702ce22305
sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
77 lines
2.6 KiB
C++
77 lines
2.6 KiB
C++
--- ./HashTable/HashTableTranslated.cpp.orig 2004-03-01 13:51:29.000000000 -0300
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+++ ./HashTable/HashTableTranslated.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -50,9 +50,9 @@
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Allocator<PositionPacked>& hitListAllocator,
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Allocator<PositionInHitList>& arrayAllocator
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):
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- queryFrame_(0),
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HashTablePacked( monitoringStream, name,
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- hitListAllocator, arrayAllocator )
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+ hitListAllocator, arrayAllocator ),
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+ queryFrame_(0)
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{
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hitListFormat_ = g32BitPackedProtein;
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bitsPerSymbol_ = gResidueBits;
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@@ -135,12 +135,12 @@
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Allocator<PositionPacked>& hitListAllocator,
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Allocator<PositionInHitList>& arrayAllocator
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):
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+ HashTablePacked( monitoringStream, name,
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+ hitListAllocator, arrayAllocator ),
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+ codonEncoder_(5),
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queryFrame_(0),
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queryMult_(1),
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- codonEncoder_(5),
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- pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein ),
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- HashTablePacked( monitoringStream, name,
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- hitListAllocator, arrayAllocator )
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+ pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein )
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{
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hitListFormat_ = g32BitPackedProtein;
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bitsPerSymbol_ = gResidueBits;
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@@ -249,14 +249,14 @@
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Allocator<PositionPacked>& hitListAllocator,
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Allocator<PositionInHitList>& arrayAllocator
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) :
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+ HashTableGeneric( monitoringStream, name, arrayAllocator ),
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hashFwd_( monitoringStream, name+(string)"_fwd",
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hitListAllocator, arrayAllocator ),
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hashRev_( monitoringStream, name+(string)"_rev",
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hitListAllocator, arrayAllocator ),
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pHash_(&hashFwd_),
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codonEncoder_(5),
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- pMatchSequence_( &HashTableTranslated::matchSequenceProtein ),
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- HashTableGeneric( monitoringStream, name, arrayAllocator )
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+ pMatchSequence_( &HashTableTranslated::matchSequenceProtein )
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{
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bitsPerSymbol_=gResidueBits;
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hitListFormat_ = gTranslated;
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@@ -344,8 +344,8 @@
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// Change encoding mode
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SequenceReaderModeFlagReplace mode('X');
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- assert(ttCodon['X']==ttProtein['X']);
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- assert(ttCodon['X']!=nv);
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+ assert(ttCodon[(int)'X']==ttProtein[(int)'X']);
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+ assert(ttCodon[(int)'X']!=nv);
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codonEncoder_.changeMode( &mode );
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@@ -418,7 +418,7 @@
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seq->link( translatedSeq );
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// NB sequences are numbered 1...n not 0...n-1
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- for ( unsigned int i(1); i <= numSeqs ; i++ )
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+ for ( int i(1); i <= numSeqs ; i++ )
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{
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// cout << "hashing sequence " << i << endl;
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if( sequenceReader.getNextSequence( thisSeq, eDNAWordSizeForHashing) == -1 )
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@@ -520,7 +520,7 @@
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int HashTableTranslated::getHitTypeSize( void ) const
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{
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assert(1==0);
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- return NULL;
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+ return 0;
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}
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void HashTableTranslated::allocateHitList( unsigned long size )
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{
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