working on chimeras

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 5af8e959a6caa3edd98a33a21fa680bd5815d2dc..d672fc3df2a405a1057781dacd84c4a9f2b50d6f 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -160,14 +160,16 @@ int AlignCommand::execute(){
                        templateDB = new KmerDB(templateFileName, kmerSize);
                }
                
-               if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000);        }
-               else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);                       }
+               int longestBase = templateDB->getLongestBase();
+               
+               if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
+               else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
                else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
                else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
                else {
                        mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
                        mothurOutEndLine();
-                       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);
+                       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
                }
                
                string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
@@ -184,7 +186,7 @@ int AlignCommand::execute(){
                        inFASTA.close();
                        
                        lines.push_back(new linePair(0, numFastaSeqs));
-                       
+               
                        driver(lines[0], alignFileName, reportFileName);
                        
                }
@@ -197,7 +199,7 @@ int AlignCommand::execute(){
                        
                        string input;
                        while(!inFASTA.eof()){
-                               getline(inFASTA, input);
+                               input = getline(inFASTA);
                                if (input.length() != 0) {
                                        if(input[0] == '>'){    int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);       }
                                }
@@ -262,13 +264,14 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                
                ifstream inFASTA;
                openInputFile(candidateFileName, inFASTA);
+
                inFASTA.seekg(line->start);
-               
+
                for(int i=0;i<line->numSeqs;i++){
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);
                        report.setCandidate(candidateSeq);
-                       
+       
                        Sequence temp = templateDB->findClosestSequence(candidateSeq);
                        Sequence* templateSeq = &temp;
                        
@@ -276,7 +279,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                        report.setSearchParameters(search, templateDB->getSearchScore());
                        
                        Nast nast(alignment, candidateSeq, templateSeq);
+
                        report.setAlignmentParameters(align, alignment);
+
                        report.setNastParameters(nast);
                        
                        alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;