From df6b6ecbf074e4ad98de70147fe6533d9f478279 Mon Sep 17 00:00:00 2001
From: kgalinsky <kgalinsky@a16988d2-67c9-4db9-a897-0603be59747b>
Date: Wed, 28 Oct 2009 21:55:20 +0000
Subject: [PATCH] Updated trunk to 0.4.2

git-svn-id: https://jcvi-tools.svn.sourceforge.net/svnroot/jcvi-tools/JCVI-Translator/trunk@7 a16988d2-67c9-4db9-a897-0603be59747b
---
 Changes                      |  3 +++
 lib/JCVI/Translator.pm       |  3 +--
 lib/JCVI/Translator/Utils.pm | 45 +++++++++++++++++++++++++++++++++++-
 3 files changed, 48 insertions(+), 3 deletions(-)

diff --git a/Changes b/Changes
index 3776f57..4f981c1 100644
--- a/Changes
+++ b/Changes
@@ -1,5 +1,8 @@
 Revision history for JCVI-Translator
 
+0.4.2   Apr 1 2009
+ - Added find method into utils
+
 0.4.1   Mar 31 2009
  - Minor fixes in documentation
  - Use "my $self = shift->SUPER::new(@_)" in constructors
diff --git a/lib/JCVI/Translator.pm b/lib/JCVI/Translator.pm
index 7d3fa0b..2dfc483 100644
--- a/lib/JCVI/Translator.pm
+++ b/lib/JCVI/Translator.pm
@@ -67,7 +67,7 @@ use strict;
 use warnings;
 
 use version;
-our $VERSION = qv('0.4.1');
+our $VERSION = qv('0.4.2');
 
 use base qw(Class::Accessor::Fast);
 __PACKAGE__->mk_accessors(qw(id names _table _starts _reverse));
@@ -391,7 +391,6 @@ sub add_translation {
         { regex => qr/^${nuc_match}{3}$/ },
         { regex => qr/^$aa_match$/ },
         { type  => Params::Validate::HASHREF, default => {} }
-
     );
 
     my %p = validate(
diff --git a/lib/JCVI/Translator/Utils.pm b/lib/JCVI/Translator/Utils.pm
index 64affe7..2a2c93b 100644
--- a/lib/JCVI/Translator/Utils.pm
+++ b/lib/JCVI/Translator/Utils.pm
@@ -54,7 +54,7 @@ our $DEFAULT_SANITIZED = 0;
 =cut
 
 sub _new {
-    my $self  = shift->SUPER::_new();
+    my $self = shift->SUPER::_new();
 
     $self->_regexes( [] );
     foreach my $rc ( 0 .. 1 ) {
@@ -135,6 +135,49 @@ sub regex {
     return $regex;
 }
 
+=head2 find
+
+    my $locations = $translator->find( $seq_ref, $residue );
+    my $locations = $translator->find( $seq_ref, $residue, \%params );
+
+Find the indexes of a given residue in a sequence. Valid options for the params
+hash are:
+
+    strand:     1 or -1; default = 1
+
+=cut
+
+sub find {
+    my $self = shift;
+
+    my ( $seq_ref, $residue, @p );
+
+    ( $seq_ref, $residue, $p[0] ) = validate_pos(
+        @_, { type => Params::Validate::SCALARREF },
+        1, { default => {}, type => Params::Validate::HASHREF }
+    );
+
+    my %p = validate(
+        @p,
+        {
+            strand => {
+                default => 1,
+                regex   => qr/^[+-]?1$/,
+                type    => Params::Validate::SCALAR
+            }
+        }
+    );
+
+    my $regex = $self->regex( $residue, $p{strand} );
+
+    my @positions;
+    while ( $$seq_ref =~ m/(?=$regex)/ig ) {
+        push @positions, pos($$seq_ref);
+    }
+    
+    return \@positions;
+}
+
 =head2 getORF
 
     my $orf_hash = $translator->getORF( $seq_ref );