removed line option

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 004a3bf05a901262ca1233e16ceb862d9b5f9ebd..d88bec0147095a1ed8e57e14c7e771548f86ffe6 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -27,7 +27,6 @@ HeatMapSimCommand::HeatMapSimCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Groups.clear();
                Estimators.clear();
@@ -37,7 +36,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"groups","line","label", "calc"};
+                       string AlignArray[] =  {"groups","label", "calc"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -57,13 +56,6 @@ HeatMapSimCommand::HeatMapSimCommand(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 { 
@@ -71,13 +63,10 @@ HeatMapSimCommand::HeatMapSimCommand(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);                     
@@ -142,15 +131,15 @@ HeatMapSimCommand::HeatMapSimCommand(string option){
 void HeatMapSimCommand::help(){
        try {
                mothurOut("The heatmap.sim command can only be executed after a successful read.otu command.\n");
-               mothurOut("The heatmap.sim command parameters are groups, calc, line and label.  No parameters are required, but you may not use line and label at the same time.\n");
+               mothurOut("The heatmap.sim 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 in your heatmap.\n");
-               mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes.\n");
-               mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels).\n");
-               mothurOut("Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund).\n");
-               mothurOut("The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used.\n");
+               mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n");
+               mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
+               mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\n");
+               mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
                validCalculator->printCalc("heat", cout);
                mothurOut("The default value for calc is jclass-thetayc.\n");
-               mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify.\n");
+               mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 
        }
@@ -178,8 +167,6 @@ int HeatMapSimCommand::execute(){
        
                if (abort == true)  { return 0; }
                
-               int count = 1;  
-               
                //if the users entered no valid calculators don't execute command
                if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
                
@@ -196,20 +183,17 @@ int HeatMapSimCommand::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;
-
                
                //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();
                                heatmap->getPic(lookup, heatCalculators);
                                        
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
-                               userLines.erase(count);
                        }
                                
                        if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -231,7 +215,6 @@ int HeatMapSimCommand::execute(){
                        //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
@@ -247,7 +230,7 @@ int HeatMapSimCommand::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);