gentoo-overlay/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch

 libMems/CompactGappedAlignment.h | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/libMems/CompactGappedAlignment.h b/libMems/CompactGappedAlignment.h
index bf78477..942d4aa 100644
--- a/libMems/CompactGappedAlignment.h
+++ b/libMems/CompactGappedAlignment.h
@@ -13,7 +13,7 @@
 #include "config.h"
 #endif
 
-#include "libGenome/gnDebug.h"
+#include "libGenome/gnDebug.h"
 #include "libGenome/gnFilter.h"
 #include "libGenome/gnSequence.h"
 #include "libMems/SparseAbstractMatch.h"
@@ -103,15 +103,15 @@ public:
 	/** Eliminates any columns that contain only gap characters */
 	void CondenseGapColumns();
 
-	void swap( CompactGappedAlignment& other ){ swap(&other); }
-
-protected:
-	// for use by derived classes in order to swap contents
-	void swap( CompactGappedAlignment* other ){
-		std::swap( align_matrix, other->align_matrix );
-		std::swap( bcount, other->bcount );
-		BaseType::swap( other );
-	}
+	void swap( CompactGappedAlignment& other ){ swap(&other); }
+
+protected:
+	// for use by derived classes in order to swap contents
+	void swap( CompactGappedAlignment* other ){
+		std::swap( align_matrix, other->align_matrix );
+		std::swap( bcount, other->bcount );
+		BaseType::swap( other );
+	}
 
 	std::vector< bitset_t > align_matrix;		/**< aligned positions have true values, gaps are false */
 	std::vector< std::vector< size_t > > bcount;
@@ -572,7 +572,7 @@ void CompactGappedAlignment<BaseType>::CropEnd(gnSeqI crop_amount){
 			this->SetStart(i, 0);
 		}
 	}
-	SetAlignmentLength( this->AlignmentLength() - crop_amount );
+	this->SetAlignmentLength( this->AlignmentLength() - crop_amount );
 	this->create_bitcount();
 	if( !this->validate() )
 		std::cerr << "CropEnd error\n";
@@ -806,13 +806,13 @@ void CompactGappedAlignment<BaseType>::CondenseGapColumns()
 
 }
 
-namespace std {
-template<> inline
-void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b )
-{
-	a.swap(b);
-}
-}
+namespace std {
+template<> inline
+void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b )
+{
+	a.swap(b);
+}
+}
 
 
 #endif // __CompactGappedAlignment_h__