CMakeLists.txt

@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-seq")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
 SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-seq
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.4.0
+PROJECT_NUMBER         = 2.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

bpp-seq.spec

@@ -3,7 +3,7 @@
 URL: https://github.com/BioPP/bpp-seq
 
 Name: bpp-seq
-Version: 2.4.0
+Version: 2.4.1
 Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
@@ -78,6 +78,8 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Fri Aug 10 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1
+- Compatibility update gcc8
 * Fri Mar 03 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
 - Increased interface number
 - Removed dynamic exceptions declarations.

debian/changelog

+libbpp-seq (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Ref: #897784
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Sun, 19 Aug 2018 11:45:47 +0200
+
 libbpp-seq (2.4.0-2) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,10 +7,10 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.80),
-               libbpp-core-dev (>= 2.4.0)
+               libbpp-core-dev (>= 2.4.1)
 Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-seq.git
+Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq
+Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 
 Package: libbpp-seq-dev
@@ -18,7 +18,7 @@ Architecture: any
 Section: libdevel
 Depends: libbpp-seq12 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-core-dev (>= 2.4.0)
+         libbpp-core-dev (>= 2.4.1)
 Description: Bio++ Sequence library development files
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.
@@ -35,7 +35,7 @@ Multi-Arch: same
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libbpp-core4 (>= 2.4.0)
+         libbpp-core4 (>= 2.4.1)
 Pre-Depends: ${misc:Pre-Depends}
 Description: Bio++ Sequence library
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence

src/Bpp/Seq/Alphabet/DefaultAlphabet.h

@@ -55,9 +55,6 @@ namespace bpp
     public LetterAlphabet
   {
   protected:
-    void registerState(AlphabetState* st) {
-      AbstractAlphabet::registerState(st);
-    }
     std::string chars_;
 		
   public:

src/Bpp/Seq/Alphabet/LetterAlphabet.h

@@ -83,7 +83,7 @@ namespace bpp {
 
   public:
     bool isCharInAlphabet(char state) const {
-      return letters_[static_cast<unsigned int>(state)] != LETTER_UNDEF_VALUE;
+      return letters_[static_cast<size_t>(state)] != LETTER_UNDEF_VALUE;
     }
     bool isCharInAlphabet(const std::string& state) const {
       return isCharInAlphabet(state[0]);
@@ -98,20 +98,20 @@ namespace bpp {
     void registerState(AlphabetState* st) {
       AbstractAlphabet::registerState(st);
       if (caseSensitive_) {
-        letters_[static_cast<unsigned int>(st->getLetter()[0])] = st->getNum();
+        letters_[static_cast<size_t>(st->getLetter()[0])] = st->getNum();
       } else {
-        letters_[static_cast<unsigned int>(tolower(st->getLetter()[0]))] = st->getNum();
-        letters_[static_cast<unsigned int>(toupper(st->getLetter()[0]))] = st->getNum();
+        letters_[static_cast<size_t>(tolower(st->getLetter()[0]))] = st->getNum();
+        letters_[static_cast<size_t>(toupper(st->getLetter()[0]))] = st->getNum();
       }
     }
 
     void setState(size_t pos, AlphabetState* st) {
       AbstractAlphabet::setState(pos, st);
       if (caseSensitive_) {
-        letters_[static_cast<unsigned int>(st->getLetter()[0])] = st->getNum();
+        letters_[static_cast<size_t>(st->getLetter()[0])] = st->getNum();
       } else {
-        letters_[static_cast<unsigned int>(tolower(st->getLetter()[0]))] = st->getNum();
-        letters_[static_cast<unsigned int>(toupper(st->getLetter()[0]))] = st->getNum();
+        letters_[static_cast<size_t>(tolower(st->getLetter()[0]))] = st->getNum();
+        letters_[static_cast<size_t>(toupper(st->getLetter()[0]))] = st->getNum();
       }
     }
 

src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h

@@ -81,7 +81,7 @@ namespace bpp
  * C RICJ880106    0.849
  * I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
  *       0.      0.      0.      1.      0.      0.      1.      0.      0.      0.
- *       0.      0.      0.      0.      0.      0.      0.      0.      0.      0. * Soit:
+ *       0.      0.      0.      0.      0.      0.      0.      0.      0.      0.
  * //
  * @endcode
  *

src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h

@@ -94,16 +94,17 @@ public:
 
   double getIndex(int state1, int state2) const
   {
-    size_t stateIndex1 = alpha_->getStateIndex(state1);
-    size_t stateIndex2 = alpha_->getStateIndex(state2);
-    return property_(stateIndex1, stateIndex2);
+    if (state1 < 0 || state1 > 19)
+      throw BadIntException(state1, "AAIndex2Entry::getIndex(). Invalid state1.", alpha_);
+    if (state2 < 0 || state2 > 19)
+      throw BadIntException(state2, "AAIndex2Entry::getIndex(). Invalid state2.", alpha_);
+    double d = property_(static_cast<size_t>(state1), static_cast<size_t>(state2));
+    return d;
   }
 
   double getIndex(const std::string& state1, const std::string& state2) const
   {
-    size_t stateIndex1 = alpha_->getStateIndex(state1);
-    size_t stateIndex2 = alpha_->getStateIndex(state2);
-    return property_(stateIndex1, stateIndex2);
+    return getIndex(alpha_->charToInt(state1), alpha_->charToInt(state2));
   }
 
   LinearMatrix<double>* getIndexMatrix() const { return new LinearMatrix<double>(property_); }

src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h

@@ -47,7 +47,7 @@
 namespace bpp
 {
 /**
- * @brief Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html
+ * @brief Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html (Note: original webpage is not available anymore)
  *
  *
  */

src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp

@@ -57,16 +57,17 @@ BLOSUM50::BLOSUM50() :
 
 double BLOSUM50::getIndex(int state1, int state2) const
 {
-  size_t stateIndex1 = alpha_->getStateIndex(state1);
-  size_t stateIndex2 = alpha_->getStateIndex(state2);
-  return distanceMatrix_(stateIndex1, stateIndex2);
+  if (state1 < 0 || state1 > 19)
+    throw BadIntException(state1, "BLOSUM50::getIndex(). Invalid state1.", alpha_);
+  if (state2 < 0 || state2 > 19)
+    throw BadIntException(state2, "BLOSUM50::getIndex(). Invalid state2.", alpha_);
+  double d = distanceMatrix_(static_cast<size_t>(state1), static_cast<size_t>(state2));
+  return d;
 }
 
 double BLOSUM50::getIndex(const std::string& state1, const std::string& state2) const
 {
-  return distanceMatrix_(
-      static_cast<size_t>(alpha_->charToInt(state1)),
-      static_cast<size_t>(alpha_->charToInt(state2)));
+  return getIndex(alpha_->charToInt(state1), alpha_->charToInt(state2));
 }
 
 LinearMatrix<double>* BLOSUM50::getIndexMatrix() const

src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp

@@ -63,13 +63,15 @@ GranthamAAChemicalDistance::~GranthamAAChemicalDistance() {}
 
 double GranthamAAChemicalDistance::getIndex(int state1, int state2) const
 {
-  size_t stateIndex1 = alpha_->getStateIndex(state1);
-  size_t stateIndex2 = alpha_->getStateIndex(state2);
-  double d = distanceMatrix_(stateIndex1, stateIndex2);
+  if (state1 < 0 || state1 > 19)
+    throw BadIntException(state1, "GranthamAAChemicalDistance::getIndex(). Invalid state1.", alpha_);
+  if (state2 < 0 || state2 > 19)
+    throw BadIntException(state2, "GranthamAAChemicalDistance::getIndex(). Invalid state2.", alpha_);
+  double d = distanceMatrix_(static_cast<size_t>(state1), static_cast<size_t>(state2));
   if (sign_ == SIGN_NONE)
     return NumTools::abs<double>(d);
   if (sign_ == SIGN_PC1)
-    return signMatrix_(stateIndex1, stateIndex2) * NumTools::abs<double>(d);
+    return signMatrix_(static_cast<size_t>(state1), static_cast<size_t>(state2)) * NumTools::abs<double>(d);
   return d;
 }
 

src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp

@@ -58,18 +58,17 @@ MiyataAAChemicalDistance::MiyataAAChemicalDistance() :
 
 double MiyataAAChemicalDistance::getIndex(int state1, int state2) const
 {
-  size_t stateIndex1 = alpha_->getStateIndex(state1);
-  size_t stateIndex2 = alpha_->getStateIndex(state2);
-  double d = distanceMatrix_(stateIndex1, stateIndex2);
+  if (state1 < 0 || state1 > 19)
+    throw BadIntException(state1, "MiyataAAChemicalDistance::getIndex(). Invalid state1.", alpha_);
+  if (state2 < 0 || state2 > 19)
+    throw BadIntException(state2, "MiyataAAChemicalDistance::getIndex(). Invalid state2.", alpha_);
+  double d = distanceMatrix_(static_cast<size_t>(state1), static_cast<size_t>(state2));
   return sym_ ? NumTools::abs<double>(d) : d;
 }
 
 double MiyataAAChemicalDistance::getIndex(const string& state1, const string& state2) const
 {
-  double d = distanceMatrix_(
-      static_cast<size_t>(alpha_->charToInt(state1)),
-      static_cast<size_t>(alpha_->charToInt(state2)));
-  return sym_ ? NumTools::abs(d) : d;
+  return getIndex(alpha_->charToInt(state1), alpha_->charToInt(state2));
 }
 
 Matrix<double>* MiyataAAChemicalDistance::getIndexMatrix() const

src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp

@@ -63,15 +63,15 @@ SimpleScore::SimpleScore(const Alphabet* alphabet, double match, double mismatch
 
 double SimpleScore::getIndex(int state1, int state2) const
 {
-  size_t stateIndex1 = alphabet_->getStateIndex(state1);
-  size_t stateIndex2 = alphabet_->getStateIndex(state2);
+  size_t stateIndex1 = alphabet_->getStateIndex(state1)-1;
+  size_t stateIndex2 = alphabet_->getStateIndex(state2)-1;
   return distanceMatrix_(stateIndex1, stateIndex2);
 }
 
 double SimpleScore::getIndex(const std::string& state1, const std::string& state2) const
 {
-  size_t stateIndex1 = alphabet_->getStateIndex(state1);
-  size_t stateIndex2 = alphabet_->getStateIndex(state2);
+  size_t stateIndex1 = alphabet_->getStateIndex(state1)-1;
+  size_t stateIndex2 = alphabet_->getStateIndex(state2)-1;
   return distanceMatrix_(stateIndex1, stateIndex2);
 }
 

src/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h

@@ -65,13 +65,13 @@ public:
   {}
 
   UserAlphabetIndex1(const UserAlphabetIndex1& uAlph) :
-    alph_(uAlph.alph_),//->clone()),
+    alph_(uAlph.alph_),
     index_(uAlph.index_)
   {}
 
   UserAlphabetIndex1& operator=(const UserAlphabetIndex1& uAlph)
   {
-    alph_  = uAlph.alph_;//->clone();
+    alph_  = uAlph.alph_;
     index_ = uAlph.index_;
     return *this;
   }    
@@ -83,22 +83,22 @@ public:
 public:
   double getIndex(int state) const
   {
-    return index_[alph_->getStateIndex(state)];
+    return index_[alph_->getStateIndex(state)-1];
   }
 
   void setIndex(int state, double val) 
   {
-    index_[alph_->getStateIndex(state)] = val;
+    index_[alph_->getStateIndex(state)-1] = val;
   }
 
   double getIndex(const std::string& state) const
   {
-    return index_[alph_->getStateIndex(state)];
+    return index_[alph_->getStateIndex(state)-1];
   }
 
   void setIndex(const std::string& state, double val) 
   {
-    index_[alph_->getStateIndex(state)] = val;
+    index_[alph_->getStateIndex(state)-1] = val;
   }
 
   std::vector<double>* getIndexVector() const { return new std::vector<double>(index_); }

src/Bpp/Seq/GeneticCode/GeneticCode.cpp

@@ -87,7 +87,7 @@ vector<int> GeneticCode::getSynonymous(int aminoacid) const
       if (translate(i) == aminoacid)
         synonymes.push_back(i);
     }
-    catch (StopCodonException)
+    catch (StopCodonException&)
     { }
   }
   return synonymes;
@@ -108,7 +108,7 @@ std::vector<std::string> GeneticCode::getSynonymous(const std::string& aminoacid
       if (translate(i) == aa)
         synonymes.push_back(codonAlphabet_.intToChar(i));
     }
-    catch (StopCodonException)
+    catch (StopCodonException&)
     { }
   }
   return synonymes;

src/Bpp/Seq/SequenceTools.cpp

@@ -155,7 +155,7 @@ Sequence* SequenceTools::getComplement(const Sequence& sequence)
 Sequence* SequenceTools::transcript(const Sequence& sequence)
 {
   // Alphabet type checking
-  if (AlphabetTools::isDNAAlphabet(sequence.getAlphabet()))
+  if (!AlphabetTools::isDNAAlphabet(sequence.getAlphabet()))
   {
     throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", sequence.getAlphabet());
   }
@@ -168,7 +168,7 @@ Sequence* SequenceTools::transcript(const Sequence& sequence)
 Sequence* SequenceTools::reverseTranscript(const Sequence& sequence)
 {
   // Alphabet type checking
-  if (AlphabetTools::isRNAAlphabet(sequence.getAlphabet()))
+  if (!AlphabetTools::isRNAAlphabet(sequence.getAlphabet()))
   {
     throw AlphabetException ("SequenceTools::reverseTranscript : Sequence must be RNA", sequence.getAlphabet());
   }

src/Bpp/Seq/SymbolList.cpp

@@ -157,7 +157,7 @@ string BasicSymbolList::getChar(size_t pos) const
   {
     c = alphabet_->intToChar(content_[pos]);
   }
-  catch(BadIntException bie)
+  catch(BadIntException& bie)
   {
     //This should never happen!
   }
@@ -372,7 +372,7 @@ string EdSymbolList::getChar(size_t pos) const
   string c = "";
   try {
     c = alphabet_->intToChar(content_[pos]);
-	} catch(BadIntException bie) {
+  } catch(BadIntException& bie) {
     //This should never happen!
   }
   return c;