From 7efa497c0ebb7a939b916d70f99e280c55071ef7 Mon Sep 17 00:00:00 2001
From: Robert Buels <rbuels@gmail.com>
Date: Mon, 21 Jan 2013 11:09:40 -0500
Subject: [PATCH] move ExternalSorter perl module into Bio::JBrowse namespace

---
 bin/ucsc-to-json.pl                           | 4 ++--
 src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm      | 6 +++---
 src/perl5/{ => Bio/JBrowse}/ExternalSorter.pm | 8 ++++----
 src/perl5/Bio/JBrowse/HashStore.pm            | 4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)
 rename src/perl5/{ => Bio/JBrowse}/ExternalSorter.pm (94%)

diff --git a/bin/ucsc-to-json.pl b/bin/ucsc-to-json.pl
index be78d075cb..89ecae52fa 100755
--- a/bin/ucsc-to-json.pl
+++ b/bin/ucsc-to-json.pl
@@ -115,7 +115,7 @@ =head1 EXAMPLE
 use JSON 2;
 use GenomeDB;
 use NameHandler;
-use ExternalSorter;
+use Bio::JBrowse::ExternalSorter;
 
 my $trackdb = "trackDb";
 my ($indir, $tracks, $arrowheadClass, $subfeatureClasses, $clientConfig, $db,
@@ -274,7 +274,7 @@ =head1 EXAMPLE
     };
 
     my %chromCounts;
-    my $sorter = ExternalSorter->new($compare, $sortMem);
+    my $sorter = Bio::JBrowse::ExternalSorter->new($compare, $sortMem);
     for_columns("$indir/" . $trackMeta->{tableName},
                 sub { 
                     $chromCounts{$_[0]->[$chromCol]} += 1;
diff --git a/src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm b/src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
index 42e33eba82..7cf33ce8b5 100644
--- a/src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
+++ b/src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
@@ -3,7 +3,7 @@ package Bio::JBrowse::Cmd::NCFormatter;
 use base 'Bio::JBrowse::Cmd';
 
 use GenomeDB;
-use ExternalSorter;
+use Bio::JBrowse::ExternalSorter;
 
 sub _format {
     my ( $self, %args ) = @_;
@@ -13,9 +13,9 @@ sub _format {
     my $types = $self->opt('type');
     @$types = split /,/, join ',', @$types;
 
-    # The ExternalSorter will get flattened [chrom, [start, end, ...]]
+    # The Bio::JBrowse::ExternalSorter will get flattened [chrom, [start, end, ...]]
     # arrays from the feature_stream
-    my $sorter = ExternalSorter->new(
+    my $sorter = Bio::JBrowse::ExternalSorter->new(
         do {
             my $startIndex = $feature_stream->startIndex;
             my $endIndex = $feature_stream->endIndex;
diff --git a/src/perl5/ExternalSorter.pm b/src/perl5/Bio/JBrowse/ExternalSorter.pm
similarity index 94%
rename from src/perl5/ExternalSorter.pm
rename to src/perl5/Bio/JBrowse/ExternalSorter.pm
index f16925dd93..8b710ed113 100644
--- a/src/perl5/ExternalSorter.pm
+++ b/src/perl5/Bio/JBrowse/ExternalSorter.pm
@@ -1,11 +1,11 @@
 =head1 NAME
 
-ExternalSorter - efficiently sort arrayrefs with a given comparison function
+Bio::JBrowse::ExternalSorter - efficiently sort arrayrefs with a given comparison function
 
 =head1 SYNOPSIS
 
   # make a new sorter that sorts by column 4, then column 3
-  my $sorter = ExternalSorter->new(
+  my $sorter = Bio::JBrowse::ExternalSorter->new(
                 sub ($$) {
                         $_[0]->[4] <=> $_[1]->[4]
                         ||
@@ -29,7 +29,7 @@ ExternalSorter - efficiently sort arrayrefs with a given comparison function
 =cut
 
 
-package ExternalSorter;
+package Bio::JBrowse::ExternalSorter;
 
 use strict;
 use warnings;
@@ -128,7 +128,7 @@ sub flush {
 
     # each segment must have at least one element
     return if ($#sorted < 0);
-    croak "ExternalSorter is already finished"
+    croak "Bio::JBrowse::ExternalSorter is already finished"
         if $self->{finished};
 
     my $fh = File::Temp->new( $self->{tmpDir} ? (DIR => $self->{tmpDir}) : (),
diff --git a/src/perl5/Bio/JBrowse/HashStore.pm b/src/perl5/Bio/JBrowse/HashStore.pm
index 7cd3914b6e..f4632b97ff 100644
--- a/src/perl5/Bio/JBrowse/HashStore.pm
+++ b/src/perl5/Bio/JBrowse/HashStore.pm
@@ -36,7 +36,7 @@ use File::Path ();
 
 use Cache::Ref::FIFO ();
 
-use ExternalSorter;
+use Bio::JBrowse::ExternalSorter;
 
 my $bucket_class = 'Bio::JBrowse::HashStore::Bucket';
 
@@ -137,7 +137,7 @@ reading them back in sorted order.
 sub sort_stream {
     my ( $self, $in_stream ) = @_;
 
-    my $sorter = ExternalSorter->new(
+    my $sorter = Bio::JBrowse::ExternalSorter->new(
         sub ($$) {
             $_[0]->[0] cmp $_[1]->[0]
         }, 32_000_000 );