merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / getlinecommand.cpp

diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index a7ca17fc34297c58869f0d578f52ec70e1fc3367..6802978a0c3e527aed6a30a7a8ecce1726c19b57 100644 (file)
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -3,16 +3,27 @@
  *  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 "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 != "") { cout << "There are no valid parameters for the get.line command." << endl; abort = true; }
+                       
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.line command." << endl; 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";
@@ -24,6 +35,25 @@ GetlineCommand::GetlineCommand(){
        }       
                        
 }
+//**********************************************************************************************************************
+
+void GetlineCommand::help(){
+       try {
+               cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
+               cout << "You may not use any parameters with the get.line command." << "\n";
+               cout << "The get.line command should be in the following format: " << "\n";
+               cout << "get.line()" << "\n";
+               cout << "Example get.line()." << "\n";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the GetlineCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
 
 //**********************************************************************************************************************
 
@@ -34,19 +64,19 @@ GetlineCommand::~GetlineCommand(){
 
 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)
-                       {
+                       if(count == 0) {
                                cout << line << "\n";
                                in >> numBins;
                                line++;