702ce22305
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)
54 lines
2.1 KiB
C
54 lines
2.1 KiB
C
--- ./QueryManager/MatchStore.h.orig 2004-03-01 13:51:29.000000000 -0300
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+++ ./QueryManager/MatchStore.h 2008-06-12 15:39:31.000000000 -0300
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@@ -93,20 +93,20 @@
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virtual SequenceNumber getSubjectNum( void ) const
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{ return subjectNum_; }
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// virtual inline string getSubjectName( void ) const;
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- virtual inline const char* getSubjectName( void ) const;
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+ virtual const char* getSubjectName( void ) const;
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virtual SequenceOffset getSubjectStart( void ) const
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{ return subjectStart_; }
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virtual SequenceOffset getSubjectEnd( void ) const
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{ return subjectEnd_; }
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- virtual inline SequenceNumber getQueryNum( void ) const;
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- virtual inline string getQueryName( void ) const;
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+ virtual SequenceNumber getQueryNum( void ) const;
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+ virtual string getQueryName( void ) const;
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virtual SequenceOffset getQueryStart( void ) const
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{ return queryStart_; }
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virtual SequenceOffset getQueryEnd( void ) const
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{ return queryEnd_; }
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- virtual inline int getQuerySize( void ) const;
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+ virtual int getQuerySize( void ) const;
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virtual int getNumBases(void ) const
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{ return numBases_; }
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virtual bool isQueryForward( void ) const
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@@ -127,7 +127,6 @@
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SequenceOffset subjectEnd,
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bool isQueryForward,
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bool isSubjectForward ):
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- myStore_( myStore ),
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subjectNum_( subjectNum ),
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numBases_( numBases ),
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queryStart_( queryStart ),
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@@ -135,7 +134,8 @@
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subjectStart_( subjectStart ),
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subjectEnd_( subjectEnd ),
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isQueryForward_( isQueryForward ),
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- isSubjectForward_( isSubjectForward ){}
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+ isSubjectForward_( isSubjectForward ),
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+ myStore_( myStore ) {}
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SequenceNumber subjectNum_;
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SequenceOffset numBases_;
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@@ -444,7 +444,7 @@
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(
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unsigned int maxToSort = 1<<30,
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double partialThreshold = 0.0
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- ) : sorter_(), maxToSort_(maxToSort), partialThreshold_(partialThreshold) {}
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+ ) : maxToSort_(maxToSort), partialThreshold_(partialThreshold), sorter_() {}
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// TBD should be virtual???
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void operator()(MatchStore& store )
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{
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