addressing issue #37 - changed deprecated functions to lambda expressions

Author: terencewtli

chromosome_utils.cpp

@@ -110,12 +110,12 @@ extract_regions_chrom_fasta(const string &chrom_name,
     in.read(buffer, region_size);
 
     std::remove_if(buffer, buffer + region_size,
-                   std::bind2nd(std::equal_to<char>(), '\n'));
+                    [](const char x) {return x == '\n';});
     buffer[orig_region_size] = '\0';
 
     sequences.push_back(buffer);
     std::transform(sequences.back().begin(), sequences.back().end(),
-                   sequences.back().begin(), std::ptr_fun(&toupper));
+                   sequences.back().begin(), [](const char x) {return toupper(x);});
     assert(i->get_width() == sequences.back().length());
   }
   in.close();
@@ -146,15 +146,14 @@ extract_regions_chrom_fasta(const string &chrom_name,
     buffer[region_size] = '\0';
     in.read(buffer, region_size);
 
-    std::remove_if(
-                   buffer, buffer + region_size,
-                   std::bind2nd(std::equal_to<char>(), '\n'));
+    std::remove_if(buffer, buffer + region_size,
+                    [](const char x) {return x == '\n';});
     buffer[orig_region_size] = '\0';
 
     sequences.push_back(buffer);
-    std::transform(
-                   sequences.back().begin(), sequences.back().end(),
-                   sequences.back().begin(), std::ptr_fun(&toupper));
+    std::transform(sequences.back().begin(), sequences.back().end(),
+                   sequences.back().begin(), [](const char x) {return toupper(x);});
+
     if (i->neg_strand())
       revcomp_inplace(sequences.back());
     assert(i->get_width() == sequences.back().length());

sim_utils.cpp

@@ -224,10 +224,10 @@ prob_to_quality_scores_solexa(const vector<vector<double> > &prb,
   quality = prb;
   for (size_t i = 0; i < prb.size(); ++i) {
     std::transform(prb[i].begin(), prb[i].end(),
-		   quality[i].begin(), std::bind2nd(std::plus<double>(), 1e-3));
+		   quality[i].begin(), [](double x) {return x + 1e-3;});	
     const double column_sum = accumulate(quality[i].begin(), quality[i].end(), 0.0);
     std::transform(quality[i].begin(), quality[i].end(),
-		   quality[i].begin(), std::bind2nd(std::divides<double>(), column_sum));
+		   quality[i].begin(), [&column_sum](double x) {return x / column_sum;});
   }
   for (size_t i = 0; i < quality.size(); ++i)
     for (size_t j = 0; j < smithlab::alphabet_size; ++j) {
@@ -269,11 +269,11 @@ add_sequencing_errors(mt19937 &generator, const double max_errors,
 
   for (size_t i = 0; i < quality_scores.size(); ++i) {
     std::transform(quality_scores[i].begin(), quality_scores[i].end(),
-		   quality_scores[i].begin(), std::bind2nd(std::plus<double>(), 1e-3));
+		   quality_scores[i].begin(), [](double x) {return x + 1e-3;});
     const double column_sum = accumulate(quality_scores[i].begin(),
 					 quality_scores[i].end(), 0.0);
     std::transform(quality_scores[i].begin(), quality_scores[i].end(),
-		   quality_scores[i].begin(), std::bind2nd(std::divides<double>(), column_sum));
+		   quality_scores[i].begin(), [&column_sum](double x) {return x / column_sum;});
   }
 
   for (size_t i = 0; i < quality_scores.size(); ++i)