Changeset 4334

Timestamp:

Mar 25, 2023, 4:32:55 AM (2 months ago)

Author:

Peter

Message:

new class NeedlemanWunsch?.

Location:

trunk

Files:

• test/Makefile.am (modified) (1 diff)
• test/needleman_wunsch2.cc (added)
• yat/utility/Aligner.cc (modified) (3 diffs)
• yat/utility/Aligner.h (modified) (6 diffs)
• yat/utility/Cigar.h (modified) (1 diff)
• yat/utility/Makefile.am (modified) (2 diffs)
• yat/utility/NeedlemanWunsch.cc (added)
• yat/utility/NeedlemanWunsch.h (added)

trunk/test/Makefile.am

@@ -109 +109 @@
   test/ncc.test \
   test/needleman_wunsch.test \
+  test/needleman_wunsch2.test \
   test/negative_binomial.test \
   test/negative_binomial_mixture.test \

trunk/yat/utility/Aligner.cc

@@ -157 +157 @@
 
 
+  double Aligner::insertion_penalty(void) const
+  {
+    return vertical_gap_;
+  }
+
+
+  double Aligner::open_insertion_penalty(void) const
+  {
+    return open_vertical_gap_;
+  }
+
+
+  double Aligner::deletion_penalty(void) const
+  {
+    return horizon_gap_;
+  }
+
+
+  double Aligner::open_deletion_penalty(void) const
+  {
+    return open_horizon_gap_;
+  }
+
+
   // ================ Cigar =======================
 
@@ -315 +339 @@
 
 
+  Aligner::Cigar::const_reverse_iterator Aligner::Cigar::rbegin(void) const
+  {
+    return const_reverse_iterator(cigar_.rbegin());
+  }
+
+
   uint32_t Aligner::Cigar::reference_length(void) const
   {
     return length(2);
+  }
+
+
+  Aligner::Cigar::const_reverse_iterator Aligner::Cigar::rend(void) const
+  {
+    return const_reverse_iterator(cigar_.rend());
   }
 
@@ -337 +373 @@
     assert(i<cigar_.size());
     return cigar_[i];
+  }
+
+
+  bool Aligner::Cigar::operator==(const Aligner::Cigar& other) const
+  {
+    return cigar_ == other.cigar_;
+  }
+
+
+  bool Aligner::Cigar::operator!=(const Aligner::Cigar& other) const
+  {
+    return cigar_ != other.cigar_;
   }
 

trunk/yat/utility/Aligner.h

@@ -86 +86 @@
        vertical_gap.
 
-       \param horizon_gap Penalty for extending a horizontal gap
-
-       \param open_horizon_gap Penalty for open a horizontal
+       \param horizontal_gap Penalty for extending a horizontal gap
+
+       \param open_horizontal_gap Penalty for open a horizontal
        gap. Total penalty for a horizontal gap is open_horizon_gap + N
        * horizon_gap.
      */
     Aligner(double vertical_gap, double open_vertical_gap,
-            double horizon_gap, double open_horizon_gap);
+            double horizontal_gap, double open_horizontal_gap);
 
     /**
@@ -192 +192 @@
 
       /**
+         \since New in yat 0.21
+       */
+      typedef
+      CigarIterator<std::deque<uint32_t>::const_reverse_iterator>
+      const_reverse_iterator;
+
+      /**
          Default constructor
        */
@@ -289 +296 @@
 
       /**
+         \return reverse iterator pointing to the beginning
+
+         \since New in yat 0.21
+       */
+      const_reverse_iterator rbegin(void) const;
+
+      /**
          \brief Translate CIGAR to a reference length.
 
@@ -301 +315 @@
 
       /**
+         \return reverse iterator pointing to the end
+
+         \since New in yat 0.21
+       */
+      const_reverse_iterator rend(void) const;
+
+      /**
         \brief reverse the CIGAR
 
@@ -316 +337 @@
        */
       size_t size(void) const;
+
+      /**
+         \since New in yat 0.21
+       */
+      bool operator==(const Cigar& other) const;
+
+      /**
+         \since New in yat 0.21
+       */
+      bool operator!=(const Cigar& other) const;
     private:
       std::deque<uint32_t> cigar_;
@@ -337 +368 @@
     const Cigar cigar(size_t i, size_t j) const;
 
+    /**
+       Same as vertical_gap in Constructor
+
+       \since New in yat 0.21
+     */
+    double insertion_penalty(void) const;
+
+    /**
+       Same as open_vertical_gap in Constructor
+
+       \since New in yat 0.21
+     */
+    double open_insertion_penalty(void) const;
+
+    /**
+       Same as horizontal_gap in Constructor
+
+       \since New in yat 0.21
+     */
+    double deletion_penalty(void) const;
+
+    /**
+       Same as open_horizontal_gap in Constructor
+
+       \since New in yat 0.21
+     */
+    double open_deletion_penalty(void) const;
   private:
     direction& directions(size_t i, size_t j);

trunk/yat/utility/Cigar.h

@@ -82 +82 @@
 // 2, (3rd column below) is 1 iff operation consumes reference
 // sequence.
+//
+// CIGAR          Type Reference Query String
+// BAM_CMATCH      3    1         1     M
+// BAM_CINS        1    0         1     I
+// BAM_CDEL        2    1         0     D
+// BAM_CREF_SKIP   2    1         0     N
+// BAM_CSOFT_CLIP  1    0         1     S
+// BAM_CHARD_CLIP  0    0         0     H
+// BAM_CPAD        0    0         0     P
+// BAM_CEQUAL      3    1         1     =
+// BAM_CDIFF       3    1         1     X
+// BAM_CBACK       0    0         0     B
 #define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3)
 #endif // end of backport

trunk/yat/utility/Makefile.am

@@ -53 +53 @@
   yat/utility/MultiMinimizer.cc \
   yat/utility/MultiMinimizerDerivative.cc \
+  yat/utility/NeedlemanWunsch.cc \
   yat/utility/NelderMeadSimplex.cc \
   yat/utility/NelderMeadSimplex2.cc \
@@ -144 +145 @@
   $(srcdir)/yat/utility/MultiMinimizerDerivative.h \
   $(srcdir)/yat/utility/multiprocess.h \
+  $(srcdir)/yat/utility/NeedlemanWunsch.h \
   $(srcdir)/yat/utility/NelderMeadSimplex.h \
   $(srcdir)/yat/utility/NelderMeadSimplex2.h \