-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
#include "myutils.h"\r
#include "chime.h"\r
#include "seqdb.h"\r
#include "hspfinder.h"\r
#include <algorithm>\r
#include <set>\r
-#include "mothurout.h"\r
\r
bool SearchChime(Ultra &U, const SeqData &QSD, float QAb, \r
const AlnParams &AP, const AlnHeuristics &AH, HSPFinder &HF,\r
\r
void Usage()\r
{\r
- //printf("\n");\r
- //printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);\r
- //printf("http://www.drive5.com/uchime\n");\r
- //printf("\n");\r
- //printf("This software is donated to the public domain\n");\r
- //printf("\n");\r
-\r
- //printf(\r
-//#include "help.h"\r
- //);\r
+ printf("\n");\r
+ printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);\r
+ printf("http://www.drive5.com/uchime\n");\r
+ printf("\n");\r
+ printf("This software is donated to the public domain\n");\r
+ printf("\n");\r
+\r
+ printf(\r
+#include "help.h"\r
+ );\r
}\r
\r
void SetBLOSUM62()\r
\r
int uchime_main(int argc, char *argv[])\r
{\r
- MothurOut* m;\r
- m = MothurOut::getInstance();\r
\r
MyCmdLine(argc, argv);\r
\r
return 0;\r
}\r
\r
- \r
+ printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);\r
+ printf("by Robert C. Edgar\n");\r
+ printf("http://drive5.com/uchime\n");\r
+ printf("This code is donated to the public domain.\n");\r
+ printf("\n");\r
if (!optset_w)\r
opt_w = 8;\r
\r
unsigned HitCount = 0;\r
for (unsigned i = 0; i < QuerySeqCount; ++i)\r
{\r
- \r
- if (m->control_pressed) { break; }\r
- \r
unsigned QuerySeqIndex = Order[i];\r
\r
SeqData QSD;\r
\r
WriteChimeHit(g_fUChime, Hit);\r
\r
- //ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));\r
- //report progress\r
- if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine(); }\r
- }\r
- if (!m->control_pressed) { \r
- //report progress\r
- if((QuerySeqCount) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(QuerySeqCount) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine(); }\r
+ ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));\r
}\r
\r
Log("\n");\r