*/
#include "getgroupcommand.h"
+#include "inputdata.h"
//**********************************************************************************************************************
vector<string> GetgroupCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,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);
+ 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); }
try {
string helpString = "";
helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\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");
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";
exit(1);
}
}
+
//**********************************************************************************************************************
GetgroupCommand::GetgroupCommand(){
try {
abort = true; calledHelp = true;
setParameters();
- vector<string> tempOutNames;
- outputTypes["bootgroup"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
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 = ""; }
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 the user changes the output directory command factory will send this info to us in the output parameter
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
- //open shared file
- m->openInputFile(sharedfile, in);
-
- //open output file
- outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
- m->openOutputFile(outputFile, out);
-
- 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;
+ 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);
}
}
+//**********************************************************************************************************************