fixed some bugs and added scriptengine

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 3787cef08a3fd8b6d142d915ed0b79e7698539ae..24ef1d12e08262a335f7c29104120f7cddc81e1b 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -12,10 +12,34 @@
 
 //***************************************************************************************************************
 
-SeqSummaryCommand::SeqSummaryCommand(){
+SeqSummaryCommand::SeqSummaryCommand(string option){
        try {
-               globaldata = GlobalData::getInstance();
-               if(globaldata->getFastaFile() == "")            {       cout << "you need to at least enter a fasta file name" << endl; }
+               abort = false;
+               
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
+               
+               else {
+                       //valid paramters for this command
+                       string Array[] =  {"fasta"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
+                       
+                       //check to make sure all parameters are valid for command
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //check for required parameters
+                       fastafile = validParameter.validFile(parameters, "fasta", true);
+                       if (fastafile == "not open") { abort = true; }
+                       else if (fastafile == "not found") { fastafile = ""; cout << "fasta is a required parameter for the summary.seqs command." << endl; abort = true;  }    
+                       
+               }
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SeqSummaryCommand class Function SeqSummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -26,6 +50,25 @@ SeqSummaryCommand::SeqSummaryCommand(){
                exit(1);
        }       
 }
+//**********************************************************************************************************************
+
+void SeqSummaryCommand::help(){
+       try {
+               cout << "The summary.seqs command reads a fastafile and ...." << "\n";
+               cout << "The summary.seqs command parameter is fasta and it is required." << "\n";
+               cout << "The summary.seqs command should be in the following format: " << "\n";
+               cout << "summary.seqs(fasta=yourFastaFile) " << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";       
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SeqSummaryCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SeqSummaryCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
 
 //***************************************************************************************************************
 
@@ -35,13 +78,15 @@ SeqSummaryCommand::~SeqSummaryCommand(){    /*      do nothing      */      }
 
 int SeqSummaryCommand::execute(){
        try{
-
+               
+               if (abort == true) { return 0; }
+               
                ifstream inFASTA;
-               openInputFile(globaldata->getFastaFile(), inFASTA);
+               openInputFile(fastafile, inFASTA);
                int numSeqs = 0;
 
                ofstream outSummary;
-               string summaryFile = globaldata->getFastaFile() + ".summary";
+               string summaryFile = fastafile + ".summary";
                openOutputFile(summaryFile, outSummary);
                
                vector<int> startPosition;