[Bioperl-guts-l] bioperl-live/Bio/DB SeqHound.pm,1.5,1.6

Heikki Lehvaslaiho heikki at dev.open-bio.org
Thu Sep 28 14:32:12 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/DB
In directory dev.open-bio.org:/tmp/cvs-serv10233

Modified Files:
	SeqHound.pm 
Log Message:
using lexically scoped file handles


Index: SeqHound.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqHound.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** SeqHound.pm	26 Sep 2006 22:03:06 -0000	1.5
--- SeqHound.pm	28 Sep 2006 18:32:10 -0000	1.6
***************
*** 520,573 ****
  
  	#set up verbosity level if need record in the log file
! 	#$self->verbose(1);
! 	open (LOG, ">>shoundlog") 
! 	and print STDERR "Writing into the log file shoundlog\n" if $self->verbose > 0;
! 	my $now = strftime("%a %b %e %H:%M:%S %Y", localtime);
! 	if ($lcontent eq ""){
! 		open (LOG, ">>shoundlog") 
! 		and print LOG "$now		$funcname. No reply.\n" if $self->verbose>0;
! 		close (LOG) if $self->verbose>0;
  		return;
! 	}
! 	elsif ($lcontent =~ /HTTP::Request error/){
! 		open (LOG, ">>shoundlog")
! 		and print LOG "$now		$funcname. Http::Request error problem.\n" if $self->verbose>0;
! 		close (LOG) if $self->verbose>0;
  		return;
! 	}
! 	elsif ($lcontent =~ /SEQHOUND_ERROR/){
! 		open (LOG, ">>shoundlog")
! 		and print LOG "$now	$funcname error. SEQHOUND_ERROR found.\n" if $self->verbose>0;
! 		close (LOG) if $self->verbose>0;
  		return;
! 	}
! 	elsif ($lcontent =~ /SEQHOUND_NULL/){
!         	open (LOG, ">>shoundlog") 
! 		and print LOG "$now	$funcname Value not found in the database. SEQHOUND_NULL found.\n" if $self->verbose>0;
! 		close (LOG) if $self->verbose>0;
  		return;
!       	}
! 	else{
      		chomp $lcontent;
        		my @lines = split(/\n/, $lcontent, 2);
!      	 	if ($lines[1] =~ /^-1/){
!            		open (LOG, ">>shoundlog") 
! 			and print LOG "$now	$funcname Value not found in the database. -1 found.\n" if $self->verbose>0;
! 			close (LOG) if $self->verbose>0;
!            		return;
! 		}
!         	elsif ($lines[1]  =~ /^0/){
!           		open (LOG, ">>shoundlog") 
! 			and print LOG "$now	$funcname failed.\n" if $self->verbose>0;
! 			close (LOG) if $self->verbose>0;
! 	  		return;
!          	}
!          	else{
!            		$result = $lines[1];
           	}
        		
!    	}
!    	close (LOG) if $self->verbose>0 ;
!  
  	#a list of functions in SeqHound which can wrap into Bio::seqIO object
  	if ($outtype eq 'Bio::SeqIO'){
--- 520,569 ----
  
  	#set up verbosity level if need record in the log file
! 	$self->verbose(1);
! 
! 
!         if ($self->verbose>0) {
!             my $now = strftime("%a %b %e %H:%M:%S %Y", localtime);
!             if ($lcontent eq "") {
!                 print STDERR "Writing into the log file shoundlog\n";
! 		open (my $LOG, ">>shoundlog");
! 		print $LOG "$now		$funcname. No reply.\n";
  		return;
!             } elsif ($lcontent =~ /HTTP::Request error/) {
!                 print STDERR "Writing into the log file shoundlog\n";
! 		open (my $LOG, ">>shoundlog");
! 		print $LOG "$now		$funcname. Http::Request error problem.\n";
  		return;
!             } elsif ($lcontent =~ /SEQHOUND_ERROR/) {
!                 print STDERR "Writing into the log file shoundlog\n";
! 		open (my $LOG, ">>shoundlog");
! 		print $LOG "$now	$funcname error. SEQHOUND_ERROR found.\n";
  		return;
!             } elsif ($lcontent =~ /SEQHOUND_NULL/) {
!                 print STDERR "Writing into the log file shoundlog\n";
!         	open (my $LOG, ">>shoundlog");
! 		print $LOG "$now	$funcname Value not found in the database. SEQHOUND_NULL found.\n";
  		return;
!             } else {
      		chomp $lcontent;
        		my @lines = split(/\n/, $lcontent, 2);
!      	 	if ($lines[1] =~ /^-1/) {
!                     print STDERR "Writing into the log file shoundlog\n";
!                     open (my $LOG, ">>shoundlog");
!                     print $LOG "$now	$funcname Value not found in the database. -1 found.\n";
!                     return;
! 		} elsif ($lines[1]  =~ /^0/) {
!                     print STDERR "Writing into the log file shoundlog\n";
!                     open (my $LOG, ">>shoundlog");
!                     print $LOG "$now	$funcname failed.\n";
!                     return;
!          	} else {
!                     $result = $lines[1];
           	}
        		
!             }
! 
!         }
! 
  	#a list of functions in SeqHound which can wrap into Bio::seqIO object
  	if ($outtype eq 'Bio::SeqIO'){



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