Merge pull request #1747 from dib-lab/feature/cython_hash_classes

[WIP] Convert Counttable interface to cython

Author: standage

include/khmer/_cpy_counttable.hh

@@ -74,21 +74,18 @@ Contact: [email protected]
 
 #include "_cpy_readparsers.hh"
 
-#include "_cpy_hashtable.hh" 
-#include "_cpy_nodetable.hh"
-#include "_cpy_counttable.hh"
-#include "_cpy_smallcounttable.hh"
+#include "_cpy_hashtable.hh"
 
 #include "_cpy_hashgraph.hh"
 #include "_cpy_subsetpartition.hh"
 #include "_cpy_countgraph.hh"
 #include "_cpy_nodegraph.hh"
 #include "_cpy_smallcountgraph.hh"
 
-#include "_cpy_graphlabels.hh" 
-#include "_cpy_hashset.hh" 
+#include "_cpy_graphlabels.hh"
+#include "_cpy_hashset.hh"
 #include "_cpy_readaligner.hh"
- 
+
 
 namespace khmer {
 

include/khmer/_cpy_khmer.hh

@@ -500,27 +500,27 @@ public:
     hash_dna(const char * kmer) const
     {
         if (!(strlen(kmer) >= _ksize)) {
-            throw oxli_exception("Supplied kmer string doesn't match the underlying k-size.");
+            throw oxli_value_exception("Supplied kmer string doesn't match the underlying k-size.");
         }
         return _hash_murmur(kmer, _ksize);
     }
 
     inline virtual HashIntoType
     hash_dna_top_strand(const char * kmer) const
     {
-        throw oxli_exception("not implemented");
+        throw oxli_value_exception("not implemented");
     }
 
     inline virtual HashIntoType
     hash_dna_bottom_strand(const char * kmer) const
     {
-        throw oxli_exception("not implemented");
+        throw oxli_value_exception("not implemented");
     }
 
     inline virtual std::string
     unhash_dna(HashIntoType hashval) const
     {
-        throw oxli_exception("not implemented");
+        throw oxli_value_exception("not implemented");
     }
 
     virtual KmerHashIteratorPtr new_kmer_iterator(const char * sp) const

include/khmer/_cpy_nodetable.hh

@@ -159,8 +159,14 @@ public:
         PAIR_MODE_ERROR_ON_UNPAIRED
     };
 
-    explicit ReadParser(std::unique_ptr<SeqIO> pf);
-    explicit ReadParser(ReadParser& other);
+    ReadParser(std::unique_ptr<SeqIO> pf);
+
+    ReadParser(ReadParser& other);
+    ReadParser& operator=(ReadParser& other);
+
+    ReadParser(ReadParser&&) noexcept;
+    ReadParser& operator=(ReadParser&&) noexcept;
+
     virtual ~ReadParser();
 
     Read get_next_read();
@@ -185,7 +191,13 @@ private:
 public:
     FastxReader();
     FastxReader(const std::string& infile);
+
     FastxReader(FastxReader& other);
+    FastxReader& operator=(FastxReader& other);
+
+    FastxReader(FastxReader&&) noexcept;
+    FastxReader& operator=(FastxReader&&) noexcept;
+
     ~FastxReader();
 
     Read get_next_read();
@@ -221,14 +233,16 @@ inline PartitionID _parse_partition_id(std::string name)
 }
 
 // Alias for generic/templated ReadParser pointer
-template<typename T> using ReadParserPtr = std::unique_ptr<ReadParser<T>>;
+template<typename T> using ReadParserPtr = std::shared_ptr<ReadParser<T>>;
+template<typename T> using WeakReadParserPtr = std::weak_ptr<ReadParser<T>>;
 
 // Convenience function
 template<typename SeqIO>
 ReadParserPtr<SeqIO> get_parser(const std::string& filename);
 
 // Alias for instantiated ReadParsers
-typedef std::unique_ptr<ReadParser<FastxReader>> FastxParserPtr;
+typedef std::shared_ptr<ReadParser<FastxReader>> FastxParserPtr;
+typedef std::weak_ptr<ReadParser<FastxReader>> WeakFastxParserPtr;
 
 } // namespace read_parsers