added pca command

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 96e1a7899c4fec8d769c46aede121bb8de240c07..f0f7243115f267b6654ab8cb25ceb05b2ef96029 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -93,7 +93,7 @@ AlignCommand::AlignCommand(string option){
                        temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
                        flip = isTrue(temp); 
                        
-                       temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.80";                  }
+                       temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
                        convert(temp, threshold); 
                        
                        search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
@@ -131,12 +131,12 @@ void AlignCommand::help(){
                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");
-               mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -2.0.\n");
+               mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
+               mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
                mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse compement if a sequence falls below the threshold.  The default is false.\n");
                mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. \n");
                mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
-               mothurOut("The default for the threshold parameter is 0.80, meaning at least 80% of the bases must remain or the sequence is reported as potentially reversed.\n");
+               mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
                mothurOut("The align.seqs command should be in the following format: \n");
                mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
                mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
@@ -231,6 +231,15 @@ int AlignCommand::execute(){
                        rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
                        rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
                        
+                       //append alignment and report files
+                       for(int i=1;i<processors;i++){
+                               appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+                               remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+                               
+                               appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
+                               remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
+                       }
+                       
                        vector<string> nonBlankAccnosFiles;
                        //delete blank accnos files generated with multiple processes
                        for(int i=0;i<processors;i++){  
@@ -253,16 +262,6 @@ int AlignCommand::execute(){
                                }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
                                mothurOutEndLine();
                        }
-                       
-                       //append other files
-                       for(int i=1;i<processors;i++){
-                               appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
-                               remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
-                               
-                               appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
-                               remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
-                       }
-                       
                }
 #else
                ifstream inFASTA;
@@ -316,7 +315,7 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
                openInputFile(candidateFileName, inFASTA);
 
                inFASTA.seekg(line->start);
-
+               
                for(int i=0;i<line->numSeqs;i++){
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
@@ -392,7 +391,13 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
                                if (needToDeleteCopy) {   delete copy;   }
                        }
                        delete candidateSeq;
+                       
+                       //report progress
+                       if((i+1) % 100 == 0){   mothurOut(toString(i+1)); mothurOutEndLine();           }
+                       
                }
+               //report progress
+               if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine();         }
                
                alignmentFile.close();
                inFASTA.close();