* Mothur
*
* Created by Thomas Ryabin on 1/30/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "getlabelcommand.h"
+//**********************************************************************************************************************
-
-
-
-
-GetlabelCommand::GetlabelCommand(){
+GetlabelCommand::GetlabelCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->mothurOutEndLine(); abort = true; }
+ }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function GetlabelCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetlabelCommand class function GetlabelCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void GetlabelCommand::help(){
+ try {
+ m->mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("You may not use any parameters with the get.label command.\n");
+ m->mothurOut("The get.label command should be in the following format: \n");
+ m->mothurOut("get.label()\n");
+ m->mothurOut("Example get.label().\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetlabelCommand", "help");
exit(1);
- }
-
+ }
}
//**********************************************************************************************************************
int GetlabelCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
filename = globaldata->inputFileName;
ifstream in;
openInputFile(filename, in);
string label;
int numBins = 0;
int count = -1;
- while(in.good())
- {
+ while(in.good()) {
+
+ if (m->control_pressed) { in.close(); return 0; }
+
if(count > numBins)
count = 0;
- if(count == 0)
- {
- cout << label << "\n";
+ if(count == 0) {
+ m->mothurOut(label); m->mothurOutEndLine();
in >> numBins;
}
in >> label;
count++;
}
+
+ in.close();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetlabelCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetlabelCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetlabelCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}