Remove deprecated feature usage

ChangeLog

@@ -1,3 +1,11 @@
+2022-05-11 Vladimir Nikolic <[email protected]>
+
+  * Release version 2.3.5
+
+    General:
+	* Fixed compile errors when using the -DNDEBUG flag.
+
+
 2021-12-20 Vladimir Nikolic <[email protected]>
 
   * Release version 2.3.4

Common/Functional.h

@@ -5,16 +5,22 @@
 
 /** A functor that always returns true. */
 template <typename Arg>
-struct True : std::unary_function<Arg, bool> {
+struct True {
 	bool operator()(const Arg&) const { return true; }
+
+	typedef Arg argument_type;
+	typedef bool result_type;
 };
 
 /** A functor to adapt a pointer to a member variable. */
 template <typename Arg, typename Result>
-struct MemVar : std::unary_function<Arg, Result>
+struct MemVar
 {
 	MemVar(Result Arg::* p) : m_p(p) { }
 	Result operator()(const Arg& arg) const { return arg.*m_p; }
+
+	typedef Arg argument_type;
+	typedef Result result_type;
   private:
 	Result Arg::* m_p;
 };
@@ -28,15 +34,17 @@ MemVar<Arg, Result> mem_var(Result Arg::* p)
 
 /** A functor, f1(f2(x)). */
 template <typename F1, typename F2>
-struct unary_compose : std::unary_function <
-		typename F2::argument_type, typename F1::result_type>
+struct unary_compose
 {
 	unary_compose(const F1& f1, const F2& f2) : f1(f1), f2(f2) { }
 	typename F1::result_type operator()(
 			const typename F2::argument_type& x) const
 	{
 		return f1(f2(x));
 	}
+
+	typedef typename F2::argument_type argument_type;
+	typedef typename F1::result_type result_type;
   private:
 	F1 f1;
 	F2 f2;
@@ -51,8 +59,7 @@ unary_compose<F1, F2> compose1(const F1& f1, const F2& f2)
 
 /** A functor, f(g1(x), g2(x)). */
 template <typename F, typename G1, typename G2>
-struct binary_compose : std::unary_function <
-		typename G1::argument_type, typename F::result_type>
+struct binary_compose
 {
 	binary_compose(const F& f, const G1& g1, const G2& g2)
 		: f(f), g1(g1), g2(g2) { }
@@ -61,6 +68,9 @@ struct binary_compose : std::unary_function <
 	{
 		return f(g1(x), g2(x));
 	}
+
+	typedef typename G1::argument_type argument_type;
+	typedef typename G1::result_type result_type;
   private:
 	F f;
 	G1 g1;

FilterGraph/FilterGraph.cc

@@ -382,7 +382,7 @@ removeContigs(Graph& g, vector<vertex_descriptor>& sc)
 }
 
 /** Return the value of the bit at the specified index. */
-struct Marked : unary_function<vertex_descriptor, bool>
+struct Marked
 {
 	typedef vector<bool> Data;
 	Marked(const Graph& g, const Data& data)
@@ -391,6 +391,9 @@ struct Marked : unary_function<vertex_descriptor, bool>
 	{}
 	bool operator()(vertex_descriptor u) const { return m_data[get(vertex_contig_index, m_g, u)]; }
 
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 	const Data& m_data;
@@ -434,7 +437,7 @@ struct sortContigs
 	}
 };
 
-struct ShorterThanX : unary_function<vertex_descriptor, bool>
+struct ShorterThanX
 {
 	const Graph& g;
 	const vector<bool>& seen;
@@ -451,9 +454,12 @@ struct ShorterThanX : unary_function<vertex_descriptor, bool>
 		return g[y].length < x && !get(vertex_removed, g, y) &&
 		       !seen[get(vertex_contig_index, g, y)];
 	}
+
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
 };
 
-struct LongerThanX : unary_function<vertex_descriptor, bool>
+struct LongerThanX
 {
 	const Graph& g;
 	const vector<bool>& seen;
@@ -470,9 +476,12 @@ struct LongerThanX : unary_function<vertex_descriptor, bool>
 		return g[y].length > x && !get(vertex_removed, g, y) &&
 		       !seen[get(vertex_contig_index, g, y)];
 	}
+
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
 };
 
-struct CoverageLessThan : unary_function<vertex_descriptor, bool>
+struct CoverageLessThan
 {
 	const Graph& g;
 	const vector<bool>& seen;
@@ -491,6 +500,9 @@ struct CoverageLessThan : unary_function<vertex_descriptor, bool>
 		return meanCoverage < minCov && !get(vertex_removed, g, u) &&
 		       !seen[get(vertex_contig_index, g, u)];
 	}
+
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
 };
 
 static void
@@ -549,7 +561,7 @@ getSequence(const Graph& g, vertex_descriptor u)
 }
 
 /** Return whether the specified edge is inconsistent. */
-struct is_edge_inconsistent : unary_function<edge_descriptor, bool>
+struct is_edge_inconsistent
 {
 	const Graph& g;
 
@@ -574,6 +586,9 @@ struct is_edge_inconsistent : unary_function<edge_descriptor, bool>
 				return true;
 		return false;
 	}
+
+	typedef edge_descriptor argument_type;
+	typedef bool result_type;
 };
 
 template<typename It>

Graph/ContigGraphAlgorithms.h

@@ -18,7 +18,7 @@ using boost::graph_traits;
 
 /** Return true if the edge e is a palindrome. */
 template<typename Graph>
-struct IsPalindrome : std::unary_function<typename graph_traits<Graph>::edge_descriptor, bool>
+struct IsPalindrome
 {
 	IsPalindrome(const Graph& g)
 	  : m_g(g)
@@ -28,6 +28,9 @@ struct IsPalindrome : std::unary_function<typename graph_traits<Graph>::edge_des
 		return source(e, m_g) == get(vertex_complement, m_g, target(e, m_g));
 	}
 
+	typedef typename graph_traits<Graph>::edge_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 };
@@ -223,7 +226,7 @@ assemble(Graph& g, OutIt out)
 
 /** Return true if the edge e is +ve sense. */
 template<typename Graph>
-struct IsPositive : std::unary_function<typename graph_traits<Graph>::edge_descriptor, bool>
+struct IsPositive
 {
 	IsPositive(const Graph& g)
 	  : m_g(g)
@@ -233,6 +236,9 @@ struct IsPositive : std::unary_function<typename graph_traits<Graph>::edge_descr
 		return !get(vertex_sense, m_g, source(e, m_g)) && !get(vertex_sense, m_g, target(e, m_g));
 	}
 
+	typedef typename graph_traits<Graph>::edge_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 };
@@ -284,7 +290,7 @@ pruneTips_if(Graph& g, OutputIt result, Pred p)
 
 /** Return true if the vertex is a normal 1-in 0-out tip. */
 template<typename Graph>
-struct IsTip : std::unary_function<typename graph_traits<Graph>::vertex_descriptor, bool>
+struct IsTip
 {
 	IsTip(const Graph& g)
 	  : m_g(g)
@@ -294,6 +300,9 @@ struct IsTip : std::unary_function<typename graph_traits<Graph>::vertex_descript
 		return in_degree(v, m_g) == 1;
 	}
 
+	typedef typename graph_traits<Graph>::vertex_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 };

Misc/samtobreak.hs

@@ -279,7 +279,7 @@ parseArgs = do
   where
   help = putStr (usageInfo usage options) >> exitSuccess
   tryHelp = "Try 'abyss-samtobreak --help' for more information."
-  version = "abyss-samtobreak (ABySS) 2.3.4\n"
+  version = "abyss-samtobreak (ABySS) 2.3.5\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

PathOverlap/PathOverlap.cpp

@@ -507,7 +507,7 @@ mergePaths(const Paths& paths, const OverlapMap& overlaps, const ContigPath& mer
 }
 
 /** Return true if the edge e is a path overlap. */
-struct IsPathOverlap : unary_function<edge_descriptor, bool>
+struct IsPathOverlap
 {
 	IsPathOverlap(const Graph& g, const OverlapMap& pmap, const IsPositive<Graph>& pred)
 	  : m_g(g)
@@ -522,6 +522,9 @@ struct IsPathOverlap : unary_function<edge_descriptor, bool>
 		return stranded && getOverlap(m_pmap, source(e, m_g), target(e, m_g));
 	}
 
+	typedef edge_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 	const OverlapMap& m_pmap;

SimpleGraph/SimpleGraph.cpp

@@ -305,7 +305,6 @@ static unsigned calculatePathLength(const Graph& g,
 
 /** Compare the lengths of two paths. */
 struct ComparePathLength
-		: binary_function<ContigPath, ContigPath, bool>
 {
 	ComparePathLength(const Graph& g, const ContigNode& origin)
 		: m_g(g), m_origin(origin) { }
@@ -315,6 +314,10 @@ struct ComparePathLength
 		return lenA < lenB
 			|| (lenA == lenB && a.size() < b.size());
 	}
+
+	typedef ContigPath first_argument_type;
+	typedef ContigPath second_argument_type;
+	typedef bool result_type;
   private:
 	const Graph& m_g;
 	const ContigNode& m_origin;

bin/abyss-pe

@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or [email protected].'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.4"
+	@echo "abyss-pe (ABySS) 2.3.5"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.3.4, [email protected], abyss,
+AC_INIT(ABySS, 2.3.5, [email protected], abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.4" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.5" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.4" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.5" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.4" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.5" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br