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--- ./QueryManager/QueryManager.cpp.orig 2004-03-01 13:51:29.000000000 -0300
+++ ./QueryManager/QueryManager.cpp 2008-06-12 15:39:31.000000000 -0300
@@ -164,8 +164,8 @@
// MatchPolicy member function definitions
MatchPolicy::MatchPolicy( HashTableGeneric& subjectTable ) :
- subjectTable_( subjectTable ),
- queryWordLength_( subjectTable.getWordLength() )
+ queryWordLength_( subjectTable.getWordLength() ),
+ subjectTable_( subjectTable )
{}
@@ -203,8 +203,8 @@
MatchPolicyProteinProtein::MatchPolicyProteinProtein
( HashTablePackedProtein& subjectTable ) :
-subjectTable_( subjectTable ),
-MatchPolicy( subjectTable )
+MatchPolicy( subjectTable ),
+subjectTable_( subjectTable )
{
subjectTable_.setQueryProtein();
@@ -386,9 +386,9 @@
QueryManager::QueryManager
( SequenceReader& querySeqs,
HashTableGeneric& subjectSeqs, ostream& monitoringStream ) :
- queryReader_( querySeqs ),
subjectTable_( subjectSeqs ),
- monitoringStream_( monitoringStream )
+ monitoringStream_( monitoringStream ),
+ queryReader_( querySeqs )
{
monitoringStream_ << "constructing QueryManager\n";
@@ -518,7 +518,7 @@
task( store );
- if ( queryReader_.getLastSequenceNumber() == queryEnd ) break;
+ if ( (int)queryReader_.getLastSequenceNumber() == queryEnd ) break;
// clear the query sequence ready to read in next query
querySeqFwd.clear();
@@ -530,7 +530,7 @@
} // ~while
while ( numBasesInLast != -1 );
- if ( ( queryReader_.getLastSequenceNumber() < queryEnd )
+ if ( ( (int)queryReader_.getLastSequenceNumber() < queryEnd )
&& ( queryEnd != - 1 ) )
{
monitoringStream_ << "Info: requested final sequence (" << queryEnd
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