final fixes for 1.7

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 958f29b39213c3fda29e810af8832fef4afa83e1..57eebb0eb096ef8cc554ba4f0eaee8f470c5b6d2 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -22,10 +22,6 @@
 #include "blastalign.hpp"
 #include "noalign.hpp"
 
-#include "kmerdb.hpp"
-#include "suffixdb.hpp"
-#include "blastdb.hpp"
-
 #include "nast.hpp"
 #include "nastreport.hpp"
 
@@ -126,7 +122,7 @@ void AlignCommand::help(){
                mothurOut("The template and candidate parameters are required.\n");
                mothurOut("The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.\n");
                mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
-               mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 7.\n");
+               mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
                mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
                mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
                mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0.\n");
@@ -149,19 +145,9 @@ int AlignCommand::execute(){
        try {
                if (abort == true) {    return 0;       }
                
-               if(search == "kmer")                    {       templateDB = new KmerDB(templateFileName, kmerSize);    }
-               else if(search == "suffix")             {       templateDB = new SuffixDB(templateFileName);                    }
-               else if(search == "blast")              {       templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch);        }
-               else {
-                       mothurOut(search + " is not a valid search option. I will run the command using kmer, ksize=8.");
-                       mothurOutEndLine();
-                       kmerSize = 8;
-                       
-                       templateDB = new KmerDB(templateFileName, kmerSize);
-               }
-               
+               templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
                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);            }
@@ -272,25 +258,32 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                for(int i=0;i<line->numSeqs;i++){
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);
+
+                       if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
+                               alignment->resize(candidateSeq->getUnaligned().length()+1);
+                       }
+       
                        report.setCandidate(candidateSeq);
        
                        Sequence temp = templateDB->findClosestSequence(candidateSeq);
+
                        Sequence* templateSeq = &temp;
-                       
+
                        report.setTemplate(templateSeq);
                        report.setSearchParameters(search, templateDB->getSearchScore());
-                       
+                               
                        Nast nast(alignment, candidateSeq, templateSeq);
 
                        report.setAlignmentParameters(align, alignment);
-
+       
                        report.setNastParameters(nast);
-
+       
                        alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
-                       
+                               
                        report.print();
                        
-                       delete candidateSeq;            
+                       delete candidateSeq;
+               
                }
                
                alignmentFile.close();