X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=uchime_main.cpp;h=77266c05366a6240f0279453bfa98a7ffd389cb0;hb=7a4bfe757a51d6b33c0c90db3b76f4d881bcf067;hp=18bd8bb4fbb8cd7cde71c4044901ff4054e55f94;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git

diff --git a/uchime_main.cpp b/uchime_main.cpp
index 18bd8bb..77266c0 100644
--- a/uchime_main.cpp
+++ b/uchime_main.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
-
 #include "myutils.h"
 #include "chime.h"
 #include "seqdb.h"
@@ -8,7 +6,6 @@
 #include "hspfinder.h"
 #include <algorithm>
 #include <set>
-#include "mothurout.h"
 
 bool SearchChime(Ultra &U, const SeqData &QSD, float QAb, 
   const AlnParams &AP, const AlnHeuristics &AH, HSPFinder &HF,
@@ -21,16 +18,16 @@ bool g_UchimeDeNovo = false;
 
 void Usage()
 	{
-	//printf("\n");
-	//printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);
-	//printf("http://www.drive5.com/uchime\n");
-	//printf("\n");
-	//printf("This software is donated to the public domain\n");
-	//printf("\n");
-
-	//printf(
-//#include "help.h"
-		//);
+	printf("\n");
+	printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);
+	printf("http://www.drive5.com/uchime\n");
+	printf("\n");
+	printf("This software is donated to the public domain\n");
+	printf("\n");
+
+	printf(
+#include "help.h"
+		);
 	}
 
 void SetBLOSUM62()
@@ -92,8 +89,6 @@ float GetAbFromLabel(const string &Label)
 
 int uchime_main(int argc, char *argv[])
 	{
-	MothurOut* m;
-	m = MothurOut::getInstance();
 		
 	MyCmdLine(argc, argv);
 
@@ -109,7 +104,11 @@ int uchime_main(int argc, char *argv[])
 		return 0;
 		}
 
-		
+	printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);
+	printf("by Robert C. Edgar\n");
+	printf("http://drive5.com/uchime\n");
+	printf("This code is donated to the public domain.\n");
+	printf("\n");
 	if (!optset_w)
 		opt_w = 8;
 	
@@ -174,9 +173,6 @@ int uchime_main(int argc, char *argv[])
 	unsigned HitCount = 0;
 	for (unsigned i = 0; i < QuerySeqCount; ++i)
 		{
-			
-		if (m->control_pressed) { break; }
-			
 		unsigned QuerySeqIndex = Order[i];
 
 		SeqData QSD;
@@ -201,13 +197,7 @@ int uchime_main(int argc, char *argv[])
 
 		WriteChimeHit(g_fUChime, Hit);
 
-		//ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));
-			//report progress
-			if((i+1) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(i+1) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine();		}
-		}
-		if (!m->control_pressed) { 
-			//report progress
-			if((QuerySeqCount) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(QuerySeqCount) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine();		}
+		ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));
 		}
 
 	Log("\n");