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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__
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