
+               mothurOut("The collect.shared command should be in the following format: \n");
+               mothurOut("collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n");
+               mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
                mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
                mothurOut("The default value for groups is all the groups in your groupfile.\n");
                validCalculator->printCalc("shared", cout);
-               mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
+               mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
                
@@ -221,8 +210,6 @@ int CollectSharedCommand::execute(){
                
                if (abort == true) {    return 0;       }
                
-               int count = 1;
-               
                //if the users entered no valid calculators don't execute command
                if (cDisplays.size() == 0) { return 0; }
                
@@ -236,15 +223,14 @@ int CollectSharedCommand::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, "collect");
                util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
-               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){
                                
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);
@@ -254,10 +240,9 @@ int CollectSharedCommand::execute(){
                                mothurOut(order->getLabel()); mothurOutEndLine();
                                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;
                                order = input->getSharedOrderVector(lastLabel);
@@ -278,7 +263,6 @@ int CollectSharedCommand::execute(){
                        //get next line to process
                        delete order;
                        order = input->getSharedOrderVector();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -294,7 +278,7 @@ int CollectSharedCommand::execute(){
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                        if (order != NULL) {  delete order;  }
                        order = input->getSharedOrderVector(lastLabel);