GNU autotools based build

.gitignore

@@ -0,0 +1,40 @@
+# http://www.gnu.org/software/autoconf
+
+/autom4te.cache
+/aclocal.m4
+/compile
+/configure
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+/test-driver
+/INSTALL
+
+# http://www.gnu.org/software/automake
+
+Makefile.in
+
+# autoscan
+
+/autoscan.log
+/configure.scan
+/config.h.in
+
+# configure
+
+Makefile
+/config.h
+/config.log
+/config.status
+.deps
+
+# make
+
+*.o
+rapsearch
+prerapsearch
+
+# other
+
+*~

Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = Src

Src/HashSearch.cpp

@@ -18,8 +18,7 @@
 #include <boost/serialization/vector.hpp>
 #include <boost/bind.hpp>
 #include <boost/thread/mutex.hpp>
-#include <boost/chrono/thread_clock.hpp>
-#include "threadpool.hpp"
+#include <boost/threadpool.hpp>
 #include "weight.h"
 #include "aa.h"
 #include "n2a.h"
@@ -1052,8 +1051,6 @@ void CHashSearch::Searching(int k, CQrPckg& Query, CDbPckg& Db)
 	muMonitor.unlock();
 
 	int nFoundHit = 0;
-	//using namespace boost::chrono;
-	//thread_clock::time_point start = thread_clock::now();
 
 	MRESULT mRes;
 	for (int nStep = 0; nStep < m_nIdxScl; ++nStep)
@@ -1539,8 +1536,6 @@ int CHashSearch::ExtendSeq2Set(int nSeed, uint unLocalSeedLen, vector<uchar>& vE
 		VNAMES& vQNames, VNAMES& vDNames,
 		MRESULT& mRes, int nTreadID)
 {
-	//using namespace boost::chrono;
-	//thread_clock::time_point st = thread_clock::now();
 	// find a proper range for the comparisons
 	int nSt = 0;
 	int nEd = 0;

Src/Makefile.am

@@ -0,0 +1,4 @@
+bin_PROGRAMS = rapsearch prerapsearch
+
+rapsearch_SOURCES = main.cpp HashSearch.cpp BlastStat.cpp Seg.cpp mergeUnit.cpp
+prerapsearch_SOURCES = BuildHash.cpp HashSearch.cpp BlastStat.cpp Seg.cpp mergeUnit.cpp