finished up adding N code to trim.flows

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index e75f63c3fe80a4eaad7a2bccfae3ad266346b9e4..06dbad975bc6f6b3035024f1260108e65470db64 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -40,7 +40,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "pairwise.seqs";               }
        string getCommandCategory()             { return "Sequence Processing"; }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
        string getDescription()         { return "calculates pairwise distances from an unaligned fasta file"; }
 
@@ -126,7 +128,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
                outFile.setf(ios::fixed, ios::showpoint);
                outFile << setprecision(4);
                
-               pDataArray->count = pDataArray->end;
+               pDataArray->count = 0;
         
         int startTime = time(NULL);
         
@@ -160,6 +162,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
         if(pDataArray->start == 0){    outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
                
                for(int i=pDataArray->start;i<pDataArray->end;i++){
+            pDataArray->count++;
             
                        string name = pDataArray->alignDB.get(i).getName();
                        //pad with spaces to make compatible
@@ -199,7 +202,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
                        }
                        
                }
-               pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+               pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
                
                outFile.close();
         delete alignment;