1 files changed, 0 insertions, 75 deletions
diff --git a/biology/ssaha/files/patch-SequenceEncoder.cpp b/biology/ssaha/files/patch-SequenceEncoder.cpp
deleted file mode 100644
index 5832a96a40bb..000000000000
--- a/biology/ssaha/files/patch-SequenceEncoder.cpp
+++ /dev/null
@@ -1,75 +0,0 @@
---- ./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) ) );