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)
75 lines
2.4 KiB
C++
75 lines
2.4 KiB
C++
--- ./SequenceReader/SequenceEncoder.cpp.orig 2004-03-01 13:51:29.000000000 -0300
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+++ ./SequenceReader/SequenceEncoder.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -54,10 +54,10 @@
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ostream& monitoringStream):
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monitoringStream_( monitoringStream ),
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tt_(tt), sourceData_( sourceData ), bitsPerSymbol_(bitsPerSymbol),
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+ symbolMask_((1<<bitsPerSymbol)-1),
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pState_( new SequenceReaderModeIgnore( monitoringStream ) ),
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wordFlag_(0),
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- doubleBitShift_(bitsPerSymbol<<1),
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- symbolMask_((1<<bitsPerSymbol)-1)
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+ doubleBitShift_(bitsPerSymbol<<1)
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// numSymbolPairs_(wordLength>>1),
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// oddNumSymbols_(wordLength%1==1),
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{
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@@ -71,13 +71,13 @@
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ett_( rhs.ett_ ),
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sourceData_( rhs.sourceData_ ),
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bitsPerSymbol_( rhs.bitsPerSymbol_ ),
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+ symbolMask_(rhs.symbolMask_),
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wordLength_( rhs.wordLength_ ),
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// pSeq_( rhs.pSeq_ ),// don't want 2 encoders linking to same seq
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pState_( rhs.pState_->clone() ),
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wordFlag_(0),
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// numSymbolPairs_(rhs.numSymbolPairs_),
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// oddNumSymbols_(rhs.oddNumSymbols_),
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- symbolMask_(rhs.symbolMask_),
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doubleBitShift_(rhs.doubleBitShift_)
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{
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monitoringStream_ << "copy constructing SequenceEncoder" << endl;
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@@ -218,7 +218,7 @@
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{
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pTemp = (uchar*)p;
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// cout << basesInLast << " doing odd char at end " << *pTemp << endl;
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- encodeChar( *p, thisWord, wordFlag_, basesInLast );
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+ encodeChar( *pTemp, thisWord, wordFlag_, basesInLast );
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}
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pSeq_->setNumBasesInLast(basesInLast);
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@@ -453,7 +453,7 @@
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for( ; i!=lastWord ; ++i )
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{
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- if (toCarry!=~0)
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+ if (toCarry!=(Word)~0)
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(*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
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? flaggedChar
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: ( toCarry | (((*i) >> (4*gCodonBits + 2*gBaseBits))&maskBase ));
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@@ -488,7 +488,7 @@
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for( ; i!=lastWord ; ++i )
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{
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- if (toCarry!=~0)
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+ if (toCarry!=(Word)~0)
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(*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
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? flaggedChar
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: ( toCarry | (((*i) >> (4*gCodonBits + gBaseBits))&mask2Bases ));
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@@ -610,7 +610,7 @@
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do
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{
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i--;
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- if (toCarry!=~0)
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+ if (toCarry!=(Word)~0)
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(*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
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? flaggedChar
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: ( toCarry | ( ((*i) & mask2Bases ) << gBaseBits ) );
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@@ -650,7 +650,7 @@
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do
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{
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i--;
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- if (toCarry!=~0)
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+ if (toCarry!=(Word)~0)
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(*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
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? flaggedChar
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: ( toCarry | ( ((*i) & maskBase ) << (2*gBaseBits) ) );
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