diff options
Diffstat (limited to 'biology/ssaha/files/patch-QueryManager.cpp')
-rw-r--r-- | biology/ssaha/files/patch-QueryManager.cpp | 54 |
1 files changed, 54 insertions, 0 deletions
diff --git a/biology/ssaha/files/patch-QueryManager.cpp b/biology/ssaha/files/patch-QueryManager.cpp new file mode 100644 index 000000000000..bb80ea676c1d --- /dev/null +++ b/biology/ssaha/files/patch-QueryManager.cpp @@ -0,0 +1,54 @@ +--- ./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 |