X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chopseqscommand.h;h=a9cfc102fb957ea775b14211db4e1f1e1118c50f;hp=fa3f559056161945021e10f9b1892db742a6116e;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=4d3ecf0d35c014b176345d21383343e7a58d2445

diff --git a/chopseqscommand.h b/chopseqscommand.h
index fa3f559..a9cfc10 100644
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -25,8 +25,9 @@ class ChopSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "chop.seqs";		}
 		string getCommandCategory()		{ return "Sequence Processing"; }
-		string getOutputFileNameTag(string, string);
+		
         string getHelpString();	
+        string getOutputPattern(string);	
 		string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
 		string getDescription()		{ return "trim sequence length"; }
 	
@@ -40,7 +41,7 @@ class ChopSeqsCommand : public Command {
             linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
         };
     
-		string fastafile, outputDir, keep;
+		string fastafile, outputDir, keep, namefile, groupfile, countfile;
 		bool abort, countGaps, Short;
 		int numbases, processors;
 		vector<string> outputNames;
@@ -59,7 +60,7 @@ struct chopData {
 	string outFasta, outAccnos, keep; 
 	unsigned long long start;
 	unsigned long long end;
-	int numbases;
+	int numbases, count;
     bool countGaps, Short, wroteAccnos;
 	MothurOut* m;
 	string namefile;
@@ -107,7 +108,7 @@ static DWORD WINAPI MyChopThreadFunction(LPVOID lpParam){
 
 		bool done = false;
         bool wroteAccnos = false;
-		int count = 0;
+		pDataArray->count = 0;
 
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 						
@@ -237,14 +238,14 @@ static DWORD WINAPI MyChopThreadFunction(LPVOID lpParam){
 					outAcc << seq.getName() << endl;
 					pDataArray->wroteAccnos = true;
 				}
-                count++;
+                pDataArray->count++;
 			}
             //report progress
-			if((count) % 1000 == 0){	pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine();		}
+			if((pDataArray->count) % 1000 == 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
 			
 		}
 		//report progress
-		if((count) % 1000 != 0){	pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine();		}
+		if((pDataArray->count) % 1000 != 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
         
 		
 		in.close();