diff options
Diffstat (limited to 'sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch')
| -rw-r--r-- | sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch | 643 |
1 files changed, 0 insertions, 643 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch deleted file mode 100644 index 36718d161ac0..000000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch +++ /dev/null @@ -1,643 +0,0 @@ - include/algo/gnomon/gnomon_model.hpp | 8 +- - include/corelib/ncbiexpt.hpp | 4 +- - include/corelib/ncbimisc.hpp | 2 + - include/corelib/ncbiobj.hpp | 2 +- - include/corelib/ncbistl.hpp | 2 +- - include/corelib/ncbistr.hpp | 2 +- - include/serial/impl/stltypes.hpp | 14 +- - include/serial/iterator.hpp | 6 +- - include/util/bitset/bmfunc.h | 263 +++++++++++++------------ - include/util/bitset/bmserial.h | 6 +- - include/util/linkedset.hpp | 8 +- - include/util/rangemap.hpp | 2 +- - src/algo/blast/gumbel_params/njn_approx.hpp | 1 + - src/algo/blast/gumbel_params/sls_alp_data.hpp | 1 + - src/serial/stdtypes.cpp | 8 +- - 15 files changed, 167 insertions(+), 162 deletions(-) - -diff --git a/include/algo/gnomon/gnomon_model.hpp b/include/algo/gnomon/gnomon_model.hpp -index 66e7765..ca4d765 100644 ---- a/include/algo/gnomon/gnomon_model.hpp -+++ b/include/algo/gnomon/gnomon_model.hpp -@@ -627,11 +627,11 @@ public: - CModelCluster(TSignedSeqRange limits) : m_limits(limits) {} - void Insert(const Model& a) { - m_limits.CombineWith(a.Limits()); -- push_back(a); -+ this->push_back(a); - } - void Splice(CModelCluster& c) { // elements removed from c and inserted into *this - m_limits.CombineWith(c.Limits()); -- splice(list<Model>::end(),c); -+ this->splice(list<Model>::end(),c); - } - TSignedSeqRange Limits() const { return m_limits; } - bool operator<(const CModelCluster& c) const { return Precede(m_limits, c.m_limits); } -@@ -663,9 +663,9 @@ class NCBI_XALGOGNOMON_EXPORT CModelClusterSet : public set<Cluster> { - pair<Titerator,Titerator> lim = set<Cluster>::equal_range(clust); - for(Titerator it = lim.first; it != lim.second;) { - clust.Splice(const_cast<Cluster&>(*it)); -- erase(it++); -+ this->erase(it++); - } -- const_cast<Cluster&>(*insert(lim.second,Cluster(clust.Limits()))).Splice(clust); -+ const_cast<Cluster&>(*this->insert(lim.second,Cluster(clust.Limits()))).Splice(clust); - } - }; - -diff --git a/include/corelib/ncbiexpt.hpp b/include/corelib/ncbiexpt.hpp -index 1d3cce3..1055d66 100644 ---- a/include/corelib/ncbiexpt.hpp -+++ b/include/corelib/ncbiexpt.hpp -@@ -843,7 +843,7 @@ const TTo* UppermostCast(const TFrom& from) - exception_class(const exception_class& other) \ - : base_class(other) \ - { \ -- x_Assign(other); \ -+ this->x_Assign(other); \ - } \ - public: \ - virtual ~exception_class(void) throw() {} \ -@@ -1166,7 +1166,7 @@ public: - : TBase( other) - { - m_Errno = other.m_Errno; -- x_Assign(other); -+ this->x_Assign(other); - } - - /// Destructor. -diff --git a/include/corelib/ncbimisc.hpp b/include/corelib/ncbimisc.hpp -index 87236c7..b540038 100644 ---- a/include/corelib/ncbimisc.hpp -+++ b/include/corelib/ncbimisc.hpp -@@ -47,6 +47,8 @@ - # include <ctype.h> - #endif - -+// for free() -+#include <stdlib.h> - - #if defined(_DEBUG) && !defined(NCBI_NO_STRICT_CTYPE_ARGS) - # define NCBI_STRICT_CTYPE_ARGS -diff --git a/include/corelib/ncbiobj.hpp b/include/corelib/ncbiobj.hpp -index de4c454..084a041 100644 ---- a/include/corelib/ncbiobj.hpp -+++ b/include/corelib/ncbiobj.hpp -@@ -2128,7 +2128,7 @@ public: - CIRef<Interface, TThisType> ref( - dynamic_cast<Interface*>(proxy->GetLockedObject()), *this); - if (ref.NotNull()) { -- Unlock(ref.GetPointer()); -+ this->Unlock(ref.GetPointer()); - } - return ref; - } -diff --git a/include/corelib/ncbistl.hpp b/include/corelib/ncbistl.hpp -index afd71d2..38768c4 100644 ---- a/include/corelib/ncbistl.hpp -+++ b/include/corelib/ncbistl.hpp -@@ -36,7 +36,7 @@ - - - #include <common/ncbi_export.h> -- -+#include <string> - - // Get rid of some warnings in MSVC++ 6.00 - #if (_MSC_VER >= 1200) -diff --git a/include/corelib/ncbistr.hpp b/include/corelib/ncbistr.hpp -index e515dc6..5800223 100644 ---- a/include/corelib/ncbistr.hpp -+++ b/include/corelib/ncbistr.hpp -@@ -2439,7 +2439,7 @@ public: - : TBase(other) - { - m_Pos = other.m_Pos; -- x_Assign(other); -+ this->x_Assign(other); - } - - /// Destructor. -diff --git a/include/serial/impl/stltypes.hpp b/include/serial/impl/stltypes.hpp -index abfa8b8..28254ae 100644 ---- a/include/serial/impl/stltypes.hpp -+++ b/include/serial/impl/stltypes.hpp -@@ -437,7 +437,7 @@ public: - } - static bool InitIterator(TTypeInfoIterator& iter) - { -- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); -+ TStlIterator stl_iter = CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).begin(); - if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { - void* data = &iter.m_IteratorData; - new (data) TStlIterator(stl_iter); -@@ -445,7 +445,7 @@ public: - else { - iter.m_IteratorData = new TStlIterator(stl_iter); - } -- return stl_iter != Get(iter.GetContainerPtr()).end(); -+ return stl_iter != CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).end(); - } - static void ReleaseIterator(TTypeInfoIterator& iter) - { -@@ -466,7 +466,7 @@ public: - - static bool NextElement(TTypeInfoIterator& iter) - { -- return ++It(iter) != Get(iter.GetContainerPtr()).end(); -+ return ++It(iter) != CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).end(); - } - static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) - { -@@ -503,7 +503,7 @@ public: - - static bool EraseElement(TTypeInfoIterator& iter) - { -- TStlIterator& it = It(iter); -+ TStlIterator& it = CStlClassInfoFunctionsI::It(iter); - Container* c = static_cast<Container*>(iter.GetContainerPtr()); - it = c->erase(it); - return it != c->end(); -@@ -511,7 +511,7 @@ public: - static void EraseAllElements(TTypeInfoIterator& iter) - { - Container* c = static_cast<Container*>(iter.GetContainerPtr()); -- c->erase(It(iter), c->end()); -+ c->erase(CStlClassInfoFunctionsI::It(iter), c->end()); - } - - static void SetIteratorFunctions(CStlOneArgTemplate* info) -@@ -542,7 +542,7 @@ public: - } - static bool EraseElement(TTypeInfoIterator& iter) - { -- TStlIterator& it = It(iter); -+ TStlIterator& it = CStlClassInfoFunctionsI_set::It(iter); - Container* c = static_cast<Container*>(iter.GetContainerPtr()); - TStlIterator erase = it++; - c->erase(erase); -@@ -551,7 +551,7 @@ public: - static void EraseAllElements(TTypeInfoIterator& iter) - { - Container* c = static_cast<Container*>(iter.GetContainerPtr()); -- c->erase(It(iter), c->end()); -+ c->erase(CStlClassInfoFunctionsI_set::It(iter), c->end()); - } - - static void SetIteratorFunctions(CStlOneArgTemplate* info) -diff --git a/include/serial/iterator.hpp b/include/serial/iterator.hpp -index eabb01b..402d7ac 100644 ---- a/include/serial/iterator.hpp -+++ b/include/serial/iterator.hpp -@@ -491,13 +491,13 @@ protected: - CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) - : m_NeedType(needType) - { -- Init(beginInfo); -+ this->Init(beginInfo); - } - CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, - const string& filter) - : m_NeedType(needType) - { -- Init(beginInfo, filter); -+ this->Init(beginInfo, filter); - } - - virtual bool CanSelect(const CConstObjectInfo& object) -@@ -599,7 +599,7 @@ public: - - CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo) - { -- Init(beginInfo); -+ this->Init(beginInfo); - return *this; - } - -diff --git a/include/util/bitset/bmfunc.h b/include/util/bitset/bmfunc.h -index bf09e2d..5489213 100644 ---- a/include/util/bitset/bmfunc.h -+++ b/include/util/bitset/bmfunc.h -@@ -1794,6 +1794,72 @@ void gap_and_to_bitset(unsigned* dest, const T* buf) - } - } - -+/*! -+ Function calculates number of 1 bits in the given array of words in -+ the range between left anf right bits (borders included) -+ Make sure the addresses are aligned. -+ -+ @ingroup bitfunc -+*/ -+inline -+bm::id_t bit_block_calc_count_range(const bm::word_t* block, -+ bm::word_t left, -+ bm::word_t right) -+{ -+ BM_ASSERT(left <= right); -+ unsigned nword, nbit; -+ nbit = left & bm::set_word_mask; -+ const bm::word_t* word = -+ block + (nword = unsigned(left >> bm::set_word_shift)); -+ if (left == right) // special case (only 1 bit to check) -+ { -+ return (*word >> nbit) & 1; -+ } -+ bm::id_t count = 0; -+ -+ unsigned acc; -+ unsigned bitcount = right - left + 1; -+ -+ if (nbit) // starting position is not aligned -+ { -+ unsigned right_margin = nbit + (right - left); -+ -+ if (right_margin < 32) -+ { -+ unsigned mask = -+ block_set_table<true>::_right[nbit] & -+ block_set_table<true>::_left[right_margin]; -+ acc = *word & mask; -+ -+ BM_INCWORD_BITCOUNT(count, acc); -+ return count; -+ } -+ else -+ { -+ acc = *word & block_set_table<true>::_right[nbit]; -+ BM_INCWORD_BITCOUNT(count, acc); -+ bitcount -= 32 - nbit; -+ } -+ ++word; -+ } -+ -+ // now when we are word aligned, we can count bits the usual way -+ for ( ;bitcount >= 32; bitcount -= 32) -+ { -+ acc = *word++; -+ BM_INCWORD_BITCOUNT(count, acc); -+ } -+ -+ if (bitcount) // we have a tail to count -+ { -+ acc = (*word) & block_set_table<true>::_left[bitcount-1]; -+ BM_INCWORD_BITCOUNT(count, acc); -+ } -+ -+ return count; -+} -+ -+ - - /*! - \brief Compute bitcount of bit block AND masked by GAP block. -@@ -1825,6 +1891,72 @@ bm::id_t gap_bitset_and_count(const unsigned* block, const T* buf) - return count; - } - -+/*! -+ Function calculates if there is any number of 1 bits -+ in the given array of words in the range between left anf right bits -+ (borders included). Make sure the addresses are aligned. -+ -+ @ingroup bitfunc -+*/ -+inline -+bm::id_t bit_block_any_range(const bm::word_t* block, -+ bm::word_t left, -+ bm::word_t right) -+{ -+ BM_ASSERT(left <= right); -+ -+ unsigned nbit = left; // unsigned(left & bm::set_block_mask); -+ unsigned nword = unsigned(nbit >> bm::set_word_shift); -+ nbit &= bm::set_word_mask; -+ -+ const bm::word_t* word = block + nword; -+ -+ if (left == right) // special case (only 1 bit to check) -+ { -+ return (*word >> nbit) & 1; -+ } -+ unsigned acc; -+ unsigned bitcount = right - left + 1; -+ -+ if (nbit) // starting position is not aligned -+ { -+ unsigned right_margin = nbit + (right - left); -+ if (right_margin < 32) -+ { -+ unsigned mask = -+ block_set_table<true>::_right[nbit] & -+ block_set_table<true>::_left[right_margin]; -+ acc = *word & mask; -+ return acc; -+ } -+ else -+ { -+ acc = *word & block_set_table<true>::_right[nbit]; -+ if (acc) -+ return acc; -+ bitcount -= 32 - nbit; -+ } -+ ++word; -+ } -+ -+ // now when we are word aligned, we can check bits the usual way -+ for ( ;bitcount >= 32; bitcount -= 32) -+ { -+ acc = *word++; -+ if (acc) -+ return acc; -+ } -+ -+ if (bitcount) // we have a tail to count -+ { -+ acc = (*word) & block_set_table<true>::_left[bitcount-1]; -+ if (acc) -+ return acc; -+ } -+ -+ return 0; -+} -+ - - /*! - \brief Bitcount test of bit block AND masked by GAP block. -@@ -2939,137 +3071,6 @@ bm::id_t bit_block_calc_count_change(const bm::word_t* block, - } - - --/*! -- Function calculates number of 1 bits in the given array of words in -- the range between left anf right bits (borders included) -- Make sure the addresses are aligned. -- -- @ingroup bitfunc --*/ --inline --bm::id_t bit_block_calc_count_range(const bm::word_t* block, -- bm::word_t left, -- bm::word_t right) --{ -- BM_ASSERT(left <= right); -- unsigned nword, nbit; -- nbit = left & bm::set_word_mask; -- const bm::word_t* word = -- block + (nword = unsigned(left >> bm::set_word_shift)); -- if (left == right) // special case (only 1 bit to check) -- { -- return (*word >> nbit) & 1; -- } -- bm::id_t count = 0; -- -- unsigned acc; -- unsigned bitcount = right - left + 1; -- -- if (nbit) // starting position is not aligned -- { -- unsigned right_margin = nbit + (right - left); -- -- if (right_margin < 32) -- { -- unsigned mask = -- block_set_table<true>::_right[nbit] & -- block_set_table<true>::_left[right_margin]; -- acc = *word & mask; -- -- BM_INCWORD_BITCOUNT(count, acc); -- return count; -- } -- else -- { -- acc = *word & block_set_table<true>::_right[nbit]; -- BM_INCWORD_BITCOUNT(count, acc); -- bitcount -= 32 - nbit; -- } -- ++word; -- } -- -- // now when we are word aligned, we can count bits the usual way -- for ( ;bitcount >= 32; bitcount -= 32) -- { -- acc = *word++; -- BM_INCWORD_BITCOUNT(count, acc); -- } -- -- if (bitcount) // we have a tail to count -- { -- acc = (*word) & block_set_table<true>::_left[bitcount-1]; -- BM_INCWORD_BITCOUNT(count, acc); -- } -- -- return count; --} -- -- --/*! -- Function calculates if there is any number of 1 bits -- in the given array of words in the range between left anf right bits -- (borders included). Make sure the addresses are aligned. -- -- @ingroup bitfunc --*/ --inline --bm::id_t bit_block_any_range(const bm::word_t* block, -- bm::word_t left, -- bm::word_t right) --{ -- BM_ASSERT(left <= right); -- -- unsigned nbit = left; // unsigned(left & bm::set_block_mask); -- unsigned nword = unsigned(nbit >> bm::set_word_shift); -- nbit &= bm::set_word_mask; -- -- const bm::word_t* word = block + nword; -- -- if (left == right) // special case (only 1 bit to check) -- { -- return (*word >> nbit) & 1; -- } -- unsigned acc; -- unsigned bitcount = right - left + 1; -- -- if (nbit) // starting position is not aligned -- { -- unsigned right_margin = nbit + (right - left); -- if (right_margin < 32) -- { -- unsigned mask = -- block_set_table<true>::_right[nbit] & -- block_set_table<true>::_left[right_margin]; -- acc = *word & mask; -- return acc; -- } -- else -- { -- acc = *word & block_set_table<true>::_right[nbit]; -- if (acc) -- return acc; -- bitcount -= 32 - nbit; -- } -- ++word; -- } -- -- // now when we are word aligned, we can check bits the usual way -- for ( ;bitcount >= 32; bitcount -= 32) -- { -- acc = *word++; -- if (acc) -- return acc; -- } -- -- if (bitcount) // we have a tail to count -- { -- acc = (*word) & block_set_table<true>::_left[bitcount-1]; -- if (acc) -- return acc; -- } -- -- return 0; --} - - - -diff --git a/include/util/bitset/bmserial.h b/include/util/bitset/bmserial.h -index 519cd2b..00f6c01 100644 ---- a/include/util/bitset/bmserial.h -+++ b/include/util/bitset/bmserial.h -@@ -1381,7 +1381,7 @@ deserializer<BV, DEC>::deserialize_gap(unsigned char btype, decoder_type& dec, - case set_block_arrgap: - case set_block_arrgap_egamma: - { -- unsigned arr_len = read_id_list(dec, btype, this->id_array_); -+ unsigned arr_len = this->read_id_list(dec, btype, this->id_array_); - gap_len = gap_set_array(gap_temp_block_, this->id_array_, arr_len); - break; - } -@@ -1390,7 +1390,7 @@ deserializer<BV, DEC>::deserialize_gap(unsigned char btype, decoder_type& dec, - (sizeof(gap_word_t) == 2 ? dec.get_16() : dec.get_32()); - case set_block_arrgap_egamma_inv: - case set_block_arrgap_inv: -- gap_len = read_gap_block(dec, btype, gap_temp_block_, gap_head); -+ gap_len = this->read_gap_block(dec, btype, gap_temp_block_, gap_head); - break; - default: - BM_ASSERT(0); -@@ -2763,7 +2763,7 @@ serial_stream_iterator<DEC>::get_gap_block(bm::gap_word_t* dst_block) - this->block_type_ == set_block_bit_1bit); - BM_ASSERT(dst_block); - -- read_gap_block(this->decoder_, -+ this->read_gap_block(this->decoder_, - this->block_type_, - dst_block, - this->gap_head_); -diff --git a/include/util/linkedset.hpp b/include/util/linkedset.hpp -index 0d2cba1..1d09a28 100644 ---- a/include/util/linkedset.hpp -+++ b/include/util/linkedset.hpp -@@ -422,10 +422,10 @@ public: - { - iterator iter = m_Container.insert(value); - if ( iter == begin() ) -- insertToStart(get(iter)); -+ this->insertToStart(get(iter)); - else { - iterator prev = iter; -- insertAfter(get(--prev), get(iter)); -+ this->insertAfter(get(--prev), get(iter)); - } - return iter; - } -@@ -433,10 +433,10 @@ public: - void erase(iterator iter) - { - if ( iter == begin() ) -- removeFromStart(get(iter)); -+ this->removeFromStart(get(iter)); - else { - iterator prev = iter; -- removeAfter(get(--prev), get(iter)); -+ this->removeAfter(get(--prev), get(iter)); - } - m_Container.erase(iter); - } -diff --git a/include/util/rangemap.hpp b/include/util/rangemap.hpp -index 22cf3dd..b30b39d 100644 ---- a/include/util/rangemap.hpp -+++ b/include/util/rangemap.hpp -@@ -640,7 +640,7 @@ public: - // insert element - iterator ret; - ret.m_Range = range_type::GetWhole(); -- ret.m_SelectIter = insertLevel(selectKey); -+ ret.m_SelectIter = this->insertLevel(selectKey); - ret.m_SelectIterEnd = this->m_SelectMap.end(); - ret.m_LevelIter = ret.m_SelectIter->second.insert(value); - return ret; -diff --git a/src/algo/blast/gumbel_params/njn_approx.hpp b/src/algo/blast/gumbel_params/njn_approx.hpp -index a79da93..5909cdf 100644 ---- a/src/algo/blast/gumbel_params/njn_approx.hpp -+++ b/src/algo/blast/gumbel_params/njn_approx.hpp -@@ -38,6 +38,7 @@ Contents: - - #include <corelib/ncbistl.hpp> - #include <float.h> -+#include <math.h> - - BEGIN_NCBI_SCOPE - BEGIN_SCOPE(blast) -diff --git a/src/algo/blast/gumbel_params/sls_alp_data.hpp b/src/algo/blast/gumbel_params/sls_alp_data.hpp -index 5cee936..9ff4a4c 100644 ---- a/src/algo/blast/gumbel_params/sls_alp_data.hpp -+++ b/src/algo/blast/gumbel_params/sls_alp_data.hpp -@@ -44,6 +44,7 @@ Contents: Contains input data - #include <float.h> - #include <ctime> - #include <stdlib.h> -+#include <math.h> - #include <limits> - - #ifndef NCBI_OS_MSWIN -diff --git a/src/serial/stdtypes.cpp b/src/serial/stdtypes.cpp -index 6eb0ac3..cdf5356 100644 ---- a/src/serial/stdtypes.cpp -+++ b/src/serial/stdtypes.cpp -@@ -720,7 +720,7 @@ public: - if ( IsSigned() ) { - // signed -> unsigned - // check for negative value -- if ( IsNegative(value) ) -+ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(value) ) - ThrowIntegerOverflow(); - } - if ( sizeof(value) > sizeof(result) ) { -@@ -751,7 +751,7 @@ public: - // unsigned -> signed - if ( sizeof(value) == sizeof(result) ) { - // same size - check for sign change only -- if ( IsNegative(result) ) -+ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(result) ) - ThrowIntegerOverflow(); - } - } -@@ -786,7 +786,7 @@ public: - if ( IsSigned() ) { - // signed -> unsigned - // check for negative value -- if ( IsNegative(value) ) -+ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(value) ) - ThrowIntegerOverflow(); - } - if ( sizeof(value) > sizeof(result) ) { -@@ -817,7 +817,7 @@ public: - // unsigned -> signed - if ( sizeof(value) == sizeof(result) ) { - // same size - check for sign change only -- if ( IsNegative(result) ) -+ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(result) ) - ThrowIntegerOverflow(); - } - } |