X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=filterseqscommand.h;h=ed7cfd1f98ddb6f44c8c7f690447d8dea1d4f6f0;hp=4405c33f52165d5c89cbe47e8513147cb14dd879;hb=c48d91112209b841444923670dca5454da0e2a4d;hpb=91a27e0483827c06c21c4fe89558923bbfe86573

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 4405c33..ed7cfd1 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -24,7 +24,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "filter.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }
 	string getDescription()		{ return "removes columns from alignments based on a criteria defined by the user"; }
 	
@@ -151,7 +153,7 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
 			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
 		}
 		
-		pDataArray->count = pDataArray->end;
+		pDataArray->count = 0;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 			
 			if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
@@ -164,12 +166,12 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
                 if(pDataArray->trump != '*')			{	pDataArray->F.doTrump(current);		}
                 if(pDataArray->m->isTrue(pDataArray->vertical) || pDataArray->soft != 0)	{	pDataArray->F.getFreqs(current);	}
 			}
-            
+            pDataArray->count++;
             //report progress
-			if((i) % 100 == 0){	pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();		}
+			if((i) % 100 == 0){	pDataArray->m->mothurOutJustToScreen(toString(i)+"\n"); 		}
 		}
 		
-        if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
+        if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); 		}
         
 		in.close();
 		
@@ -201,7 +203,7 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
 			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
 		}
 		
-		pDataArray->count = pDataArray->end;
+		pDataArray->count = 0;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 			
 			if (pDataArray->m->control_pressed) { in.close(); out.close(); pDataArray->count = 1; return 1; }
@@ -219,12 +221,12 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
                 
                 out << '>' << seq.getName() << endl << filterSeq << endl;
             }
-            
+            pDataArray->count++;
             //report progress
-			if((i) % 100 == 0){	pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();		}
+			if((i) % 100 == 0){	pDataArray->m->mothurOutJustToScreen(toString(i)+"\n"); 		}
 		}
 		
-        if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
+        if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); 		}
         
 		in.close();
         out.close();