moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / getgroupcommand.cpp

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 9014031d5a58556493b712282fbf4bfc5535d5e2..cf47661bb6a8084740262d8a6b4b157181a2b0ab 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -10,7 +10,7 @@
 #include "getgroupcommand.h"
 
 //**********************************************************************************************************************
-GetgroupCommand::GetgroupCommand(string option){
+GetgroupCommand::GetgroupCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
@@ -19,24 +19,39 @@ GetgroupCommand::GetgroupCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option != "") { mothurOut("There are no valid parameters for the get.group command."); mothurOutEndLine(); abort = true; }
+                       //valid paramters for this command
+                       string Array[] =  {"outputdir","inputdir"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
-                       if ((globaldata->getSharedFile() == "")) { mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); mothurOutEndLine(); abort = true; }
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
+                       //check to make sure all parameters are valid for command
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               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 = "";         }
+                       
+                       if ((globaldata->getSharedFile() == "")) { m->mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); m->mothurOutEndLine(); abort = true; }
                                
                        if (abort == false) {
                                //open shared file
                                sharedfile = globaldata->getSharedFile();
-                               openInputFile(sharedfile, in);
+                               m->openInputFile(sharedfile, in);
                
                                //open output file
-                               outputFile = getRootName(sharedfile) + "bootGroups";
-                               openOutputFile(outputFile, out);
+                               if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
+                               outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
+                               m->openOutputFile(outputFile, out);
 
                        }
                }
        }
        catch(exception& e) {
-               errorOut(e, "GetgroupCommand", "GetgroupCommand");
+               m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
                exit(1);
        }
 }
@@ -44,16 +59,16 @@ GetgroupCommand::GetgroupCommand(string option){
 
 void GetgroupCommand::help(){
        try {
-               mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
-               //mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
-               mothurOut("You may not use any parameters with the get.group command.\n");
-               mothurOut("The get.group command should be in the following format: \n");
-               mothurOut("get.group()\n");
-               mothurOut("Example get.group().\n");
+               m->mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
+               //m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
+               m->mothurOut("You may not use any parameters with the get.group command.\n");
+               m->mothurOut("The get.group command should be in the following format: \n");
+               m->mothurOut("get.group()\n");
+               m->mothurOut("Example get.group().\n");
                
        }
        catch(exception& e) {
-               errorOut(e, "GetgroupCommand", "help");
+               m->errorOut(e, "GetgroupCommand", "help");
                exit(1);
        }
 }
@@ -79,7 +94,7 @@ int GetgroupCommand::execute(){
                holdLabel = label;
                
                //output first group
-               mothurOut(groupN); mothurOutEndLine();
+               m->mothurOut(groupN); m->mothurOutEndLine();
                out << groupN << '\t' << groupN << endl;        
                        
                //get rest of line
@@ -87,15 +102,19 @@ int GetgroupCommand::execute(){
                        in >> inputData;
                }
                
+               if (m->control_pressed) { in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+
                if (in.eof() != true) { in >> nextLabel; }
                
                //read the rest of the groups info in
                while ((nextLabel == holdLabel) && (in.eof() != true)) {
+                       if (m->control_pressed) { in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+                       
                        in >> groupN >> num;
                        count++;
                        
                        //output next group
-                       mothurOut(groupN); mothurOutEndLine();
+                       m->mothurOut(groupN); m->mothurOutEndLine();
                        out << groupN << '\t' << groupN << endl;                                
                        
                        //fill vector.  
@@ -108,11 +127,19 @@ int GetgroupCommand::execute(){
                
                in.close();
                out.close();
+               
+               if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(outputFile); m->mothurOutEndLine();        
+               m->mothurOutEndLine();
+               
                return 0;       
        }
 
        catch(exception& e) {
-               errorOut(e, "GetgroupCommand", "execute");
+               m->errorOut(e, "GetgroupCommand", "execute");
                exit(1);
        }
 }