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--- ./SequenceReader/SequenceReaderFasta.cpp.orig 2004-03-01 13:51:29.000000000 -0300
+++ ./SequenceReader/SequenceReaderFasta.cpp 2008-06-12 15:39:31.000000000 -0300
@@ -135,9 +135,9 @@
seqStopChar_( rhs.seqStopChar_ ),
pInputFileStream_( new ifstream( rhs.fileName_.c_str() ) ),
fileName_( rhs.fileName_.c_str() ),
- seqPositions_( rhs.seqPositions_ ),
// lastSourceSeqNum_(0),
- pEncoder_( rhs.pEncoder_->clone() )
+ pEncoder_( rhs.pEncoder_->clone() ),
+ seqPositions_( rhs.seqPositions_ )
{
monitoringStream_ << "copy constructing SequenceReaderFile" << this
<< endl;
@@ -603,7 +603,7 @@
throw SSAHAException
("Requested seq start exceeds requested seq end in SequenceReaderFile::extractSource");
} // ~if
- else if (seqEnd>lastSourceSeq_.size() )
+ else if (seqEnd>(SequenceOffset)lastSourceSeq_.size() )
{
throw SSAHAException
("Requested last byte exceeds end of seq in SequenceReaderFile::extractSource");
@@ -628,7 +628,7 @@
computeNumSequencesInFile(); // ensure have scanned to end of file
fileFile << fileName_ << endl;
SeqIndexInfo* pIndex = new SeqIndexInfo[seqPositions_.size()];
- for (int i(0) ; i < seqPositions_.size() ; i++)
+ for (unsigned int i(0) ; i < seqPositions_.size() ; i++)
{
pIndex[i].fileNum=fileNumber;
pIndex[i].seqPos=seqPositions_[i];
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