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