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--- ./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 )
{
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