1 files changed, 48 insertions, 0 deletions
diff --git a/biology/ssaha/files/patch-HashTableGeneric.cpp b/biology/ssaha/files/patch-HashTableGeneric.cpp
new file mode 100644
index 000000000000..0d1ffb441303
--- /dev/null
+++ b/biology/ssaha/files/patch-HashTableGeneric.cpp
@@ -0,0 +1,48 @@
+--- ./HashTable/HashTableGeneric.cpp.orig	2005-06-21 05:48:27.000000000 -0300
++++ ./HashTable/HashTableGeneric.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -63,18 +63,18 @@
+ ( ostream& monitoringStream,
+   const string& name,
+   Allocator<PositionInHitList>& arrayAllocator ) : 
+-  isInitialized_( false ), 
+-  monitoringStream_( monitoringStream ),
+   name_( name ),
+-  bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
++  isInitialized_( false ), 
+   maxNumHits_( defaultMaxNumHits ),
++  bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
+   hitListFormat_( gNotSpecified ),
++  monitoringStream_( monitoringStream ),
+   pArrayAllocator_
+   ( arrayAllocator.clone(&pWordPositionInHitList_,
+ 			 name+(string)".head",
+ 			 monitoringStream_) ),
+-  pSequenceSizes_(NULL),
+-  pNameReader_(NULL)
++  pNameReader_(NULL),
++  pSequenceSizes_(NULL)
+   {
+     monitoringStream_ << "constructing HashTableGeneric\n";
+     if (name_=="")
+@@ -290,7 +290,7 @@
+   WordSequence thisSeq;
+     
+   // 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++ )
+   {
+     if( sequenceReader.getNextSequence( thisSeq, wordLength_) == -1 ) 
+     {
+@@ -973,10 +973,10 @@
+ 
+ SequenceAdapterWithOverlap::SequenceAdapterWithOverlap
+ ( int bitsPerSymbol, int wordLength, int stepLength ) :
++SequenceAdapter(),
+ bitsPerSymbol_( bitsPerSymbol ), 
+ wordLength_( wordLength ), 
+-stepLength_( stepLength ),
+-SequenceAdapter() 
++stepLength_( stepLength )
+ {
+ 
+   maskLeft_  = new Word[ wordLength_ ];