[Bioperl-guts-l] bioperl-live/Bio/SearchIO EventHandlerI.pm, 1.10, 1.11 FastHitEventBuilder.pm, 1.9, 1.10 SearchResultEventBuilder.pm, 1.38, 1.39 blast.pm, 1.95, 1.96

[Christopher John Fields]

Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO
In directory dev.open-bio.org:/tmp/cvs-serv17263/Bio/SearchIO

Modified Files:
	EventHandlerI.pm FastHitEventBuilder.pm 
	SearchResultEventBuilder.pm blast.pm 
Log Message:
Moved start_iteration, end_iteration to EventHandlerI; modified
 SearchIO::blast to play nice when using other event handlers

Index: blast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blast.pm,v
retrieving revision 1.95
retrieving revision 1.96
diff -C2 -d -r1.95 -r1.96
*** blast.pm	27 Apr 2006 00:57:07 -0000	1.95
--- blast.pm	29 Apr 2006 21:43:02 -0000	1.96
***************
*** 1921,1928 ****
          }
          else {
!             $self->throw(
!                 -class => 'Bio::SearchIO::InternalParserError',
!                 -text  => "Can't handle elements of type '$type'.",
!                 -value => $type
              );
          }
--- 1921,1927 ----
          }
          else {
!             $self->debug( # changed 4/29/2006 to play nice with other event handlers
!                 "Bio::SearchIO::InternalParserError ".
!                 "\nCan't handle elements of type \'$type.\'"
              );
          }

Index: EventHandlerI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/EventHandlerI.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** EventHandlerI.pm	27 Sep 2005 14:54:03 -0000	1.10
--- EventHandlerI.pm	29 Apr 2006 21:43:02 -0000	1.11
***************
*** 165,168 ****
--- 165,200 ----
  }
  
+ =head2 start_iteration
+ 
+  Title   : start_iteration
+  Usage   : $handler->start_iteration()
+  Function: Starts an Iteration event cycle
+  Returns : none
+  Args    : type of event and associated hashref
+ 
+ 
+ =cut
+ 
+ sub start_iteration {
+    my ($self, at args) = @_;
+    $self->throw_not_implemented
+ }
+ 
+ =head2 end_iteration
+ 
+  Title   : end_iteration
+  Usage   : $handler->end_iteration()
+  Function: Ends an Iterationevent cycle
+  Returns : Bio::Search::Iteration::IterationI object
+  Args    : type of event and associated hashref
+ 
+ 
+ =cut
+ 
+ sub end_iteration {
+    my ($self, at args) = @_;
+    $self->throw_not_implemented();
+ }
+ 
  =head2 register_factory
  

Index: FastHitEventBuilder.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/FastHitEventBuilder.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** FastHitEventBuilder.pm	27 Apr 2006 15:18:36 -0000	1.9
--- FastHitEventBuilder.pm	29 Apr 2006 21:43:02 -0000	1.10
***************
*** 130,134 ****
     my ($self,$type) = @_;
     # these are the events we recognize
!    return ( $type eq 'hit' || $type eq 'result' || $type eq 'iteration' || $type eq 'hsp');
  }
  
--- 130,134 ----
     my ($self,$type) = @_;
     # these are the events we recognize
!    return ( $type eq 'hit' || $type eq 'result' );
  }
  
***************
*** 289,305 ****
  }
  
- # NOOP so this can behave like a IteratedSearchResultBuilder 
- sub start_iteration {}
- 
- # NOOP so this can behave like a IteratedSearchResultBuilder 
- sub end_iteration {}
- 
- # NOOP so this can behave like a SearchResultBuilder
- # junks HSPs
- sub start_hsp {}
- 
- # NOOP so this can behave like a SearchResultBuilder
- # junks HSPs
- sub end_hsp {}
- 
  1;
--- 289,291 ----

Index: SearchResultEventBuilder.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/SearchResultEventBuilder.pm,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** SearchResultEventBuilder.pm	27 Apr 2006 00:57:06 -0000	1.38
--- SearchResultEventBuilder.pm	29 Apr 2006 21:43:02 -0000	1.39
***************
*** 127,131 ****
     my ($self,$type) = @_;
     # these are the events we recognize
!    return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' || $type eq 'iteration' );
  }
  
--- 127,131 ----
     my ($self,$type) = @_;
     # these are the events we recognize
!    return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' );
  }
  
***************
*** 430,438 ****
  }
  
- # NOOP so this can behave like a IteratedSearchResultBuilder 
- sub start_iteration {}
- 
- # NOOP so this can behave like a IteratedSearchResultBuilder 
- sub end_iteration {}
- 
  1;
--- 430,432 ----