Changeset 867 for trunk/yat/utility

Timestamp:

Sep 13, 2007, 9:36:50 PM (15 years ago)

Author:

Peter

Message:

adding function doing a SSEARCH between two strings

Location:

trunk/yat/utility

Files:

• Alignment.cc (modified) (1 diff)
• Alignment.h (modified) (1 diff)

trunk/yat/utility/Alignment.cc

@@ -33 +33 @@
 namespace yat {
 namespace utility {
+
+  unsigned int ssearch(std::string first, std::string second)
+  {
+    matrix m(first.size(), second.size());
+    for (size_t i=0; i<first.size(); ++i)
+      for (size_t j=0; j<second.size(); ++j)
+        m(i,j) = (first[i]==second[j] ? 1 : 0);
+    std::vector<std::pair<size_t, size_t> > path;
+    return static_cast<unsigned int>(NeedlemanWunsch(m,path,0));
+  }
+
 
   double NeedlemanWunsch(const utility::matrix& s,

trunk/yat/utility/Alignment.h

@@ -60 +60 @@
                          const double gap);
 
+  /**
+     SSearch does a rigorous Smith-Waterman (Needleman-Wunsch with no gap
+     cost) search for similarity between a sequnces. For long sequences this
+     may be very expensive (both in time and space) and BLAST or FASTA is
+     preferable.
+
+     @return number of matches
+   */
+  unsigned int ssearch(std::string first, std::string second);
+
 }}} // of namespace utility, yat, and theplu