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;
   }
 };