pat's edits of screen.seqs and summary.seqs

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 242e9a8fe0e3ba7a7f199846ae0e80cba10f0edb..08c291d2bd28e1f74efdb0562c2c1ccc329d9a25 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -41,9 +41,11 @@
 AlignCommand::AlignCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               candidateFileName = globaldata->getCandidateFile();
-               templateFileName = globaldata->getFastaFile();
-               openInputFile(candidateFileName, in);
+               if(globaldata->getFastaFile() == "" && globaldata->getPhylipFile() == "" && globaldata->getNexusFile() == "" && globaldata->getClustalFile() == ""){
+                       cout << "you forgot a template file" << endl;
+               }
+               openInputFile(globaldata->getCandidateFile(), in);
+               
                convert(globaldata->getKSize(), kmerSize);
                convert(globaldata->getMatch(), match);
                convert(globaldata->getMismatch(), misMatch);
@@ -73,28 +75,33 @@ int AlignCommand::execute(){
                srand( (unsigned)time( NULL ) );  //needed to assign names to temporary files
                
                Database* templateDB;
-               if(globaldata->getSearch() == "kmer")                   {       templateDB = new KmerDB(templateFileName, kmerSize);                                                            }
-               else if(globaldata->getSearch() == "suffix")    {       templateDB = new SuffixDB(templateFileName);                                                                            }
-               else if(globaldata->getSearch() == "blast")             {       templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch);        }
-               else {  cout << globaldata->getSearch() << " is not a valid search option. I will run the command using suffix." << endl;
-                               templateDB = new SuffixDB(templateFileName);            }
+               if(globaldata->getSearch() == "kmer")                   {       templateDB = new KmerDB(globaldata->getFastaFile() , kmerSize); }
+               else if(globaldata->getSearch() == "suffix")    {       templateDB = new SuffixDB(globaldata->getFastaFile());                  }
+               else if(globaldata->getSearch() == "blast")             {       templateDB = new BlastDB(globaldata->getFastaFile(), gapOpen, gapExtend, match, misMatch);      }
+               else {
+                       cout << globaldata->getSearch() << " is not a valid search option. I will run the command using kmer, ksize=8." << endl;
+                       templateDB = new KmerDB(globaldata->getFastaFile(), kmerSize);
+               }
        
                Alignment* alignment;
-               if(globaldata->getAlign() == "gotoh")                                   {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000);        }
-               else if(globaldata->getAlign() == "needleman")                  {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);                       }
-               else if(globaldata->getAlign() == "blast")                              {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
-               else if(globaldata->getAlign() == "noalign")                    {       alignment = new NoAlign();                                                                                                      }
-               else {  cout << globaldata->getAlign() << " is not a valid alignment option. I will run the command using blast." << endl;
-                               alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);    }
+               if(globaldata->getAlign() == "gotoh")                   {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000);        }
+               else if(globaldata->getAlign() == "needleman")  {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);                       }
+               else if(globaldata->getAlign() == "blast")              {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
+               else if(globaldata->getAlign() == "noalign")    {       alignment = new NoAlign();                                                                                                      }
+               else {
+                       cout << globaldata->getAlign() << " is not a valid alignment option. I will run the command using needleman." << endl;
+                       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);
+               }
                                
                int numFastaSeqs=count(istreambuf_iterator<char>(in),istreambuf_iterator<char>(), '>');
                in.seekg(0);
        
-               string candidateAligngmentFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + globaldata->getSearch() + '.' + globaldata->getAlign() + ".nast.align";
+               candidateFileName = globaldata->getCandidateFile();
+               string candidateAligngmentFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
                ofstream candidateAlignmentFile;
                openOutputFile(candidateAligngmentFName, candidateAlignmentFile);
 
-               string candidateReportFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + globaldata->getSearch() + '.' + globaldata->getAlign() + ".nast.report";
+               string candidateReportFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
                NastReport report(candidateReportFName);
 
                cout << "We are going to align the " << numFastaSeqs << " sequences in " << candidateFileName << "..." << endl;
@@ -110,6 +117,7 @@ int AlignCommand::execute(){
                        Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq);
                        report.setTemplate(templateSeq);
                        report.setSearchParameters(globaldata->getSearch(), templateDB->getSearchScore());
+                       
                                
                        Nast nast(alignment, candidateSeq, templateSeq);
                        report.setAlignmentParameters(globaldata->getAlign(), alignment);