#include "getgroupcommand.h"
//**********************************************************************************************************************
-GetgroupCommand::GetgroupCommand(string option){
+GetgroupCommand::GetgroupCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
//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() == "")) { 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; }
+ 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
}
}
catch(exception& e) {
- errorOut(e, "GetgroupCommand", "GetgroupCommand");
+ m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
exit(1);
}
}
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);
}
}
holdLabel = label;
//output first group
- mothurOut(groupN); mothurOutEndLine();
+ m->mothurOut(groupN); m->mothurOutEndLine();
out << groupN << '\t' << groupN << endl;
//get rest of line
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.
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);
}
}