Rename .h files to .hpp

yge15 · Dec 14, 2017 · 724c938 · 724c938
1 parent af6d723
commit 724c938
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Showing 15 changed files with 29 additions and 28 deletions.
diff --git a/src/Makefile b/src/Makefile
@@ -28,7 +28,7 @@ db_sort: krakendb.o quickfile.o
 
 set_lcas: krakendb.o quickfile.o krakenutil.o seqreader.o uid_mapping.o
 
-grade_classification: taxdb.h report-cols.h
+grade_classification: taxdb.hpp report-cols.hpp
 
 read_uid_mapping: quickfile.o
 
@@ -38,16 +38,16 @@ test_hll_on_db: krakendb.o hyperloglogplus.o quickfile.o
 
 dump_db_kmers: krakendb.o quickfile.o
 
-classify: classify.cpp krakendb.o quickfile.o krakenutil.o seqreader.o uid_mapping.o gzstream.o hyperloglogplus.o taxdb.h report-cols.h readcounts.hpp
+classify: classify.cpp krakendb.o quickfile.o krakenutil.o seqreader.o uid_mapping.o gzstream.o hyperloglogplus.o taxdb.hpp report-cols.hpp readcounts.hpp
 	$(CXX) $(CXXFLAGS) -o classify $^ $(LIBFLAGS)
 
-build_taxdb: taxdb.h report-cols.h quickfile.o
+build_taxdb: taxdb.hpp report-cols.hpp quickfile.o
 
 make_seqid_to_taxid_map: quickfile.o
 
 read_uid_mapping: quickfile.o krakenutil.o uid_mapping.o
 
-krakenutil.o: krakenutil.cpp krakenutil.hpp taxdb.h report-cols.h
+krakenutil.o: krakenutil.cpp krakenutil.hpp taxdb.hpp report-cols.hpp
 	$(CXX) $(CXXFLAGS) -c krakenutil.cpp
 
 krakendb.o: krakendb.cpp krakendb.hpp quickfile.hpp
@@ -65,5 +65,5 @@ quickfile.o: quickfile.cpp quickfile.hpp
 uid_mapping.o: krakenutil.hpp uid_mapping.hpp uid_mapping.cpp
 	$(CXX) $(CXXFLAGS) -c uid_mapping.cpp
 
-hyperloglogplus.o: hyperloglogplus.h hyperloglogplus.cpp
+hyperloglogplus.o: hyperloglogplus.hpp hyperloglogplus.cpp
 	$(CXX) $(CXXFLAGS) -c hyperloglogplus.cpp
diff --git a/src/build_taxdb.cpp b/src/build_taxdb.cpp
@@ -17,7 +17,7 @@
  * along with Kraken.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "taxdb.h"
+#include "taxdb.hpp"
 #include "quickfile.hpp"
 #include <iostream>
 #include <fstream>

diff --git a/src/classify.cpp b/src/classify.cpp
@@ -24,7 +24,7 @@
 #include "quickfile.hpp"
 #include "seqreader.hpp"
 #include "readcounts.hpp"
-#include "taxdb.h"
+#include "taxdb.hpp"
 #include "gzstream.h"
 #include "uid_mapping.hpp"
 #include <sstream>

diff --git a/src/count_unique.cpp b/src/count_unique.cpp
@@ -17,7 +17,7 @@
  * along with Kraken.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "hyperloglogplus.h"
+#include "hyperloglogplus.hpp"
 #include <iostream>
 #include <fstream>
 #include <random>

diff --git a/src/dump_taxdb.cpp b/src/dump_taxdb.cpp
@@ -17,7 +17,7 @@
  * along with Kraken.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "taxdb.h"
+#include "taxdb.hpp"
 #include "quickfile.hpp"
 #include <iostream>
 #include <fstream>

diff --git a/src/grade_classification.cpp b/src/grade_classification.cpp
@@ -17,7 +17,7 @@
  * along with Kraken.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "taxdb.h"
+#include "taxdb.hpp"
 #include "quickfile.hpp"
 #include <iostream>
 #include <fstream>
@@ -113,7 +113,7 @@ int main(int argc, char **argv) {
       exit(1);
     } else {
       seq_taxid = it->second;
-      if (!taxdb.hasTaxon(seq_taxid)) {
+      if (!taxdb.hppasTaxon(seq_taxid)) {
         if (ignored_taxa.count(seq_taxid) == 0) {
           cerr << "Ignoring taxon " << seq_taxid << " - not in database" << endl;
           ignored_taxa.insert(seq_taxid);

diff --git a/src/hyperloglogbias.h → src/hyperloglogplus-bias.hpp b/src/hyperloglogbias.h → src/hyperloglogplus-bias.hpp
diff --git a/src/hyperloglogplus.cpp b/src/hyperloglogplus.cpp
@@ -18,7 +18,19 @@
  */
 
 
-#include "hyperloglogplus.h"
+#include "hyperloglogplus.hpp"
+
+#include<vector>
+#include<stdexcept>
+#include<iostream>
+#include<fstream>
+#include<math.h>    //log
+#include<algorithm> //vector.count
+#include<bitset>
+#include<numeric>   //accummulate
+
+#include "hyperloglogplus-bias.hpp"
+#include "assert_helpers.h"
 
 /////////////////////////////////////////////////////////////////////
 // Helper methods for bit operations

diff --git a/src/hyperloglogplus.h → src/hyperloglogplus.hpp b/src/hyperloglogplus.h → src/hyperloglogplus.hpp
@@ -26,18 +26,7 @@
 #define HYPERLOGLOGPLUS_H_
 
 #include<vector>
-#include<stdexcept>
-#include<iostream>
-#include<fstream>
-#include<math.h>    //log
-#include<algorithm> //vector.count
-#include<bitset>
 #include<unordered_set>
-#include<numeric>   //accummulate
-
-#include "hyperloglogbias.h"
-#include "assert_helpers.h"
-
 using namespace std;
 
 //#define HLL_DEBUG

diff --git a/src/query_taxdb.cpp b/src/query_taxdb.cpp
@@ -17,7 +17,7 @@
  * along with KrakenHLL.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "taxdb.h"
+#include "taxdb.hpp"
 #include <iostream>
 #include <fstream>
 #include <unordered_map>

diff --git a/src/readcounts.hpp b/src/readcounts.hpp
@@ -21,7 +21,7 @@
 #define READCOUNTS_HPP
 
 #include "kraken_headers.hpp"
-#include "hyperloglogplus.h"
+#include "hyperloglogplus.hpp"
 
 namespace kraken {
   static size_t HLL_PRECISION = 14;

diff --git a/src/report-cols.h → src/report-cols.hpp b/src/report-cols.h → src/report-cols.hpp
diff --git a/src/set_lcas.cpp b/src/set_lcas.cpp
@@ -23,7 +23,7 @@
 #include "krakendb.hpp"
 #include "krakenutil.hpp"
 #include "seqreader.hpp"
-#include "taxdb.h"
+#include "taxdb.hpp"
 #include "readcounts.hpp"
 #include "uid_mapping.hpp"
 #include <unordered_map>

diff --git a/src/taxdb.h → src/taxdb.hpp b/src/taxdb.h → src/taxdb.hpp
@@ -33,7 +33,7 @@
 #include <iomanip>
 #include <sstream>
 #include <stdexcept>
-#include "report-cols.h"
+#include "report-cols.hpp"
 //#include "readcounts.hpp"
 
 

diff --git a/src/test_hll_on_db.cpp b/src/test_hll_on_db.cpp
@@ -17,7 +17,7 @@
  * along with Kraken.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "hyperloglogplus.h"
+#include "hyperloglogplus.hpp"
 #include "kraken_headers.hpp"
 #include "quickfile.hpp"
 #include "krakendb.hpp"