Change the default for _has_analysis() from false (zero) to true (1) to

decrease the amount of code (slightly) in most of the feature-specific
sub-classes.

modules/Bio/EnsEMBL/Collection.pm

@@ -1083,8 +1083,8 @@ sub _dbID_column {
                   in their main feature table.  For these feature
                   types, a restriction on analysis.logic_name may
                   be enforced by using the ANALYSIS argument of the
-                  constructor.  This method should return a true
-                  value if there is such an analysis_id column in
+                  constructor.  This method should return a false
+                  value if there is no such an analysis_id column in
                   the feature table.
 
   Return type   : Boolean
@@ -1097,7 +1097,7 @@ sub _dbID_column {
 
 =cut
 
-sub _has_analysis { return 0 }
+sub _has_analysis { return 1 }
 
 #-----------------------------------------------------------------------
 

modules/Bio/EnsEMBL/Collection/DnaAlignFeature.pm

@@ -31,7 +31,7 @@ sub _extra_columns {
 
 # sub _extra_where_clause { }
 
-sub _has_analysis { return 1 }
+# sub _has_analysis { return 1 }
 
 #-----------------------------------------------------------------------
 # Implemented abstract protected methods from base class

modules/Bio/EnsEMBL/Collection/Exon.pm

@@ -35,7 +35,7 @@ sub _extra_where_clause {
   );
 }
 
-# sub _has_analysis { return 0 }
+ sub _has_analysis { return 0 }
 
 #-----------------------------------------------------------------------
 # Implemented abstract protected methods from base class

modules/Bio/EnsEMBL/Collection/Gene.pm

@@ -37,7 +37,7 @@ sub _extra_where_clause {
   );
 }
 
-sub _has_analysis { return 1 }
+# sub _has_analysis { return 1 }
 
 #-----------------------------------------------------------------------
 # Implemented abstract protected methods from base class

modules/Bio/EnsEMBL/Collection/ProteinAlignFeature.pm

@@ -30,7 +30,7 @@ sub _extra_columns {
 
 # sub _extra_where_clause { }
 
-sub _has_analysis { return 1 }
+# sub _has_analysis { return 1 }
 
 #-----------------------------------------------------------------------
 # Implemented abstract protected methods from base class

modules/Bio/EnsEMBL/Collection/RepeatFeature.pm

@@ -36,7 +36,7 @@ sub _extra_where_clause {
   return 'rc.repeat_consensus_id = rf.repeat_consensus_id';
 }
 
-sub _has_analysis { return 1 }
+# sub _has_analysis { return 1 }
 
 #-----------------------------------------------------------------------
 # Implemented abstract protected methods from base class

modules/Bio/EnsEMBL/Collection/Transcript.pm

@@ -30,7 +30,7 @@ sub _extra_where_clause {
   );
 }
 
-sub _has_analysis { return 1 }
+# sub _has_analysis { return 1 }
 
 #-----------------------------------------------------------------------
 # Implemented abstract protected methods from base class