[Gmod-schema-cmts] schema/GMODTools/lib/Bio/GMOD Config2.pm, 1.5, 1.6

[Don G. <don...@us...>]

Update of /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv29196/lib/Bio/GMOD

Modified Files:
	Config2.pm 
Log Message:
no_csomesplit change for genomes with many scaffolds; validate chado variables; config updates

Index: Config2.pm
===================================================================
RCS file: /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD/Config2.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Config2.pm	28 Dec 2005 02:22:07 -0000	1.5
--- Config2.pm	15 Oct 2007 16:19:29 -0000	1.6
***************
*** 439,442 ****
--- 439,443 ----
  
    $DEBUG= delete $opts->{debug} if (defined $opts->{debug});
+   my $replacekeys= delete $opts->{replace} || 0;
    
    ##print STDERR "Config2::readConfig in=$file\n" if $DEBUG;
***************
*** 447,451 ****
  
    my $conf1 = $self->readConfigFile($file, $opts, 0);
!   $self->appendHash($confhash, $conf1, 0) if ($conf1);
       
    ## $self->{filename}= $file;
--- 448,452 ----
  
    my $conf1 = $self->readConfigFile($file, $opts, 0);
!   $self->appendHash($confhash, $conf1, $replacekeys) if ($conf1);
       
    ## $self->{filename}= $file;
***************
*** 467,471 ****
          my $inc1= delete $$conf1{include};
          if($inc1) { push(@inc, (ref($inc1) =~ /ARRAY/) ? @$inc1 : ($inc1)); }
!         $self->appendHash($confhash, $conf1, 0);
          }
        $saveConfigOk=0 unless($readConfigOk);
--- 468,472 ----
          my $inc1= delete $$conf1{include};
          if($inc1) { push(@inc, (ref($inc1) =~ /ARRAY/) ? @$inc1 : ($inc1)); }
!         $self->appendHash($confhash, $conf1, $replacekeys);
          }
        $saveConfigOk=0 unless($readConfigOk);
***************
*** 478,481 ****
--- 479,523 ----
  
  
+ sub updateVariables
+ {
+   my $self = shift;
+   my( $confhash, $opts)= @_;
+   $DEBUG= delete $opts->{debug} if (defined $opts->{debug});
+   $confhash = $self->{'conf'} unless(ref $confhash); # always exists ?
+   $confhash = {} unless(ref $confhash);
+   my $env= (ref $opts and ref $opts->{Variables}) ? $opts->{Variables} : $Variables;
+   _update1Value( $confhash, $env);
+   return $confhash;
+ }
+ 
+ 
+ sub _update1Value
+ {
+   my($val,$env)= @_;
+ 
+   if( ref($val) eq 'HASH') {  
+     foreach my $tag (sort keys %$val) { 
+       $$val{$tag} = _update1Value( $$val{$tag}, $env);
+       }
+     
+   } elsif( ref($val) eq 'ARRAY') {
+      foreach (@$val){  $_= _update1Value( $_, $env); }
+      
+   } else {
+     while ( $val =~ m/\$\{(\w+)\}/g) {
+       my $var=$1;
+       my $enval= $env->{$var}; #only if defined, leave otherwise
+       if (defined $enval) { 
+         if($enval =~ m/\$\{(\w+)\}/) { $enval= _update1Value( $enval, $env); }
+         print STDERR "UPVAL1: \$\{$var\} => $enval\n" if $DEBUG;
+         $val =~ s/\$\{$var\}/$enval/;
+         } 
+     }
+   }
+   
+   return $val;
+ }
+ 
+ 
  =head2 showConfig($confhash, $opts)