Some refactoring of _hyListNumeric; added random replication to the u…

…t_hyListNumeric.cpp; removed _hyListNumeric.cpp -- now directly pasted into the header file to make gcov work

contrib/gtest-1.7.0/cmake_install.cmake

@@ -1,4 +1,4 @@
-# Install script for directory: /Volumes/TeraMonkey/Users/sergei/hyphy/contrib/gtest-1.7.0
+# Install script for directory: /Users/sergei/hyphy/contrib/gtest-1.7.0
 
 # Set the install prefix
 IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -12,7 +12,7 @@ IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
     STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
            CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
   ELSE(BUILD_TYPE)
-    SET(CMAKE_INSTALL_CONFIG_NAME "")
+    SET(CMAKE_INSTALL_CONFIG_NAME "Release")
   ENDIF(BUILD_TYPE)
   MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
 ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)

src/core/include/hy_list.h

@@ -225,7 +225,7 @@ class _hyList : public virtual BaseObj {
   * @return A long
   */
 
-  virtual PAYLOAD Element(const long);
+  virtual PAYLOAD Element(const long) const;
 
   /**
   * Checks if list is identical to other list
@@ -329,14 +329,14 @@ class _hyList : public virtual BaseObj {
   * @return Nothing. Acts on the List object it was called from.
   */
   inline void    Swap    (const unsigned long, const unsigned long); //swap two elements
-  virtual BaseRef toStr(void);
+  virtual BaseRef toStr(void) const;
 
   /**
   * Request space for this many elements
   * @param slots The number of elements to allocate the space for
   */
 
-  void    RequestSpace(const unsigned long);
+  void    RequestSpace(const unsigned long, bool = false);
   /**
   * Trim excess memory from the list allocation 
   */

src/core/include/hy_list_numeric.h

@@ -63,27 +63,28 @@ class _hyListNumeric : public _hyListOrderable<PAYLOAD> {
         //does nothing
       _hyListNumeric();
 
-        //_hyList constructor
-      _hyListNumeric(const unsigned long);
-
         // stack copy contructor
       _hyListNumeric(const _hyListNumeric <PAYLOAD>&, const long = 0UL, const long = HY_LIST_INSERT_AT_END);
 
         // data constructor (1 member list)
       _hyListNumeric(const PAYLOAD);
 
-      // arithmetic series populator: size, first item, step
+        // data constructor from _hyListOrderable
+
+      _hyListNumeric(const _hyListOrderable<PAYLOAD>&);
+
+    // arithmetic series populator: size, first item, step
       _hyListNumeric(const unsigned long, const PAYLOAD, const PAYLOAD);
 
 
       /**
-       * Data constructor list of longs supplied as a variable
-       * @param long the first string to add to the list
-       * @param const unsigned long the number of additional long arguments supplied
-       * to the constructor
-       * @param 2-N: long to be added to the list
+       * Data constructor from a static list of PAYLOAD objects
+       * @param const unsigned long the number of PAYLOAD arguments supplied
+       * to the constructor in the second argument
+       * @param const PAYLOAD: the static list of items to pass to the constructor
        */
-      _hyListNumeric(const PAYLOAD, const unsigned long, ...);
+
+      _hyListNumeric (const unsigned long, const PAYLOAD []);
 
       /**
       * Populate a _hyListNumeric with integers incrementally.
@@ -97,7 +98,7 @@ class _hyListNumeric : public _hyListOrderable<PAYLOAD> {
 
 
       /* instead of throwing an error, returns the missing value */
-      virtual PAYLOAD Element(const long);
+      virtual PAYLOAD Element(const long) const;
 
       /**
       * SLKP: 20090508
@@ -116,18 +117,16 @@ class _hyListNumeric : public _hyListOrderable<PAYLOAD> {
       */
       void Offset(const PAYLOAD);
 
-      /**
-      * Appends a number to the passed string buffer
-      * @return void
-      */
-      void AppendNumtoStr(_StringBuffer*, const PAYLOAD) const;
-
+
+
+
       /**
       * Convert (a sorted) list into a partition string for consumption by datafilters etc
       * Example: _hyListNumeric(1,2,3,7,8,9,10).ListToPartitionString() = "1-3,7-10"
       * @return The partition string
       */
-      _String* ListToPartitionString(void) const;
+      // define this only for "long" PAYLOADS
+      _StringBuffer * ListToPartitionString(void) const;
 
 
       /**
@@ -142,13 +141,203 @@ class _hyListNumeric : public _hyListOrderable<PAYLOAD> {
       *
       */
 
-      _hyListNumeric <PAYLOAD> *CountingSort(PAYLOAD, _hyListNumeric <long> * = nil);
+      _hyListNumeric <PAYLOAD> CountingSort(PAYLOAD, _hyListNumeric <long> * = nil);
+      virtual BaseRef toStr() const;
+
+private:
+
+      /**
+       * Appends a number to the passed string buffer
+       * @return void
+       */
+      void AppendNumtoStr(_StringBuffer*, const PAYLOAD) const;
 
+};
 
-      virtual BaseRef toStr();
+  //#include "hy_list_numeric.cpp"
 
-};
+  // FUNCTION DEFINITIONS -- moved here so that gcov can view them
+
+// Does nothing
+template<typename PAYLOAD>
+_hyListNumeric<PAYLOAD>::_hyListNumeric() {
+}
+
+  //Data constructor (1 member list)
+template<typename PAYLOAD>
+_hyListNumeric<PAYLOAD>::_hyListNumeric(const PAYLOAD item) : _hyListOrderable<PAYLOAD> (item) {
+}
+
+
+  //Stack copy contructor
+template<typename PAYLOAD>
+_hyListNumeric<PAYLOAD>::_hyListNumeric(const _hyListNumeric <PAYLOAD> &l, const long from, const long to)
+{
+  this->Clone(&l, from, to); }
+
+  // Data constructor from array
+template<typename PAYLOAD>
+_hyListNumeric<PAYLOAD>::_hyListNumeric(const unsigned long number, const PAYLOAD items[]) :
+_hyListOrderable<PAYLOAD> (number, items) {
+}
+
+  // Does nothing
+template<typename PAYLOAD>
+_hyListNumeric<PAYLOAD>::_hyListNumeric(const _hyListOrderable<PAYLOAD>& source):_hyListOrderable<PAYLOAD> (source) {
+}
+
+template<typename PAYLOAD>
+_hyListNumeric<PAYLOAD>::_hyListNumeric (const unsigned long l, const PAYLOAD start, const PAYLOAD step) {
+  this->Initialize(false);
+  Populate (l, start, step);
+}
+
+
+template<typename PAYLOAD>
+PAYLOAD _hyListNumeric<PAYLOAD>::Element(const long index) const {
+  if (this->lLength) {
+    if (index >= 0L && (unsigned long)index < this->lLength) {
+      return this->lData[index];
+    } else if ((unsigned long)(-index) <= this->lLength) {
+      return this->lData[this->lLength - (-index)];
+    }
+  }
+  return _HY_LIST_NUMERIC_INVALID_VALUE_;
+}
+
+template<typename PAYLOAD>
+PAYLOAD _hyListNumeric<PAYLOAD>::Sum(void) const {
+  PAYLOAD sum = 0L;
+  for (unsigned long k = 0UL; k < this->lLength; k++) {
+    sum += this->lData[k];
+  }
+  return sum;
+}
+
+template<typename PAYLOAD>
+void _hyListNumeric<PAYLOAD>::Offset(const PAYLOAD shift) {
+  for (unsigned long k = 0UL; k < this->lLength; k++) {
+    this->lData[k] += shift;
+  }
+}
+
+template<typename PAYLOAD>
+void _hyListNumeric<PAYLOAD>::Populate (const unsigned long l, const PAYLOAD start, const PAYLOAD step) {
+  this->RequestSpace (l);
+  PAYLOAD current_value = start;
+  for (unsigned long k = 0UL; k < l; k++, current_value+=step) {
+    this->lData[k] = current_value;
+  }
+
+  this->lLength = l;
+}
+
+
+template<typename PAYLOAD>
+void _hyListNumeric<PAYLOAD>::AppendNumtoStr(_StringBuffer* s, PAYLOAD num) const{
+
+  char buffer[128];
+  snprintf(buffer, 127, "%ld", long (num));
+  (*s) << buffer;
+}
+
+
+  //Char* conversion
+template<typename PAYLOAD>
+BaseRef _hyListNumeric<PAYLOAD>::toStr(void) const {
+
+  if (this->countitems()) {
+    _StringBuffer* s = new _StringBuffer();
+
+    (*s) << '{';
+
+    for (unsigned long i = 0UL; i<this->lLength; i++) {
+      this->AppendNumtoStr(s, this->lData[i]);
+      if (i<this->lLength-1) {
+        (*s) << ',';
+      }
+    }
+    (*s) << '}';
+
+    return s;
+  } else {
+    return new _String ("{}");
+  }
+}
+
+
+template<typename PAYLOAD>
+_StringBuffer* _hyListNumeric<PAYLOAD>::ListToPartitionString (void) const {
+
+  _StringBuffer *result = new _StringBuffer (64UL);
+
+  for (unsigned long k=0UL; k<this->lLength; k++) {
+    unsigned long m;
+    for (m=k+1UL; m<this->lLength; m++)
+      if (this->lData[m]-this->lData[m-1]!=1L) {
+        break;
+      }
+    if (m>k+2) {
+      this->AppendNumtoStr(result, this->lData[k]);
+      (*result) << '-';
+      this->AppendNumtoStr(result, this->lData[m-1]);
+      if (m<this->lLength) {
+        (*result) << ',';
+      }
+      k = m-1;
+    } else {
+      this->AppendNumtoStr(result, this->lData[k]);
+      if (k<this->lLength-1) {
+        (*result) << ',';
+      }
+    }
+  }
+  return result;
+}
+
+template<typename PAYLOAD>
+_hyListNumeric <PAYLOAD>  _hyListNumeric<PAYLOAD>::CountingSort (PAYLOAD upperBound, _hyListNumeric <long> * ordering)
+{
+  if (ordering) {
+    ordering->Clear();
+  }
+
+  _hyListNumeric<PAYLOAD> result;
 
-#include "hy_list_numeric.cpp"
+  if (this->lLength) {
+    if (upperBound == _HY_LIST_NUMERIC_INVALID_VALUE_) {
+      upperBound = this->Max()+1UL;
+    }
+
+    _hyListNumeric<PAYLOAD> count;
+
+    count.RequestSpace (upperBound+1UL);
+    result.RequestSpace (this->lLength, true);
+
+
+    count.Populate(upperBound, 0UL, 0UL);
+
+    for (unsigned long pass1 = 0UL; pass1 < this->lLength; pass1++) {
+      count[this->lData[pass1]]++;
+    }
+
+    for (unsigned long pass2 = 1UL; pass2 < upperBound; pass2++) {
+      count[pass2] += count[pass2-1];
+    }
+
+    if (ordering) {
+      ordering->Populate (this->lLength, 0UL, 0UL);
+      for (long pass3 = this->lLength-1; pass3 >=0L; pass3--) {
+        result[--count[this->Element(pass3)]] = this->Element(pass3);
+        (*ordering)[count.Element(this->Element(pass3))] = pass3;
+      }
+    } else {
+      for (long pass3 = this->lLength-1; pass3 >= 0L; pass3--) {
+        result[--count[this->Element(pass3)]] = this->Element(pass3);
+      }
+    }
+  }
+  return result;
+}
 
 #endif

src/core/include/hy_strings.h

@@ -249,7 +249,7 @@ class _String : public BaseObj {
   * Converts a good ole char*
   * \n\n \b Example: \code string.toStr(); \endcode
   */
-  virtual BaseRef toStr(void);
+  virtual BaseRef toStr(void) const;
 
   /**
   * Return good ole char*

src/core/strings.cpp

@@ -1040,9 +1040,8 @@ _Parameter _String::toNum(void) {
 }
 
 //Return good ole char*
-BaseRef _String::toStr(void) {
-  AddAReference();
-  return this;
+BaseRef _String::toStr(void) const{
+  return new _String (*this);
 }
 
 _Parameter _String::ProcessTreeBranchLength(void) {

src/core/templates/hy_list.cpp

@@ -242,7 +242,7 @@ void _hyList<PAYLOAD>::append_multiple(const PAYLOAD item, const unsigned long c
 }
 
 template<typename PAYLOAD>
-void _hyList<PAYLOAD>::RequestSpace(const unsigned long slots)
+void _hyList<PAYLOAD>::RequestSpace(const unsigned long slots, bool set_length)
 {
   if (slots > laLength) {
     laLength = (slots / HY_LIST_ALLOCATION_CHUNK + 1) * HY_LIST_ALLOCATION_CHUNK;
@@ -253,6 +253,9 @@ void _hyList<PAYLOAD>::RequestSpace(const unsigned long slots)
       checkPointer(lData = (PAYLOAD *)MemAllocate(laLength * sizeof(PAYLOAD)));
     }
   }
+  if (set_length) {
+    lLength = slots;
+  }
 }
 
 template<typename PAYLOAD>
@@ -499,7 +502,7 @@ void _hyList<PAYLOAD>::Duplicate(BaseRefConst theRef)
 //Element location functions (0,llength - 1)
 //Negative indices return offsets from the end of the list
 template<typename PAYLOAD>
-PAYLOAD _hyList<PAYLOAD>::Element(const long index)
+PAYLOAD _hyList<PAYLOAD>::Element(const long index) const
 {
   if (index >= 0L && (unsigned long)index < lLength) {
     return lData[index];
@@ -701,7 +704,7 @@ void _hyList<PAYLOAD>::Swap(const unsigned long i, const unsigned long j)
 }
 
 template<typename PAYLOAD>
-BaseRef _hyList<PAYLOAD>::toStr(void)
+BaseRef _hyList<PAYLOAD>::toStr(void) const
 {
   _StringBuffer * stringified = new _StringBuffer ();
   (*stringified) << "_hyList with ";