*/
#include "getgroupcommand.h"
+#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> GetgroupCommand::getValidParameters(){
+vector<string> GetgroupCommand::setParameters(){
try {
- string Array[] = {"outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none","",false,true, true); parameters.push_back(pshared);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetgroupCommand::GetgroupCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["bootgroup"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
+ m->errorOut(e, "GetgroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetgroupCommand::getRequiredParameters(){
+string GetgroupCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n";
+ helpString += "You may not use any parameters with the get.group command.\n";
+ helpString += "The get.group command should be in the following format: \n";
+ helpString += "get.group()\n";
+ helpString += "Example get.group().\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "getRequiredParameters");
+ m->errorOut(e, "GetgroupCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> GetgroupCommand::getRequiredFiles(){
+GetgroupCommand::GetgroupCommand(){
try {
- string Array[] = {"shared"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
}
catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "getRequiredFiles");
+ m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetgroupCommand::GetgroupCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (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 input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+ }
- //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 = ""; }
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
- 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);
-
- }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); }
}
}
catch(exception& e) {
}
//**********************************************************************************************************************
-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);
- }
-}
-
-//**********************************************************************************************************************
-
-GetgroupCommand::~GetgroupCommand(){
-}
-
-//**********************************************************************************************************************
-
int GetgroupCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- 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;
+
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
- //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;
+ for (int i = 0; i < lookup.size(); i++) {
+ m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
+ delete lookup[i];
}
-
- 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->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
exit(1);
}
}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff