broke up globaldata and moved error checking and help into commands

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 8c7f07c8bb7f73025764e77fa71d3f44585a1e55..b3aa54f77a883579a29c601c2d5e737e1c1cae09 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -11,12 +11,68 @@
 
 //**********************************************************************************************************************
 
-GetSAbundCommand::GetSAbundCommand(){
+GetSAbundCommand::GetSAbundCommand(string option){
        try {
                globaldata = GlobalData::getInstance();
-               filename = getRootName(globaldata->inputFileName) + "sabund";
+               abort = false;
+               allLines = 1;
+               lines.clear();
+               labels.clear();
                
-               openOutputFile(filename, out);
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
+               
+               else {
+                       //valid paramters for this command
+                       string Array[] =  {"line","label"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       parser = new OptionParser();
+                       parser->parse(option, parameters);  delete parser;
+                       
+                       ValidParameters* validParameter = new ValidParameters();
+               
+                       //check to make sure all parameters are valid for command
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //make sure the user has already run the read.otu command
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; abort = true; }
+                       
+                       //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 { 
+                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               else { allLines = 1;  }
+                       }
+                       
+                       //make sure user did not use both the line and label parameters
+                       if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+                       //if the user has not specified any line or labels use the ones from read.otu
+                       else if((line == "") && (label == "")) {  
+                               allLines = globaldata->allLines; 
+                               labels = globaldata->labels; 
+                               lines = globaldata->lines;
+                       }
+                               
+                       delete validParameter;
+                       
+                       if (abort == false) {
+                               filename = getRootName(globaldata->inputFileName) + "sabund";
+                               openOutputFile(filename, out);
+                       }
+               }
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -28,6 +84,28 @@ GetSAbundCommand::GetSAbundCommand(){
        }       
                        
 }
+//**********************************************************************************************************************
+
+void GetSAbundCommand::help(){
+       try {
+               cout << "The get.sabund command can only be executed after a successful read.otu of a listfile." << "\n";
+               cout << "The get.sabund command parameters are line and label.  No parameters are required, and you may not use line and label at the same time." << "\n";
+               cout << "The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes." << "\n";
+               cout << "The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels)." << "\n";
+               cout << "Example get.sabund(line=1-3-5)." << "\n";
+               cout << "The default value for line and label are all lines in your inputfile." << "\n";
+               cout << "The get.sabund command outputs a .sabund file containing the lines you selected." << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the GetSAbundCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
 
 //**********************************************************************************************************************
 
@@ -38,6 +116,9 @@ GetSAbundCommand::~GetSAbundCommand(){
 
 int GetSAbundCommand::execute(){
        try {
+               
+               if (abort == true) { return 0; }
+       
                int count = 1;
                
                //using order vector so you don't have to distinguish between the list and rabund files
@@ -50,13 +131,13 @@ int GetSAbundCommand::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 = globaldata->labels;
-               set<int> userLines = globaldata->lines;
+               set<string> userLabels = labels;
+               set<int> userLines = lines;
 
                
-               while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
-                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+                       if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
                                        cout << order->getLabel() << '\t' << count << endl;
                                        sabund = new SAbundVector();
                                        *sabund = (order->getSAbundVector());