added pca command

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 9e2a08b2a493fec7ed717505d7d02112a8530b49..37e95685430184760cd0919c18a1cfeea2ec4c42 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -38,36 +38,28 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                        //check for required parameters
                        fasta = validParameter.validFile(parameters, "fasta", true);
                        if (fasta == "not open") { abort = true; }
-                       else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true;  }    
+                       else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true;  }     
                        
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 //**********************************************************************************************************************
 
 void ReverseSeqsCommand::help(){
        try {
-               cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
-               cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
-               cout << "The reverse.seqs command should be in the following format: " << "\n";
-               cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";   
+               mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+               mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+               mothurOut("The reverse.seqs command should be in the following format: \n");
+               mothurOut("reverse.seqs(fasta=yourFastaFile) \n");      
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReverseSeqsCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //***************************************************************************************************************
@@ -90,9 +82,11 @@ int ReverseSeqsCommand::execute(){
                openOutputFile(reverseFile, outFASTA);
                
                while(!inFASTA.eof()){
-                       Sequence currSeq(inFASTA);
-                       currSeq.reverseComplement();
-                       currSeq.printSequence(outFASTA);
+                       Sequence currSeq(inFASTA);  gobble(inFASTA);
+                       if (currSeq.getName() != "") {
+                               currSeq.reverseComplement();
+                               currSeq.printSequence(outFASTA);
+                       }
                }
                inFASTA.close();
                outFASTA.close();
@@ -101,11 +95,7 @@ int ReverseSeqsCommand::execute(){
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReverseSeqsCommand", "execute");
                exit(1);
        }
 }