From 7cdcfc1406977465616866fd9ca408d9cf1d6317 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 13 Oct 2004 14:05:57 +0000
Subject: [PATCH] pass xref to method xref and no longer pass it as an argument
in other methods
---
misc-scripts/xref_mapping/xref_mapper.pl | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index be890517c9..6f3ca108bb 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -3,6 +3,7 @@ use warnings;
use Getopt::Long;
use Cwd;
+use XrefMapper::db;
use vars qw(@INC);
@@ -27,6 +28,7 @@ open(FILE, $file) or die("Could not open input file '$file'");
my @all_species;
my $xref;
+#my $output=undef;
my $new=undef;
my $type;
while( my $line = <FILE> ) {
@@ -42,6 +44,9 @@ while( my $line = <FILE> ) {
if($type eq "species"){
push @all_species, $new;
}
+# elsif($type eq "output"){
+# $output = $new;
+# }
else{
$xref = $new;
}
@@ -66,9 +71,11 @@ while( my $line = <FILE> ) {
$new->species($value);
}
}
+# elsif($key eq "output"){
+# $type= "output";
+# $new = new XrefMapper::db();
+# }
else{
- my $module = "db";
- use XrefMapper::db;
$type= "xref";
$new = new XrefMapper::db();
}
@@ -82,6 +89,9 @@ if(defined($new)){ #save last one
if($type eq "species"){
push @all_species, $new;
}
+# elsif($type eq "output"){
+# $output= $new;
+# }
else{
$xref = $new;
}
@@ -89,8 +99,10 @@ if(defined($new)){ #save last one
}
for my $species ( @all_species ) {
- $species->dump_seqs($xref);
- $species->run_matching($xref);
+ $species->xref($xref);
+# $species->output($output);
+ $species->dump_seqs();
+ $species->run_matching();
$species->store();
}
--
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