Changeset 3176

Timestamp:

Mar 15, 2014, 10:10:37 AM (9 years ago)

Author:

Peter

Message:

closes #784. New class BamPairProxy? to finalize implementation of BamPairIterator?.

Location:

trunk/yat/omic

Files:

• BamPair.cc (modified) (2 diffs)
• BamPair.h (modified) (1 diff)
• BamPairIterator.h (modified) (6 diffs)

trunk/yat/omic/BamPair.cc

@@ -23 +23 @@
 
 #include "BamPair.h"
+
+#include <cassert>
 
 namespace theplu {
@@ -60 +62 @@
   }
 
+  ///////////// BamPairProxy ////////////////////
+
+  BamPairProxy::BamPairProxy(void)
+    : first_(NULL), second_(NULL) {}
+
+  BamPairProxy::BamPairProxy(const BamRead* first, const BamRead* second)
+    : first_(first), second_(second) {}
+
+  const BamRead& BamPairProxy::first(void) const
+  {
+    assert(first_);
+    return *first_;
+  }
+
+
+  const BamRead& BamPairProxy::second(void) const
+  {
+    assert(second_);
+    return *second_;
+  }
+
+
+  BamPairProxy::operator BamPair() const
+  {
+    return BamPair(*first_, *second_);
+  }
+
 }}}

trunk/yat/omic/BamPair.h

@@ -72 +72 @@
   };
 
+
+  /**
+     A proxy class that behaves like a const BamPair&.
+
+     The class is used in BamPairIterator. The class allows to create
+     an object that looks like a const reference of BamPair from two
+     BamRead pointers without copying the BamRead objects. As the
+     class is aimed at looking like a const BamPair&, implicit
+     conversion to BamPair is allowed to mimic: BamPair = const BamPair&.
+   */
+  class BamPairProxy
+  {
+  public:
+    /**
+       \brief Default constructor
+    */
+    BamPairProxy(void);
+
+    /**
+       Create a proxy from \a first and \a second.
+
+       \note if the objects pointed to by \a first and \a second goes
+       out of scope, this class becomes invalid and behaviour is
+       undefined.
+     */
+    BamPairProxy(const BamRead* first, const BamRead* second);
+
+    /**
+       \return const reference to first BamRead
+     */
+    const BamRead& first(void) const;
+
+    /**
+       \return const reference to second BamRead
+    */
+    const BamRead& second(void) const;
+
+    /**
+       Implicit conversion from BamPairProxy to BamPair.
+     */
+    operator BamPair() const;
+  private:
+    const BamRead* first_;
+    const BamRead* second_;
+  };
+
 }}}
 #endif

trunk/yat/omic/BamPairIterator.h

@@ -60 +60 @@
   class BamPairIterator
     : public boost::iterator_facade<
-    BamPairIterator<Base>, const BamPair, std::input_iterator_tag
+    BamPairIterator<Base>, const BamPair, std::input_iterator_tag,
+    const BamPairProxy
     >
   {
@@ -81 +82 @@
     Base iter_;
     Base end_;
-    BamPair x_;
+    const BamRead* mate_;
     boost::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
     typedef std::pair<int32_t, int32_t> Position;
@@ -87 +88 @@
     friend class boost::iterator_core_access;
 
-    const BamPair& dereference(void) const;
+    const BamPairProxy dereference(void) const;
     bool equal(const BamPairIterator& other) const;
     void increment(void);
@@ -143 +144 @@
 
   template<typename Base>
-  const BamPair&
+  const BamPairProxy
   BamPairIterator<Base>::dereference(void) const
   {
-    return x_;
+    return BamPairProxy(mate_, &*iter_);
   }
 
@@ -189 +190 @@
         for (; lower!=reads_->end() && lower->first == position; ++lower)
           if (same_query_name(lower->second, *iter_)) {
-            x_.first() = lower->second;
-            x_.second() = *iter_;
+            mate_ = &lower->second;
             return;
           }
@@ -199 +199 @@
           mate = siam_reads_->lower_bound(iter_->name());
         if (mate!=siam_reads_->end() && same_query_name(mate->second, *iter_)) {
-          x_.first() = mate->second;
-          x_.second() = *iter_;
+          mate_ = &mate->second;
           return;
         }