diff options
Diffstat (limited to 'sci-biology/lagan/files/lagan-2.0-fix-c++14.patch')
| -rw-r--r-- | sci-biology/lagan/files/lagan-2.0-fix-c++14.patch | 473 |
1 files changed, 0 insertions, 473 deletions
diff --git a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch deleted file mode 100644 index 9865f2756c5a..000000000000 --- a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch +++ /dev/null @@ -1,473 +0,0 @@ -Fix building with C++14, which errors out due to namespace collisions with std::end -in C++14 mode, due to crappy 'using namespace std' declared everywhere. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594148 - ---- a/src/ancseq.cpp -+++ b/src/ancseq.cpp -@@ -30,7 +30,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - #include "util.cpp" - #include "faindex.cpp" ---- a/src/ancseqrest.cpp -+++ b/src/ancseqrest.cpp -@@ -31,7 +31,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - #define fastaRowLength 50 - typedef char* pchar; ---- a/src/cutmfa.cpp -+++ b/src/cutmfa.cpp -@@ -45,7 +45,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - // TODO refactor in classes and normal make project - ---- a/src/glocal/glocal.cpp -+++ b/src/glocal/glocal.cpp -@@ -7,9 +7,9 @@ - } - - //vectors that would be needed globally --vector<Fragment> fragments; --vector<Point>startPoints; --vector<Point>endPoints; -+std::vector<Fragment> fragments; -+std::vector<Point>startPoints; -+std::vector<Point>endPoints; - long long int numFragments; - InterPoint inter; - -@@ -19,7 +19,7 @@ - RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - --vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; -+std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - - Name allNames; - ---- a/src/glocal/io.cpp -+++ b/src/glocal/io.cpp -@@ -3,9 +3,9 @@ - #include<io.h> - #include<algorithm> - --extern vector <Fragment> fragments; --extern vector <Point> startPoints; --extern vector <Point> endPoints; -+extern std::vector <Fragment> fragments; -+extern std::vector <Point> startPoints; -+extern std::vector <Point> endPoints; - extern Name allNames; - - bool PointCompare(const Point &f1, const Point &f2) { -@@ -223,8 +223,8 @@ - startPoints.push_back(startPoint); - endPoints.push_back(endPoint); - } -- sort(startPoints.begin(), startPoints.end(), PointCompare); -- sort(endPoints.begin(), endPoints.end(), PointCompare); -+ std::sort(startPoints.begin(), startPoints.end(), PointCompare); -+ std::sort(endPoints.begin(), endPoints.end(), PointCompare); - } - - ---- a/src/glocal/leftinfluence.cpp -+++ b/src/glocal/leftinfluence.cpp -@@ -154,8 +154,8 @@ - - if (second->score == -1) { return TRUE; } - -- dummy.seq1Start = max(first->seq1End, second->seq1End) + 2; -- dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; -+ dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2; -+ dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; - - if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) { - dummy.nameIter = first->nameIter; -@@ -444,7 +444,7 @@ - temp.seq1 = col - diag; - temp.seq2 = col; - -- pair<Point,LI*> pairp(temp, LeftInfluence); -+ std::pair<Point,LI*> pairp(temp, LeftInfluence); - tempinter = inter.insert(pairp); - - colInter->second = tempinter; ---- a/src/glocal/leftinfluence.h -+++ b/src/glocal/leftinfluence.h -@@ -39,15 +39,15 @@ - - - --typedef list<Fragment*> Owner; --typedef map <long long int ,Owner::iterator,longlongCompare2> CBound; -+typedef std::list<Fragment*> Owner; -+typedef std::map <long long int ,Owner::iterator,longlongCompare2> CBound; - --typedef multimap <Point ,struct LI *,paircomp> InterPoint; -+typedef std::multimap <Point ,struct LI *,paircomp> InterPoint; - --typedef map <long long int ,InterPoint::iterator,longlongCompare2> CInter; --typedef map <long long int,Owner::iterator,longlongCompare2> DBound; -+typedef std::map <long long int ,InterPoint::iterator,longlongCompare2> CInter; -+typedef std::map <long long int,Owner::iterator,longlongCompare2> DBound; - --typedef map <long long int,InterPoint::iterator,longlongCompare2> DInter; -+typedef std::map <long long int,InterPoint::iterator,longlongCompare2> DInter; - - - ---- a/src/glocal/rightinfluence.h -+++ b/src/glocal/rightinfluence.h -@@ -17,7 +17,7 @@ - }; - - --typedef map<const long long int , Fragment*,longlongCompare> Active; -+typedef std::map<const long long int , Fragment*,longlongCompare> Active; - - typedef struct RI { - //List of active regions ---- a/src/glocal/score.cpp -+++ b/src/glocal/score.cpp -@@ -4,7 +4,7 @@ - #include<rightinfluence.h> - #include<fstream> - --extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; -+extern std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; - - - float Score::getScore(Fragment *up, Fragment * down) { -@@ -36,7 +36,7 @@ - - - void initScoreFunctionPointers(char * scoreFileName) { -- ifstream SFP; -+ std::ifstream SFP; - char line[255]; - - SFP.open(scoreFileName); ---- a/src/glocal/structs.h -+++ b/src/glocal/structs.h -@@ -12,7 +12,6 @@ - #include <list> - #include <string.h> - --using namespace std; - - #define RIGHT 0 - #define LEFT 1 -@@ -49,7 +48,7 @@ - }; - - --typedef map<const char*,long long int ,ltstr> Name; -+typedef std::map<const char*,long long int ,ltstr> Name; - - - typedef struct Fragment { ---- a/src/lagan2mfa.cpp -+++ b/src/lagan2mfa.cpp -@@ -6,7 +6,6 @@ - #include <stdlib.h> - #include <stdio.h> - --using namespace std; - - // TODO refactor in classes and normal make project - ---- a/src/makecons.cpp -+++ b/src/makecons.cpp -@@ -18,7 +18,6 @@ - #include <ctype.h> - #include <time.h> - --using namespace std; - - #define fastaRowLength 50 - #define bufSize 2000 ---- a/src/utils/Glue.cpp -+++ b/src/utils/Glue.cpp -@@ -170,7 +170,7 @@ - } - - void printCoordinates (int seq, int begin, int end){ -- cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; -+ std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; - } - - int printRegion (int begin, int end){ -@@ -183,7 +183,7 @@ - score += rescoreRegion (seqs[i], seqs[j], begin, end); - } - } -- cout << score << endl; -+ std::cout << score << std::endl; - return score; - } - -@@ -223,7 +223,7 @@ - } - } - -- cout << "= score=" << score << endl; -+ std::cout << "= score=" << score << std::endl; - } - - int countLets (SafeVector<char> &data){ -@@ -355,7 +355,7 @@ - FILE* outfile; - - if (argc < 2 || argc > 3){ -- cerr << "Usage: Glue align.mfa \n" << endl; -+ std::cerr << "Usage: Glue align.mfa \n" << std::endl; - exit (1); - } - -@@ -375,7 +375,7 @@ - SafeVector<int> merged1label, merged2label; - int begin1 = 1, end1 = 1; - -- ifstream data (argv[1]); -+ std::ifstream data (argv[1]); - int alignNum = 0; - strand.push_back ('?'); // nothing for alignNum 0 - -@@ -452,7 +452,7 @@ - SafeVector<char> temp1 (begin1 - 1, 'N'); - SafeVector<char> temp2 (begin1 - 1, '-'); - -- for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++) -+ for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++) - temp2[i] = 'N'; - - merged1 = merge (temp1, merged1); -@@ -471,12 +471,12 @@ - if (isalpha(merged2[j])) pos2++; - - if (merged1label[j] == i){ -- min1 = min (min1, pos1); -- max1 = max (max1, pos1); -+ min1 = std::min (min1, pos1); -+ max1 = std::max (max1, pos1); - } - if (merged2label[j] == i){ -- min2 = min (min2, pos2); -- max2 = max (max2, pos2); -+ min2 = std::min (min2, pos2); -+ max2 = std::max (max2, pos2); - } - } - -@@ -489,6 +489,6 @@ - fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2); - } - -- printMFA (cout, merged1, string ("first"), 60); -- printMFA (cout, merged2, string ("second"), 60); -+ printMFA (std::cout, merged1, std::string ("first"), 60); -+ printMFA (std::cout, merged2, std::string ("second"), 60); - } ---- a/src/utils/MultiSequence.h -+++ b/src/utils/MultiSequence.h -@@ -12,7 +12,6 @@ - #include "Sequence.h" - #include "SafeVector.h" - --using namespace std; - - class MultiSequence { - private: -@@ -54,10 +53,10 @@ - - // Read in all of the Sequences in an MFA file and append them to the - // existing MultiSequence object. -- void addRawFromMFA (const string& filename){ -+ void addRawFromMFA (const std::string& filename){ - - // open up file for reading -- ifstream infile (filename.c_str()); -+ std::ifstream infile (filename.c_str()); - - // check for error - assert (!infile.fail()); -@@ -75,7 +74,7 @@ - - // Read in all of the Sequences in an MFA file and append them to the - // existing MultiSequence object. -- void addRawFromMFA (ifstream &infile){ -+ void addRawFromMFA (std::ifstream &infile){ - - // check for error - assert (!infile.fail()); -@@ -89,7 +88,7 @@ - } - - // Writes sequences to outfile in XMFA format. -- void writeToXMFA (ostream &outfile, int numColumns) const { -+ void writeToXMFA (std::ostream &outfile, int numColumns) const { - for (int i = 0; i < (int) sequences.size(); ++i){ - sequences[i].writeToXMFA (outfile, numColumns); - } ---- a/src/utils/Output.h -+++ b/src/utils/Output.h -@@ -2,18 +2,18 @@ - #define OUTPUT_H - - // print reversed string in MFA format --void printMFA (ostream &outfile, SafeVector<char> &data, string comment, int numColumns){ -+void printMFA (std::ostream &outfile, SafeVector<char> &data, std::string comment, int numColumns){ - - int charsWritten = 0; - -- outfile << ">" << comment << endl; -+ outfile << ">" << comment << std::endl; - for (int i = 0; i < (int) data.size(); i++){ - outfile << data[i]; - charsWritten++; -- if (charsWritten % numColumns == 0) outfile << endl; -+ if (charsWritten % numColumns == 0) outfile << std::endl; - } - -- if (charsWritten % numColumns != 0) outfile << endl; -+ if (charsWritten % numColumns != 0) outfile << std::endl; - } - - ---- a/src/utils/SafeVector.h -+++ b/src/utils/SafeVector.h -@@ -10,7 +10,6 @@ - #include <assert.h> - #include <vector> - --using namespace std; - - // class derived from the STL std::vector - template<class TYPE> -@@ -19,9 +18,9 @@ - - // miscellaneous constructors - SafeVector () {} -- SafeVector (size_t size) : vector<TYPE>(size) {} -- SafeVector (size_t size, const TYPE &value) : vector<TYPE>(size, value) {} -- SafeVector (const SafeVector &source) : vector<TYPE>(source) {} -+ SafeVector (size_t size) : std::vector<TYPE>(size) {} -+ SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {} -+ SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {} - - #ifdef ENABLE_CHECKS - ---- a/src/utils/Sequence.h -+++ b/src/utils/Sequence.h -@@ -8,15 +8,14 @@ - #include <string> - #include "SafeVector.h" - --using namespace std; - - class Sequence { - - private: - - // Read header of MFA/XMFA file. -- bool readHeader (ifstream &infile, bool &isXMFA){ -- string header; -+ bool readHeader (std::ifstream &infile, bool &isXMFA){ -+ std::string header; - - while (true){ - -@@ -24,7 +23,7 @@ - if (infile.fail() || infile.eof()) return false; - - // get new header line -- getline (infile, header); -+ std::getline (infile, header); - - // check that header line is not empty - if (header.length() != 0) break; -@@ -64,7 +63,7 @@ - int startCoord; // sequence position of first character - int endCoord; // sequence position of last character - char direction; // + or - -- string comment; // comments -+ std::string comment; // comments - - public: - -@@ -77,7 +76,7 @@ - } - - // Constructor. Reads in a sequence from the input file. -- Sequence (ifstream &infile){ -+ Sequence (std::ifstream &infile){ - - bool isXMFA = true; - -@@ -147,7 +146,7 @@ - } - - // Constructor. Gets sequence from array data. -- Sequence (SafeVector<char> data, string comment) : data(data), comment(comment) { -+ Sequence (SafeVector<char> data, std::string comment) : data(data), comment(comment) { - length = data.size() - 1; - id = 0; - startCoord = 1; -@@ -165,7 +164,7 @@ - return temp; - } - -- const string getComment () const { -+ const std::string getComment () const { - return comment; - } - -@@ -197,9 +196,9 @@ - const int getEndCoord () const { assert (isValid); return endCoord; } - - // Print XMFA header only. -- void writeXMFAHeader (ostream &outfile) const { -+ void writeXMFAHeader (std::ostream &outfile) const { - assert (isValid); -- outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; -+ outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl; - } - - // Return sequence ID. -@@ -209,20 +208,20 @@ - void setID (int id) { assert (isValid); this->id = id; } - - // Writes sequence to XMFA format. -- void writeToXMFA (ostream &outfile, int numColumns) const { -+ void writeToXMFA (std::ostream &outfile, int numColumns) const { - - assert (isValid); - - // print XMFA header -- outfile << ">" << comment << endl; -+ outfile << ">" << comment << std::endl; - // outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; - - // print character data - for (int i = 1; i <= length; ++i){ - outfile << data[i]; -- if (i % numColumns == 0) outfile << endl; -+ if (i % numColumns == 0) outfile << std::endl; - } -- if (length % numColumns != 0) outfile << endl; -+ if (length % numColumns != 0) outfile << std::endl; - } - }; - |