1 files changed, 0 insertions, 94 deletions
diff --git a/biology/ssaha/files/patch-MatchAligner.cpp b/biology/ssaha/files/patch-MatchAligner.cpp
deleted file mode 100644
index e7420b1ddec4..000000000000
--- a/biology/ssaha/files/patch-MatchAligner.cpp
+++ /dev/null
@@ -1,94 +0,0 @@
---- ./QueryManager/MatchAligner.cpp.orig	2004-03-01 13:51:29.000000000 -0300
-+++ ./QueryManager/MatchAligner.cpp	2008-06-12 15:39:31.000000000 -0300
-@@ -53,13 +53,13 @@
-   bool reverseQueryCoords,
-   bool doAlignment,
-   ostream& outputStream ):
-+  pAlign_(pAlign),
-+  outputStream_(outputStream),
-   querySource_(querySource), 
-   subjectSource_(subjectSource),
--  pAlign_(pAlign),
-   //  numCols_(numCols),
-   reverseQueryCoords_(reverseQueryCoords),
--  doAlignment_(doAlignment),
--  outputStream_(outputStream)
-+  doAlignment_(doAlignment)
- {
- } // ~MatchTaskAlign::MatchTaskAlign
- 
-@@ -194,10 +194,10 @@
-   int bandExtension,
-   ScoreTable* pTable,
-   ostream& outputStream ) :
-+  outputStream_(outputStream),
-   numCols_(numCols),
-   bandExtension_(bandExtension),
--  pTable_(pTable),
--  outputStream_(outputStream)
-+  pTable_(pTable)
- {
-   pBufSeq1_= new char [numCols+1];
-   pBufSeq2_= new char [numCols+1];
-@@ -563,17 +563,17 @@
-       //  cout << int ( ttDNA[ *(pChar++ ] << 4
-       //     | (ttDNA[ *(pChar++) ] << 2)
-       //     | ttDNA[ *(pChar++) ] ) << endl; 
--      if (    (ttDNA[ *(pChar)   ]==nv)
--           || (ttDNA[ *(pChar+1) ]==nv)
--           || (ttDNA[ *(pChar+2) ]==nv) )
-+      if (    (ttDNA[ (int) *(pChar)   ]==nv)
-+           || (ttDNA[ (int) *(pChar+1) ]==nv)
-+           || (ttDNA[ (int) *(pChar+2) ]==nv) )
-       {	
- 	*i='X';
-       } // ~if   
-       else
-       {
--	*i= gResidueNames[ ttCodon[ ttDNA[ *(pChar) ] << 4
--				  | ttDNA[ *(pChar+1) ] << 2
--				  | ttDNA[ *(pChar+2) ] ] ];
-+	*i= gResidueNames[ ttCodon[ ttDNA[ (int) *(pChar) ] << 4
-+				  | ttDNA[ (int) *(pChar+1) ] << 2
-+				  | ttDNA[ (int) *(pChar+2) ] ] ];
-       } // ~else
- 
-     } // ~for i
-@@ -983,7 +983,7 @@
- 
- void print( PathMatrix<PathType>& p )
- {
--  for (int i(0); i< p.front().size(); i++)
-+  for (size_t i(0); i< p.front().size(); i++)
-   {
-     for (vector<vector<PathType> >::iterator j(p.begin());
- 	 j!=p.end();++j)
-@@ -1249,16 +1249,16 @@
-   bandWidth_(p2Size-p1Size+1),
-   bandLength_(p1Size+1),
-   colSize_(p2Size-p1Size+1+(2*bandExtension_)),
--  fillCell_(),
-   finalFrame1_(p1FinalFrame),
-   finalFrame2_(p2FinalFrame),
-   numFrames1_((p1Trans[1]==NULL)?1:gNumReadingFrames),
-   numFrames2_((p2Trans[1]==NULL)?1:gNumReadingFrames),
-+  fillCell_(),
-+  getScore_(scoreTable),
-   v1_(colSize_, veryBadScore3D ), 
-   v2_(colSize_, veryBadScore3D ),
-   pLast_(&v1_),
--  pCurrent_(&v2_),
--  getScore_(scoreTable)
-+  pCurrent_(&v2_)
- {
-   
-   p1_[0] = p1Trans[0];
-@@ -1287,7 +1287,7 @@
- {
- 
-   //  ScoreType lastScore, prevFrameScore1, prevFrameScore2;
--  int i,j,k,l;
-+  int i,j;
- 
-   matrix.resize(bandLength_, vector<PathType3D>(colSize_) );
-