1 files changed, 82 insertions, 0 deletions
diff --git a/biology/ssaha/files/patch-GlobalDefinitions.h b/biology/ssaha/files/patch-GlobalDefinitions.h
new file mode 100644
index 000000000000..fb7851574cc7
--- /dev/null
+++ b/biology/ssaha/files/patch-GlobalDefinitions.h
@@ -0,0 +1,82 @@
+--- ./Global/GlobalDefinitions.h.orig	2004-03-01 13:51:28.000000000 -0300
++++ ./Global/GlobalDefinitions.h	2008-06-12 15:39:31.000000000 -0300
+@@ -726,8 +726,6 @@
+ template <typename T> class Allocator
+ {
+ public:
+-  typedef T MyType;
+-
+   Allocator( T** ptr, const string& name, ostream& monStream=cerr ) : 
+     ptr_(ptr), name_(name), size_(0), isAllocated_(false), 
+     monStream_( monStream )
+@@ -788,32 +786,34 @@
+  
+   virtual void allocate( unsigned long size )
+   {
+-    size_=size;
+-    (*ptr_)=new T[size_];
+-    isAllocated_=true;
++    Allocator<T>::size_=size;
++    (*Allocator<T>::ptr_)=new T[Allocator<T>::size_];
++    Allocator<T>::isAllocated_=true;
+   }
+ 
+   virtual void allocateAndZero( unsigned long size ) 
+   {
+     const unsigned char zero(0);
+     allocate(size);
+-    memset( (void*)(*ptr_), zero, size_*sizeof(MyType) );
++    memset( (void*)(*Allocator<T>::ptr_), zero, Allocator<T>::size_*sizeof(T) );
+   }
+   virtual void load( unsigned long size )
+   {
+     allocate(size);
+-    loadFromFile( name_, (char*)(*ptr_), size_*sizeof(MyType), monStream_ );
++    loadFromFile( Allocator<T>::name_, (char*)(*Allocator<T>::ptr_),
++        Allocator<T>::size_*sizeof(T), Allocator<T>::monStream_ );
+   }
+   virtual void save()
+   {
+-    saveToFile( name_, (char*)(*ptr_), size_*sizeof(MyType), monStream_ );
++    saveToFile( Allocator<T>::name_, (char*)(*Allocator<T>::ptr_),
++        Allocator<T>::size_*sizeof(T), Allocator<T>::monStream_ );
+   }
+ 
+   virtual void deallocate()
+   {
+-    if (!isAllocated_) return;
+-    delete [] (*ptr_);
+-    isAllocated_=false;
++    if (!Allocator<T>::isAllocated_) return;
++    delete [] (*Allocator<T>::ptr_);
++    Allocator<T>::isAllocated_=false;
+   }
+ protected:
+ };
+@@ -892,7 +892,7 @@
+     if (isAllocated_) return;
+     mode_ = MemoryMapper::createMap;
+     size_ = size;
+-    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(MyType));
++    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(T));
+     isAllocated_ = true;
+   }
+ 
+@@ -908,7 +908,7 @@
+     if (isAllocated_) return;
+     mode_ = MemoryMapper::readMap;
+     size_ = size;
+-    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(MyType));
++    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(T));
+     isAllocated_ = true;
+   }
+ 
+@@ -921,7 +921,7 @@
+   virtual void deallocate()
+   {
+     if (!isAllocated_) return;
+-    if(munmap((caddr_t)(*ptr_), size_*sizeof(MyType)) < 0)
++    if(munmap((caddr_t)(*ptr_), size_*sizeof(T)) < 0)
+       perror("unmap error"); // don't throw - called from destructor!
+     close(fileDesc_);
+     if (mode_.deleteFileOnExit) shm_unlink(name_.c_str());