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)
48 lines
1.6 KiB
C++
48 lines
1.6 KiB
C++
--- ./HashTable/HashTableGeneric.cpp.orig 2005-06-21 05:48:27.000000000 -0300
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+++ ./HashTable/HashTableGeneric.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -63,18 +63,18 @@
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( ostream& monitoringStream,
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const string& name,
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Allocator<PositionInHitList>& arrayAllocator ) :
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- isInitialized_( false ),
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- monitoringStream_( monitoringStream ),
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name_( name ),
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- bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
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+ isInitialized_( false ),
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maxNumHits_( defaultMaxNumHits ),
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+ bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
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hitListFormat_( gNotSpecified ),
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+ monitoringStream_( monitoringStream ),
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pArrayAllocator_
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( arrayAllocator.clone(&pWordPositionInHitList_,
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name+(string)".head",
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monitoringStream_) ),
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- pSequenceSizes_(NULL),
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- pNameReader_(NULL)
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+ pNameReader_(NULL),
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+ pSequenceSizes_(NULL)
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{
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monitoringStream_ << "constructing HashTableGeneric\n";
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if (name_=="")
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@@ -290,7 +290,7 @@
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WordSequence thisSeq;
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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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if( sequenceReader.getNextSequence( thisSeq, wordLength_) == -1 )
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{
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@@ -973,10 +973,10 @@
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SequenceAdapterWithOverlap::SequenceAdapterWithOverlap
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( int bitsPerSymbol, int wordLength, int stepLength ) :
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+SequenceAdapter(),
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bitsPerSymbol_( bitsPerSymbol ),
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wordLength_( wordLength ),
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-stepLength_( stepLength ),
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-SequenceAdapter()
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+stepLength_( stepLength )
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{
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maskLeft_ = new Word[ wordLength_ ];
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