Changeset 2470

Timestamp:

Apr 12, 2011, 5:21:45 AM (12 years ago)

Author:

Peter

Message:

merge patch release 0.7.2 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• bootstrap (modified) (2 diffs)
• m4/version.m4 (modified) (2 diffs)
• test/codon.cc (modified) (2 diffs)
• test/statistics.cc (modified) (5 diffs)
• yat/omic/Codon.cc (modified) (3 diffs)
• yat/statistics/Percentiler.h (modified) (4 diffs)

trunk/NEWS

@@ -13 +13 @@
 
 yat 0.7.x series from http://dev.thep.lu.se/yat/svn/branches/0.7-stable
+
+version 0.7.2 (released 12 April 2011)
+  - omic::Codon("ATG").amino_acid() now return 'M' (bug #664)
+  - median now works on empty ranges (bug #660)
+  - fixed bug percentiler sometimes zero weight elements (r2466)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.7.2
+
 
 version 0.7.1 (released 13 January 2011)

trunk/bootstrap

@@ -7 +7 @@
 # Copyright (C) 2006 Jari Häkkinen
 # Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2009 Peter Johansson
+# Copyright (C) 2009, 2011 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -37 +37 @@
     shift;
 done
+cmd="autoreconf --install --symlink --force";
 if test "x$verbose" = "xno"; then
-    exec >& /dev/null
+    exec > /dev/null
+else
+    cmd="$cmd --verbose"
 fi
-cmd="autoreconf --install --symlink --force --verbose";
 echo "$me: running: $cmd";
 exec $cmd;

trunk/m4/version.m4

@@ -32 +32 @@
 # DEV_BUILD - When rolling a tarball we set this to `false'. In
 # repository value remains `true'.
-m4_define([DEV_BUILD], [true])
+m4_define([DEV_BUILD], [false])
 
 # Library versioning (current:revision:age)
@@ -67 +67 @@
 # yat-0.7.0  4:0:0
 # yat-0.7.1  4:1:0
+# yat-0.7.2  4:2:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/codon.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2010 Peter Johansson
+  Copyright (C) 2010, 2011 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -53 +53 @@
     suite.err() << "error: expected end() to return false\n";
 
+  if (!suite.add(Codon("ATG").amino_acid()=='M'))
+    suite.err() << "error: Codon(\"ATG\").amino_acid() returns: `" 
+                << Codon("ATG").amino_acid() << "'\n";
+
+  if (!suite.add(Codon("ATG").start()))
+    suite.err() << "error: Codon(\"ATG\").start() returns: false\n"; 
+
   return suite.return_value();
 }

trunk/test/statistics.cc

@@ -6 +6 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   Copyright (C) 2007, 2008, 2009 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2010 Peter Johansson
+  Copyright (C) 2010, 2011 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -46 +46 @@
 void test_mad(test::Suite&);
 
+void test_median_empty(test::Suite&);
 void test_percentiler(test::Suite&);
 void test_percentiler_nan(test::Suite&);
@@ -124 +125 @@
             
   }
+  test_median_empty(suite);
   return suite.return_value();
 }
@@ -150 +152 @@
             boost::random_access_iterator_archetype<utility::DataWeight>());
   }
+}
+
+
+// test for ticket #660
+void test_median_empty(test::Suite& suite)
+{
+  std::vector<double> x;
+  double m = 0;
+  m = statistics::median(x.begin(), x.end(), true);
 }
 
@@ -260 +271 @@
                      RandomAccessIterator2 last2)
 {
-  for (double p=0; p<100; p+=10) {
+  for (double p=0; p<=100; p+=10) {
     double correct=statistics::percentile2(first1, last1, p);
     test_percentiler(suite, first2, last2, p, correct);

trunk/yat/omic/Codon.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2010 Peter Johansson
+  Copyright (C) 2010, 2011 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -138 +138 @@
     add_to_map('I', "ATT,ATC,ATA");
     add_to_map('V', "GTT,GTC,GTA,GTG");
-    add_to_map('\0',"ATG"); // start
     add_to_map('*',"TAA,TGA,TAG"); //  stop
   }
@@ -145 +144 @@
   bool Codon::start(void) const
   {
-    return iter_->second=='\0';
+    return iter_->second=='M';
   }
 

trunk/yat/statistics/Percentiler.h

@@ -6 +6 @@
 /*
   Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2010 Peter Johansson
+  Copyright (C) 2010, 2011 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -34 +34 @@
 #include <algorithm>
 #include <cmath>
+#include <limits>
 #include <numeric>
 #include <stdexcept>
@@ -99 +100 @@
       BOOST_CONCEPT_ASSERT((boost::RandomAccessIterator<RandomAccessIterator>));
       BOOST_CONCEPT_ASSERT((utility::DataIteratorConcept<RandomAccessIterator>));
+      if (first==last)
+        return std::numeric_limits<double>::quiet_NaN();
       return calculate(first, last, sorted_, 
        typename utility::weighted_iterator_traits<RandomAccessIterator>::type());
@@ -176 +179 @@
       std::vector<double>::const_iterator upper(accum_w.begin());
       double margin=1e-10;
-      while (*upper <= w_bound+margin && upper!=accum_w.end())
+      while (upper!=accum_w.end() && *upper <= w_bound+margin)
         ++upper;
-      if (upper==accum_w.end())
+      while (upper!=accum_w.begin() &&
+             (upper==accum_w.end() || 
+              trait.weight(first+(upper-accum_w.begin()))==0.0))
         --upper;
       std::vector<double>::const_iterator lower(upper);