X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.h;h=06dbad975bc6f6b3035024f1260108e65470db64;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=e75f63c3fe80a4eaad7a2bccfae3ad266346b9e4;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index e75f63c..06dbad9 100644
--- 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;