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sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
55 lines
1.7 KiB
C++
55 lines
1.7 KiB
C++
--- ./QueryManager/QueryManager.cpp.orig 2004-03-01 13:51:29.000000000 -0300
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+++ ./QueryManager/QueryManager.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -164,8 +164,8 @@
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// MatchPolicy member function definitions
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MatchPolicy::MatchPolicy( HashTableGeneric& subjectTable ) :
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- subjectTable_( subjectTable ),
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- queryWordLength_( subjectTable.getWordLength() )
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+ queryWordLength_( subjectTable.getWordLength() ),
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+ subjectTable_( subjectTable )
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{}
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@@ -203,8 +203,8 @@
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MatchPolicyProteinProtein::MatchPolicyProteinProtein
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( HashTablePackedProtein& subjectTable ) :
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-subjectTable_( subjectTable ),
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-MatchPolicy( subjectTable )
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+MatchPolicy( subjectTable ),
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+subjectTable_( subjectTable )
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{
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subjectTable_.setQueryProtein();
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@@ -386,9 +386,9 @@
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QueryManager::QueryManager
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( SequenceReader& querySeqs,
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HashTableGeneric& subjectSeqs, ostream& monitoringStream ) :
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- queryReader_( querySeqs ),
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subjectTable_( subjectSeqs ),
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- monitoringStream_( monitoringStream )
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+ monitoringStream_( monitoringStream ),
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+ queryReader_( querySeqs )
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{
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monitoringStream_ << "constructing QueryManager\n";
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@@ -518,7 +518,7 @@
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task( store );
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- if ( queryReader_.getLastSequenceNumber() == queryEnd ) break;
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+ if ( (int)queryReader_.getLastSequenceNumber() == queryEnd ) break;
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// clear the query sequence ready to read in next query
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querySeqFwd.clear();
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@@ -530,7 +530,7 @@
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} // ~while
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while ( numBasesInLast != -1 );
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- if ( ( queryReader_.getLastSequenceNumber() < queryEnd )
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+ if ( ( (int)queryReader_.getLastSequenceNumber() < queryEnd )
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&& ( queryEnd != - 1 ) )
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{
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monitoringStream_ << "Info: requested final sequence (" << queryEnd
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