some changes while testing 1.9

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 3dd58c117945a299154ebd09cc60b0688ea9f714..ca8c8a66a9445c21a7472301dce1bce71abe34b3 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-GetSAbundCommand::GetSAbundCommand(string option){
+GetSAbundCommand::GetSAbundCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
@@ -23,7 +23,7 @@ GetSAbundCommand::GetSAbundCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"label"};
+                       string Array[] =  {"label","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -36,8 +36,14 @@ GetSAbundCommand::GetSAbundCommand(string option){
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  
+                               outputDir = ""; 
+                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                       }
+
                        //make sure the user has already run the read.otu command
-                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; }
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -55,14 +61,14 @@ GetSAbundCommand::GetSAbundCommand(string option){
                        }
                                
                        if (abort == false) {
-                               filename = getRootName(globaldata->inputFileName) + "sabund";
+                               filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund";
                                openOutputFile(filename, out);
                        }
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+               m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
                exit(1);
        }
 }
@@ -70,17 +76,17 @@ GetSAbundCommand::GetSAbundCommand(string option){
 
 void GetSAbundCommand::help(){
        try {
-               mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
-               mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
-               mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
-               mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
-               mothurOut("Example get.sabund().\n");
-               mothurOut("The default value for label is all labels in your inputfile.\n");
-               mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
+               m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
+               m->mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
+               m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
+               m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
+               m->mothurOut("Example get.sabund().\n");
+               m->mothurOut("The default value for label is all labels in your inputfile.\n");
+               m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "GetSAbundCommand", "help");
+               m->errorOut(e, "GetSAbundCommand", "help");
                exit(1);
        }
 }
@@ -109,14 +115,19 @@ int GetSAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
+               if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+
+               
                while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
                        if(allLines == 1 || labels.count(order->getLabel()) == 1){
-                                       mothurOut(order->getLabel());  mothurOutEndLine();
+                                       m->mothurOut(order->getLabel());  m->mothurOutEndLine();
                                        sabund = new SAbundVector();
                                        *sabund = (order->getSAbundVector());
                                        sabund->print(out);
                                        delete sabund;
+                                       
+                                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
@@ -128,11 +139,13 @@ int GetSAbundCommand::execute(){
                                        delete order;           
                                        order = (input->getOrderVector(lastLabel));
                                        
-                                       mothurOut(order->getLabel());  mothurOutEndLine();
+                                       m->mothurOut(order->getLabel());  m->mothurOutEndLine();
                                        sabund = new SAbundVector();
                                        *sabund = (order->getSAbundVector());
                                        sabund->print(out);
                                        delete sabund;
+                                       
+                                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
@@ -152,12 +165,12 @@ int GetSAbundCommand::execute(){
                set<string>::iterator it;
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       mothurOut("Your file does not include the label " + *it); 
+                       m->mothurOut("Your file does not include the label " + *it); 
                        if (processedLabels.count(lastLabel) != 1) {
-                               mothurOut(". I will use " + lastLabel + ".");  mothurOutEndLine();
+                               m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
                                needToRun = true;
                        }else {
-                               mothurOut(". Please refer to " + lastLabel + ".");  mothurOutEndLine();
+                               m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
                        }
                }
                
@@ -166,21 +179,30 @@ int GetSAbundCommand::execute(){
                        if (order != NULL) {    delete order;   }
                        order = (input->getOrderVector(lastLabel));
                        
-                       mothurOut(order->getLabel());  mothurOutEndLine();
+                       m->mothurOut(order->getLabel());  m->mothurOutEndLine();
                        sabund = new SAbundVector();
                        *sabund = (order->getSAbundVector());
                        sabund->print(out);
                        delete sabund;
+                       
+                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+                       
                        delete order;
                }
                globaldata->gorder = NULL;
 
                out.close();
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(filename); m->mothurOutEndLine();  
+               m->mothurOutEndLine();
+               
                return 0;               
        }
 
        catch(exception& e) {
-               errorOut(e, "GetSAbundCommand", "execute");
+               m->errorOut(e, "GetSAbundCommand", "execute");
                exit(1);
        }
 }