#include "getgroupcommand.h"
-
-GetgroupCommand::GetgroupCommand(){
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::getValidParameters(){
try {
- globaldata = GlobalData::getInstance();
- groupMap = globaldata->gGroupmap;
- outputFile = globaldata->inputFileName + ".bootGroups";
- openOutputFile(outputFile, out);
+ string Array[] = {"outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetgroupCommand", "getValidParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetgroupCommand class function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+GetgroupCommand::GetgroupCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["bootgroup"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
exit(1);
- }
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetgroupCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetgroupCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetgroupCommand::GetgroupCommand(string option) {
+ try {
+ globaldata = GlobalData::getInstance();
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["bootgroup"] = tempOutNames;
+
+ //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();
+ m->openInputFile(sharedfile, in);
+
+ //open output file
+ if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
+ outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
+ m->openOutputFile(outputFile, out);
+
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void GetgroupCommand::help(){
+ try {
+ 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) {
+ m->errorOut(e, "GetgroupCommand", "help");
+ exit(1);
+ }
}
//**********************************************************************************************************************
int GetgroupCommand::execute(){
try {
- vector<string> groupNames = groupMap->namesOfGroups;
- for(int i = 0; i < groupNames.size(); i++) {
- cout << groupNames[i] << "\n";
- out << groupNames[i] << "\t" << groupNames[i] << "\n";
+
+ if (abort == true) { return 0; }
+
+ int num, inputData, count;
+ count = 0;
+ string holdLabel, nextLabel, groupN, label;
+
+ //read in first row since you know there is at least 1 group.
+ in >> label >> groupN >> num;
+ holdLabel = label;
+
+ //output first group
+ m->mothurOut(groupN); m->mothurOutEndLine();
+ out << groupN << '\t' << groupN << endl;
+
+ //get rest of line
+ for(int i=0;i<num;i++){
+ in >> inputData;
}
+
+ if (m->control_pressed) { outputTypes.clear(); 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) { outputTypes.clear(); in.close(); out.close(); remove(outputFile.c_str()); return 0; }
+
+ in >> groupN >> num;
+ count++;
+
+ //output next group
+ m->mothurOut(groupN); m->mothurOutEndLine();
+ out << groupN << '\t' << groupN << endl;
+
+ //fill vector.
+ for(int i=0;i<num;i++){
+ in >> inputData;
+ }
+
+ if (in.eof() != true) { in >> nextLabel; }
+ }
+
+ 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(); outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetgroupCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetgroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
projects / mothur.git / blobdiff