added logfile feature

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index c38bfcb5f83eb3b607b42616174cf650b0de8952..ad491aa1252ccb28553b12daf0f353533428d531 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -36,7 +36,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
                        
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
+                       if (fastafile == "not found") { mothurOut("fasta is a required parameter for the filter.seqs command."); mothurOutEndLine(); abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
 
                        //check for optional parameter and set defaults
@@ -60,40 +60,32 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the FilterSeqsCommand class function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
 
 void FilterSeqsCommand::help(){
        try {
-               cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
-               cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical.  " << "\n";
-               cout << "The fasta parameter is required." << "\n";
-               cout << "The trump parameter .... The default is ..." << "\n";
-               cout << "The soft parameter .... The default is ...." << "\n";
-               cout << "The hard parameter .... The default is ...." << "\n";
-               cout << "The vertical parameter .... The default is T." << "\n";
-               cout << "The filter.seqs command should be in the following format: " << "\n";
-               cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
-               cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
-               cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+               mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
+               mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
+               mothurOut("The fasta parameter is required.\n");
+               mothurOut("The trump parameter .... The default is ...\n");
+               mothurOut("The soft parameter .... The default is ....\n");
+               mothurOut("The hard parameter .... The default is ....\n");
+               mothurOut("The vertical parameter .... The default is T.\n");
+               mothurOut("The filter.seqs command should be in the following format: \n");
+               mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
+               mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FilterSeqsCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the FilterSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /**************************************************************************************/
@@ -206,15 +198,15 @@ int FilterSeqsCommand::execute() {
                outFilter << filter << endl;
                outFilter.close();
                
-
-               openInputFile(fastafile, inFASTA);
+               ifstream inFasta2;
+               openInputFile(fastafile, inFasta2);
                string filteredFasta = getRootName(fastafile) + "filter.fasta";
                ofstream outFASTA;
                openOutputFile(filteredFasta, outFASTA);
 
                numSeqs = 0;
-               while(!inFASTA.eof()){
-                       Sequence seq(inFASTA);
+               while(!inFasta2.eof()){
+                       Sequence seq(inFasta2);
                        string align = seq.getAligned();
                        string filterSeq = "";
        
@@ -226,10 +218,10 @@ int FilterSeqsCommand::execute() {
 
                        outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
                        numSeqs++;
-                       gobble(inFASTA);
+                       gobble(inFasta2);
                }
                outFASTA.close();
-               inFASTA.close();
+               inFasta2.close();
                
                
                int filteredLength = 0;
@@ -237,21 +229,17 @@ int FilterSeqsCommand::execute() {
                        if(filter[i] == '1'){   filteredLength++;       }
                }
                
-               cout << endl;
-               cout << "Length of filtered alignment: " << filteredLength << endl;
-               cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
-               cout << "Length of the original alignment: " << alignmentLength << endl;
-               cout << "Number of sequences used to construct filter: " << numSeqs << endl;
+               mothurOutEndLine();
+               mothurOut("Length of filtered alignment: " + toString(filteredLength)); mothurOutEndLine();
+               mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); mothurOutEndLine();
+               mothurOut("Length of the original alignment: " + toString(alignmentLength)); mothurOutEndLine();
+               mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); mothurOutEndLine();
                
                return 0;
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "FilterSeqsCommand", "execute");
                exit(1);
        }
 }