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