1 files changed, 54 insertions, 0 deletions
diff --git a/biology/ssaha/files/patch-MatchStore.h b/biology/ssaha/files/patch-MatchStore.h
new file mode 100644
index 000000000000..076639489869
--- /dev/null
+++ b/biology/ssaha/files/patch-MatchStore.h
@@ -0,0 +1,54 @@
+--- ./QueryManager/MatchStore.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/MatchStore.h	2008-06-12 15:39:31.000000000 -0300
+@@ -93,20 +93,20 @@
+   virtual SequenceNumber getSubjectNum( void ) const 
+     { return subjectNum_; }
+   //  virtual inline string  getSubjectName( void ) const;
+-  virtual inline const char*  getSubjectName( void ) const;
++  virtual const char*  getSubjectName( void ) const;
+   virtual SequenceOffset getSubjectStart( void ) const 
+     { return subjectStart_; }
+   virtual SequenceOffset getSubjectEnd( void ) const 
+     { return subjectEnd_; }
+ 
+-  virtual inline SequenceNumber getQueryNum( void ) const;
+-  virtual inline string         getQueryName( void ) const;
++  virtual SequenceNumber getQueryNum( void ) const;
++  virtual string         getQueryName( void ) const;
+   virtual SequenceOffset getQueryStart( void ) const 
+     { return queryStart_; }
+   virtual SequenceOffset getQueryEnd( void ) const 
+     { return queryEnd_; }
+   
+-  virtual inline int  getQuerySize( void ) const; 
++  virtual int  getQuerySize( void ) const; 
+   virtual int  getNumBases(void ) const 
+     { return numBases_; }
+   virtual bool isQueryForward( void ) const 
+@@ -127,7 +127,6 @@
+              SequenceOffset subjectEnd,
+              bool isQueryForward,
+              bool isSubjectForward ):
+-    myStore_( myStore ),
+     subjectNum_( subjectNum ),  
+     numBases_( numBases ),  
+     queryStart_( queryStart ),
+@@ -135,7 +134,8 @@
+     subjectStart_( subjectStart ),
+     subjectEnd_( subjectEnd ),
+     isQueryForward_( isQueryForward ),
+-    isSubjectForward_( isSubjectForward ){}
++    isSubjectForward_( isSubjectForward ),
++    myStore_( myStore )   {}
+ 
+   SequenceNumber subjectNum_;
+   SequenceOffset numBases_;
+@@ -444,7 +444,7 @@
+   ( 
+     unsigned int maxToSort = 1<<30,
+     double partialThreshold = 0.0
+-  ) : sorter_(), maxToSort_(maxToSort), partialThreshold_(partialThreshold) {}
++  ) : maxToSort_(maxToSort), partialThreshold_(partialThreshold), sorter_()  {}
+   // TBD should be virtual???
+   void operator()(MatchStore& store )
+   {