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