#include "getlinecommand.h"
-
-GetlineCommand::GetlineCommand(){
+//**********************************************************************************************************************
+GetlineCommand::GetlineCommand(string option){
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ if (option != "") { mothurOut("There are no valid parameters for the get.line command."); mothurOutEndLine(); abort = true; }
+
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the get.line command."); mothurOutEndLine(); abort = true; }
+ }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetlineCommand", "GetlineCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetlineCommand class function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void GetlineCommand::help(){
+ try {
+ mothurOut("The get.line command can only be executed after a successful read.otu command.\n");
+ mothurOut("You may not use any parameters with the get.line command.\n");
+ mothurOut("The get.line command should be in the following format: \n");
+ mothurOut("get.line()\n");
+ mothurOut("Example get.line().\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "GetlineCommand", "help");
exit(1);
- }
-
+ }
}
//**********************************************************************************************************************
int GetlineCommand::execute(){
try {
- filename = globaldata->inputFileName;
+
+ if (abort == true) { return 0; }
+
ifstream in;
- openInputFile(filename, in);
+ openInputFile(globaldata->inputFileName, in);
string label;
int numBins = 0;
int count = -1;
int line = 1;
- while(in.good())
- {
+ while(in.good()) {
if(count > numBins)
count = 0;
- if(count == 0)
- {
- cout << line << "\n";
+ if(count == 0) {
+ mothurOut(toString(line)); mothurOutEndLine();
in >> numBins;
line++;
}
in >> label;
count++;
}
+
+ in.close();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetlineCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetlineCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}