Removed testutils, removed get_-prefixes

examples/hugepages.cpp

@@ -11,14 +11,14 @@ using namespace std;
 
 template<class tCsa>
 void do_something(const tCsa &csa){
-	stop_watch sw;
+	util::stop_watch sw;
 	uint64_t sum=0;
 	sw.start();
 	for(size_t i=0; i<csa.size() and i<10000000;++i){
 		sum+=csa.psi(i);
 	}
 	sw.stop();
-	cout << sw.get_real_time() << endl;
+	cout << sw.real_time() << endl;
 	cout<<"sum="<<sum<<endl;
 }
 

examples/import_non_sdsl_data2.cpp

@@ -16,7 +16,7 @@ int main(int argc, char* argv[]){
 	util::load_vector_from_file(v, argv[1], 4);
 
 	cout << "v.size() = " << v.size() << endl;
-	cout << "v.get_int_width() = "  << (int)v.get_int_width() << endl;
+	cout << "v.width() = "  << (int)v.width() << endl;
 	cout << "v =";
 	size_t max_out = 10;
 	if ( argc > 2 ){

examples/int_vector_entry.cpp

@@ -10,7 +10,7 @@ using namespace sdsl;
 int main(int argc, char* argv[]){
 	int_vector<> v;
 	util::load_from_file(v, argv[1]);
-	cout<<"loaded vector of size "<<v.size()<<" and "<<(int)v.get_int_width()<<"-bit integers from file";
+	cout<<"loaded vector of size "<<v.size()<<" and "<<(int)v.width()<<"-bit integers from file";
 	cout<<" "<<argv[1]<<endl;
 	if ( v.size() == 0 )
 		return 0;

extras/cheatsheet/sdsl-cheatsheet.tex

@@ -172,7 +172,7 @@ \subsection{Dynamic vector}
 \end{tabular}
 
 \textit{Public~methods:} \code{operator[i]}, \code{resize(n)},
-\code{}
+\code{size()}, \code{data()}
 
 \subsection{Manipulating vectors}
 \code{util::set\_random\_bits(v)}
@@ -323,17 +323,19 @@ \subsection{Compressed Suffix Trees (CST)}
  \code{child(v,c)}, \code{edge(v, d)}, \code{lca(v,w)},
  \code{depth(v)}, \code{node\_depth}, \code{sl(v)},
  \code{wl(v,c)}, \code{sn(v)}, \code{id(v)}, \code{inv\_id(i)},
- \code{node(lb, rb)}.\\
+ \code{node(lb, rb)}, \code{nodes()}, \code{size()},
+ \code{begin()}, \code{end()}, \code{begin\_bottom\_up()},
+ \code{end\_bottom\_up}.\\
 \textit{Public~members:} \code{csa}, \code{lcp}.
 
 \subsection{Range Minimum/Maximum Query (RMQ)}
 \begin{tabular}{@{}ll@{}}
 \href{\sdslgit/include/sdsl/rmq_support_sparse_table.hpp}{\sdslrmqsupportsparsetable} &
-$n\Order{\log n}$ word structure.\\
+$\Order{n \log^2 n}$.\\
 \href{\sdslgit/include/sdsl/rmq_succinct_sada.hpp}{\sdslrmqsuccinctsada} &
 $4n+o(n)$ bit \\
 \href{\sdslgit/include/sdsl/rmq_succinct_sct.hpp}{\sdslrmqsuccinctsct} &
-$2n+o(n)$ bit based on Super-Cartesian-Tree\\
+$2n+o(n)$ bit \\
 \end{tabular}
 
 \section{Constructing data structures}
@@ -384,8 +386,8 @@ \subsection{Store \sdsl\ structures}
 
 
 \section{Utility methods}
-\code{util::get\_pid()}, % reomve get?
-\code{util::get\_id()}, % remove get?
+\code{util::pid()}, 
+\code{util::id()}, 
 \code{util::to\_string(x)},
 \code{util::to\_latex\_string(x)}
 
@@ -404,14 +406,14 @@ \section{Construction}
 \code{util::store\_to\_cache(x, key, config)}
 
 \section{Helper}
-\code{stop\_watch}\\
+\code{util::stop\_watch}\\
 \textit{Public methods:} \code{start()}, \code{stop()},
-\code{get\_user\_time()},  % get rid of prefix "get_" ???
-\code{get\_sys\_time()},
-\code{get\_real\_time()},
-\code{get\_abs\_user\_time()},
-\code{get\_abs\_sys\_time()},
-\code{get\_abs\_real\_time()},
+\code{user\_time()},  
+\code{sys\_time()},
+\code{real\_time()},
+\code{abs\_user\_time()},
+\code{abs\_sys\_time()},
+\code{abs\_real\_time()},
 
 
 \code{paths\_from\_config\_file(file, prefix)}
@@ -424,6 +426,22 @@ \section{Performance}
 TODO: insert time space graph for different
 construction processes.
 
+\section{Bitmagic}
+Let \code{x} be a 64-bit word. Positions in
+$x$ start from $0$.
+\settowidth{\MyLen}{\code{num\_bytes=1} }
+\begin{tabular}{@{}p{\the\MyLen}%
+                @{}p{\linewidth-\the\MyLen}@{}}
+%\begin{tabular}{@{}ll@{}}
+\textit{Method}      & \textit{Description}  \\
+\code{b1Cnt(x)}  & Count the number of set bits in \code{x}.\\
+\code{i1BP(x,i)} & Get the position of the $i$-th set bit in \code{x},
+	$i~\in~[0,\code{b1Cnt(x)}\!-\!1)$.
+\end{tabular}
+
+\section{Debugging}
+Mention: gdb config file, verbose
+
 \section{Acknowledgements}
 Yuta Mori for implementing libdivsufsort, which
 is used to construct SAs.

include/sdsl/construct.hpp

@@ -78,7 +78,7 @@ template<class Index>
 void construct(Index& idx, const std::string &file, cache_config& config, uint8_t num_bytes, wt_tag){
 	int_vector<Index::alphabet_category::WIDTH> text;	
 	util::load_vector_from_file(text, file, num_bytes);
-	std::string tmp_key = util::to_string(util::get_pid())+"_"+util::to_string(util::get_id());
+	std::string tmp_key = util::to_string(util::pid())+"_"+util::to_string(util::id());
 	std::string tmp_file_name = util::cache_file_name(tmp_key, config);
 	util::store_to_file(text, tmp_file_name);
 	util::clear(text);

include/sdsl/lcp_support_tree.hpp

@@ -86,7 +86,7 @@ class _lcp_support_tree
         template<uint8_t int_width>
         _lcp_support_tree(int_vector_file_buffer<int_width>& lcp_buf, const Cst* cst = NULL) {
             m_cst = cst;
-            std::string id =  util::to_string(util::get_pid())+"_"+util::to_string(util::get_id()).c_str() + "_fc_lcp";
+            std::string id =  util::to_string(util::pid())+"_"+util::to_string(util::id()).c_str() + "_fc_lcp";
             {
                 int_vector<int_width> temp_lcp;
                 algorithm::construct_first_child_lcp(lcp_buf, temp_lcp, (int_vector_size_type) 0);

include/sdsl/lcp_support_tree2.hpp

@@ -83,8 +83,8 @@ class _lcp_support_tree2
                        int_vector_file_buffer<Cst::csa_type::alphabet_type::int_width>& bwt_buf,
                        const cst_type* cst = NULL) {
             m_cst = cst;
-            std::string small_lcp_file_name =  util::to_string(util::get_pid())+"_"+util::to_string(util::get_id()).c_str() + "_fc_lf_lcp_sml";
-            std::string big_lcp_file_name =  util::to_string(util::get_pid())+"_"+util::to_string(util::get_id()).c_str() + "_fc_lf_lcp_big";
+            std::string small_lcp_file_name =  util::to_string(util::pid())+"_"+util::to_string(util::id()).c_str() + "_fc_lf_lcp_sml";
+            std::string big_lcp_file_name =  util::to_string(util::pid())+"_"+util::to_string(util::id()).c_str() + "_fc_lf_lcp_big";
 
             algorithm::construct_first_child_and_lf_lcp<SampleDens>(lcp_buf, bwt_buf, small_lcp_file_name, big_lcp_file_name, m_big_lcp);
             // construct wavelet tree huffman from file buffer

include/sdsl/lcp_wt.hpp

@@ -198,7 +198,7 @@ template<uint8_t width>
 template<uint8_t int_width>
 lcp_wt<width>::lcp_wt(int_vector_file_buffer<int_width>& lcp_buf)
 {
-    std::string temp_file = "/tmp/lcp_sml" + util::to_string(util::get_pid()) + "_" + util::to_string(util::get_id()) ;// TODO: remove absolute file name
+    std::string temp_file = "/tmp/lcp_sml" + util::to_string(util::pid()) + "_" + util::to_string(util::id()) ;// TODO: remove absolute file name
 //	write_R_output("lcp","construct sml","begin");
     typename int_vector<>::size_type l=0, max_l=0, big_sum=0, n = lcp_buf.int_vector_size;
     {

include/sdsl/temp_write_read_buffer.hpp

@@ -52,8 +52,8 @@ class temp_write_read_buffer
             m_buf = buffer_type(buf_size, 0, width);    // initialize buffer
             m_in_buf_idx = 0;
             m_buf_cnt = 0;
-            m_file_name =  dir + "temp_write_read_buffer_" + util::to_string(util::get_pid())+"_"
-                           + util::to_string(util::get_id())+"_"
+            m_file_name =  dir + "temp_write_read_buffer_" + util::to_string(util::pid())+"_"
+                           + util::to_string(util::id())+"_"
                            + util::to_string(m_buffer_id);
             m_buffer_id++; // increase the object counter
             m_output_exists = false;

include/sdsl/test_index_performance.hpp

@@ -15,7 +15,7 @@
     along with this program.  If not, see http://www.gnu.org/licenses/ .
 */
 /*! \file test_index_performance.hpp
- *  \brief test_index_performance.hpp contains a set of functions which test the speed of operations of compressed suffix arrays and compressed suffix trees
+ *  \brief test_index_performance.hpp contains a set of benchmark methods
  *  \author Simon Gog
  */
 #ifndef INCLUDE_SDSL_TEST_INDEX_PERFORMANCE
@@ -270,16 +270,18 @@ void test_pattern_matching(const Csa& csa,
     write_R_output("csa","extract patterns","begin",times,0);
 
     size_type file_size = 0;
-    char* ccc = NULL;
-    if ((file_size=file::read_text(file_name, ccc)) == 0) {
-        throw std::logic_error("file " + std::string(file_name) + " has size 0 or could not be read");
-    }
-
-    for (size_type i=0; i<rands.size(); ++i) {
-        for (size_type j=rands[i]; j < rands[i] + pattern_len; ++j)
-            patterns[i*pattern_len + (j-rands[i])] = ccc[j];
-    }
-    delete [] ccc;
+	{
+		int_vector<8> text;
+		if ( util::load_vector_from_file(text, file_name, 1) ){
+			for (size_type i=0; i<rands.size(); ++i) {
+				for (size_type j=rands[i]; j < rands[i] + pattern_len; ++j)
+					patterns[i*pattern_len + (j-rands[i])] = text[j];
+			}
+		} else {
+			std::cerr << "ERROR: test_pattern_matching: could not open";
+			std::cerr << "file `" << file_name << "`" << std::endl;
+		}
+	}
     write_R_output("csa","extract patterns","end",times,0);
 
     size_type cnt=0;