1 files changed, 0 insertions, 77 deletions
diff --git a/biology/ssaha/files/patch-HashTableTranslated.cpp b/biology/ssaha/files/patch-HashTableTranslated.cpp
deleted file mode 100644
index e4ab9af82423..000000000000
--- a/biology/ssaha/files/patch-HashTableTranslated.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
---- ./HashTable/HashTableTranslated.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./HashTable/HashTableTranslated.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -50,9 +50,9 @@
-  		   Allocator<PositionPacked>& hitListAllocator,
- 		   Allocator<PositionInHitList>& arrayAllocator 
- 		   ):
--  queryFrame_(0),
-   HashTablePacked( monitoringStream, name, 
--		   hitListAllocator, arrayAllocator  ) 
-+		   hitListAllocator, arrayAllocator  ), 
-+  queryFrame_(0)
- {
-   hitListFormat_ = g32BitPackedProtein;
-   bitsPerSymbol_ = gResidueBits;
-@@ -135,12 +135,12 @@
-   Allocator<PositionPacked>& hitListAllocator,
-   Allocator<PositionInHitList>& arrayAllocator 
-   ):
-+  HashTablePacked( monitoringStream, name, 
-+		     hitListAllocator, arrayAllocator  ),
-+  codonEncoder_(5),
-   queryFrame_(0),
-   queryMult_(1),
--  codonEncoder_(5),
--  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein ),
--  HashTablePacked( monitoringStream, name, 
--		     hitListAllocator, arrayAllocator  ) 
-+  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein )
- {
-     hitListFormat_ = g32BitPackedProtein;
-     bitsPerSymbol_ = gResidueBits;
-@@ -249,14 +249,14 @@
-   Allocator<PositionPacked>& hitListAllocator,
-   Allocator<PositionInHitList>& arrayAllocator
-   ) :
-+  HashTableGeneric( monitoringStream, name, arrayAllocator ),
-   hashFwd_( monitoringStream, name+(string)"_fwd", 
- 	    hitListAllocator, arrayAllocator ),
-   hashRev_( monitoringStream, name+(string)"_rev", 
- 	    hitListAllocator, arrayAllocator ),
-   pHash_(&hashFwd_),
-   codonEncoder_(5),
--  pMatchSequence_( &HashTableTranslated::matchSequenceProtein ),
--  HashTableGeneric( monitoringStream, name, arrayAllocator ) 
-+  pMatchSequence_( &HashTableTranslated::matchSequenceProtein )
- {
-   bitsPerSymbol_=gResidueBits;
-   hitListFormat_ = gTranslated;
-@@ -344,8 +344,8 @@
- 
-     // Change encoding mode
-     SequenceReaderModeFlagReplace mode('X');
--    assert(ttCodon['X']==ttProtein['X']);
--    assert(ttCodon['X']!=nv);
-+    assert(ttCodon[(int)'X']==ttProtein[(int)'X']);
-+    assert(ttCodon[(int)'X']!=nv);
-     codonEncoder_.changeMode( &mode );
- 
- 
-@@ -418,7 +418,7 @@
-   seq->link( translatedSeq );
- 
-   // NB sequences are numbered 1...n not 0...n-1
--  for ( unsigned int i(1); i <= numSeqs ; i++ )
-+  for ( int i(1); i <= numSeqs ; i++ )
-   {
-     //    cout << "hashing sequence " << i << endl;
-     if( sequenceReader.getNextSequence( thisSeq, eDNAWordSizeForHashing) == -1 ) 
-@@ -520,7 +520,7 @@
- int HashTableTranslated::getHitTypeSize( void ) const 
- {
-   assert(1==0);
--  return NULL;
-+  return 0;
- }
- void HashTableTranslated::allocateHitList( unsigned long size ) 
- {