/[gentoo-x86]/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
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Contents of /sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch

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Revision 1.3 - (show annotations) (download)
Wed Nov 20 07:29:19 2013 UTC (16 months, 1 week ago) by jlec
Branch: MAIN
CVS Tags: HEAD
Changes since 1.2: +0 -0 lines
FILE REMOVED
superseeded by sci-biology/allpathslg
Upstream wants anybody to move over

1 MakeDepend.cc | 1 +
2 Vec.h | 12 ++++++------
3 feudal/BinaryStream.h | 4 ++++
4 feudal/FeudalControlBlock.cc | 1 +
5 feudal/FeudalFileReader.h | 1 +
6 feudal/MasterVec.h | 14 +++++++-------
7 feudal/SerfVec.h | 4 ++--
8 reporting/ScaffoldLayout.cc | 10 +++++-----
9 system/ProcBuf.cc | 12 ++++++------
10 9 files changed, 33 insertions(+), 26 deletions(-)
11
12 diff --git a/MakeDepend.cc b/MakeDepend.cc
13 index 93032e8..619e6f7 100644
14 --- a/MakeDepend.cc
15 +++ b/MakeDepend.cc
16 @@ -25,6 +25,7 @@
17 #include <iterator>
18 #include <iostream>
19 #include <ctype.h>
20 +#include <unistd.h>
21
22 using namespace std;
23
24 diff --git a/Vec.h b/Vec.h
25 index f26f3f4..e2d26a4 100644
26 --- a/Vec.h
27 +++ b/Vec.h
28 @@ -259,11 +259,11 @@ template <class T> class vec : public vector<T> {
29
30 template <class U>
31 void append( const vec<U>& y )
32 - { insert( this->end( ), y.begin( ), y.end( ) ); }
33 + { this->insert( this->end( ), y.begin( ), y.end( ) ); }
34
35 void append( const vec<T>& y, size_type i, size_type j ) {
36 - if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
37 - else insert( this->end( ), y.begin( ) + i, y.begin( ) + j );
38 + if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) );
39 + else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j );
40 }
41
42 // appends values in y, but only those whose indices are in entries
43 @@ -339,7 +339,7 @@ template <class T> class vec : public vector<T> {
44
45 void SetToRangeOf( const vec<T>& v, size_type i, size_type j ) {
46 AssertLe( i, j );
47 - assign(v.begin() + i, v.begin() + j);
48 + this->assign(v.begin() + i, v.begin() + j);
49 }
50
51 inline friend vec<T> RangeOf( const vec<T>& v, size_type i, size_type j ) {
52 @@ -397,12 +397,12 @@ template <class T> class vec : public vector<T> {
53 /// Erase: erase range of elements, where range is given by half-open interval.
54
55 void Erase( size_type start, size_type stop ) {
56 - erase( this->begin( ) + start, this->begin( ) + stop );
57 + this->erase( this->begin( ) + start, this->begin( ) + stop );
58 }
59
60 /// EraseValue: erase all entries having the given value.
61 void EraseValue( const T& x ) {
62 - erase(remove(this->begin(), this->end(), x), this->end());
63 + this->erase(remove(this->begin(), this->end(), x), this->end());
64 }
65
66 /// print values to ostream, separated by sep.
67 diff --git a/feudal/BinaryStream.h b/feudal/BinaryStream.h
68 index f54d8a9..c61469b 100644
69 --- a/feudal/BinaryStream.h
70 +++ b/feudal/BinaryStream.h
71 @@ -144,6 +144,10 @@ private:
72 std::ostream& mOS;
73 };
74
75 +template <typename T1, typename T2>
76 +inline size_t serializedSizeof( std::pair<T1,T2>* );
77 +
78 +
79 /// Reader of binary streams.
80 class BinaryReader
81 {
82 diff --git a/feudal/FeudalControlBlock.cc b/feudal/FeudalControlBlock.cc
83 index bc64ecd..a709320 100644
84 --- a/feudal/FeudalControlBlock.cc
85 +++ b/feudal/FeudalControlBlock.cc
86 @@ -24,6 +24,7 @@
87 #include <string.h>
88 #include <errno.h>
89 #include <iostream>
90 +#include <unistd.h>
91
92 using std::cout;
93 using std::endl;
94 diff --git a/feudal/FeudalFileReader.h b/feudal/FeudalFileReader.h
95 index b71bf6d..073a1a1 100644
96 --- a/feudal/FeudalFileReader.h
97 +++ b/feudal/FeudalFileReader.h
98 @@ -13,6 +13,7 @@
99 #include <string>
100 #include <cassert>
101 #include <sstream>
102 +#include <unistd.h>
103 #include "feudal/BinaryStream.h"
104
105 /**
106 diff --git a/feudal/MasterVec.h b/feudal/MasterVec.h
107 index e6477d9..b88e9fe 100644
108 --- a/feudal/MasterVec.h
109 +++ b/feudal/MasterVec.h
110 @@ -60,20 +60,20 @@ public:
111 /// This function is deprecated: Use reserve() instead.
112 /// The pool size argument is ignored, anyway.
113 MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
114 - { reserve(capacity); return *this; }
115 + { this->reserve(capacity); return *this; }
116
117 /// This function is deprecated: Use clear().shrink_to_fit().
118 MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
119
120 /// This function is deprecated: Use push_back().
121 MasterVec& push_back_external( T const& val )
122 - { push_back(val); return *this; }
123 + { this->push_back(val); return *this; }
124
125 /// This function is deprecated: Use push_back().
126 MasterVec& push_back_reserve( T const& val,
127 size_type growthIncr = 0,
128 float growthFact = 1.3f )
129 - { push_back(val,growthFact,growthIncr); return *this; }
130 + { this->push_back(val,growthFact,growthIncr); return *this; }
131
132 /// This function is deprecated: Use append().
133 MasterVec& Append( MasterVec const& that )
134 @@ -81,7 +81,7 @@ public:
135
136 /// This function is deprecated: Use append().
137 MasterVec& Append( MasterVec const& that, size_type from, size_type to )
138 - { append(that.begin(from),that.begin(to)); return *this; }
139 + { this->append(that.begin(from),that.begin(to)); return *this; }
140
141 MasterVec const& WriteAll( String const& fileName ) const
142 { return WriteRange(fileName,0UL,BaseT::size()); return *this; }
143 @@ -99,7 +99,7 @@ public:
144 { if ( !append ) BaseT::clear();
145 FeudalFileReader rdr(fileName.c_str(),T::fixedDataLen());
146 size_type siz = rdr.getNElements();
147 - reserve(BaseT::size()+siz);
148 + this->reserve(BaseT::size()+siz);
149 for ( size_type iii = 0; iii < siz; ++iii )
150 appendFromReader(rdr,iii);
151 return *this; }
152 @@ -148,7 +148,7 @@ public:
153 vec<int> const& entries,
154 int /*extra*/ = 0, Bool /*pre_reserved*/ = False )
155 { VirtualMasterVec<T> vVec(fileName.c_str());
156 - if ( BaseT::size() < vVec.size() ) resize(vVec.size());
157 + if ( BaseT::size() < vVec.size() ) this->resize(vVec.size());
158 vec<int>::const_iterator end(entries.end());
159 for ( vec<int>::const_iterator itr(entries.begin()); itr != end; ++itr )
160 { BaseT::operator[](*itr) = vVec[*itr]; }
161 @@ -158,7 +158,7 @@ public:
162 size_t from, size_t to,
163 int /* extra */ = 0 )
164 { VirtualMasterVec<T> vVec(fileName.c_str());
165 - if ( BaseT::size() < vVec.size() ) resize(vVec.size());
166 + if ( BaseT::size() < vVec.size() ) this->resize(vVec.size());
167 for ( ; from < to; ++from ) (*this)[from] = vVec[from];
168 return *this; }
169
170 diff --git a/feudal/SerfVec.h b/feudal/SerfVec.h
171 index e91847c..d5f053d 100644
172 --- a/feudal/SerfVec.h
173 +++ b/feudal/SerfVec.h
174 @@ -79,10 +79,10 @@ public:
175 /// Deprecated: Use assign().
176 SerfVec& SetToSubOf( SerfVec const& that, size_type pos, size_type len )
177 { if ( this != &that )
178 - { assign(that.begin(pos),that.begin(pos+len)); }
179 + { this->assign(that.begin(pos),that.begin(pos+len)); }
180 else
181 { assert(that.size()>=pos+len);
182 - erase(BaseT::begin(),BaseT::begin(pos));
183 + this->erase(BaseT::begin(),BaseT::begin(pos));
184 BaseT::resize(len); }
185 return *this; }
186
187 diff --git a/reporting/ScaffoldLayout.cc b/reporting/ScaffoldLayout.cc
188 index 7c39718..646b106 100644
189 --- a/reporting/ScaffoldLayout.cc
190 +++ b/reporting/ScaffoldLayout.cc
191 @@ -66,13 +66,13 @@ int main(int argc, char **argv)
192 // This version finds the first and last non-ambiguous sequences of
193 // END_SIZE_MIN <= length <= end_size_max
194 // --bruce
195 - int j, k;
196 + int l, k;
197 int end_size_max = min(END_SIZE_MAX, scaffold_size/2);
198 - for (j = k = 0; k < scaffold_size; k++) {
199 + for (l = k = 0; k < scaffold_size; k++) {
200 if (assembly_amb[i][k]) {
201 - if (k-j >= END_SIZE_MIN) break;
202 - else j = k+1;
203 - } else if (k-j >= end_size_max) break;
204 + if (k-l >= END_SIZE_MIN) break;
205 + else l = k+1;
206 + } else if (k-l >= end_size_max) break;
207 }
208 e.SetToSubOf( assembly[i], j, k-j );
209 ENDS.push_back_reserve(e);
210 diff --git a/system/ProcBuf.cc b/system/ProcBuf.cc
211 index 748cc6b..5b91ed3 100644
212 --- a/system/ProcBuf.cc
213 +++ b/system/ProcBuf.cc
214 @@ -189,12 +189,12 @@ basic_procbuf<charT,traits>::overflow( int_type c )
215 Assert(M_internal_put_buffer == NULL);
216 M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE];
217 M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE;
218 - setp(M_internal_put_buffer,
219 + this->setp(M_internal_put_buffer,
220 M_internal_put_buffer_end);
221 } else if (!flush())
222 return traits_type::eof();
223 if (!traits_type::eq_int_type(c, traits_type::eof()))
224 - return sputc(c);
225 + return this->sputc(c);
226 else
227 return traits_type::not_eof(c);
228 }
229 @@ -234,7 +234,7 @@ basic_procbuf<charT,traits>::pbackfail( int_type c )
230 // (which is start of buffer)
231 std::copy_backward(this->eback(), this->egptr(), this->egptr()+1);
232 *(this->gptr()) = traits_type::to_char_type(c);
233 - setg(this->eback(), this->gptr(), this->egptr()+1);
234 + this->setg(this->eback(), this->gptr(), this->egptr()+1);
235 return traits_type::not_eof(c);
236 } else
237 return traits_type::eof();
238 @@ -263,7 +263,7 @@ basic_procbuf<charT,traits>::flush( )
239 // doing wchars and we write an odd # of bytes?
240 return false;
241 } else {
242 - setp(this->pbase(), this->epptr());
243 + this->setp(this->pbase(), this->epptr());
244 return true;
245 }
246 }
247 @@ -277,7 +277,7 @@ basic_procbuf<charT,traits>::fill( )
248 Assert(M_internal_get_buffer == NULL);
249 M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE];
250 M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE;
251 - setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
252 + this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
253 }
254 // The "get" pointer should be at the end of the buffer - that's
255 // why we need to fill it.
256 @@ -312,7 +312,7 @@ basic_procbuf<charT,traits>::fill( )
257 //
258 // reset the get pointers
259 //
260 - setg(M_internal_get_buffer,
261 + this->setg(M_internal_get_buffer,
262 M_internal_get_buffer,
263 M_internal_get_buffer+numusable/sizeof(char_type));
264 return true;

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