--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Transcript.pm	Wed Feb 08 16:59:24 2012 -0500
@@ -0,0 +1,126 @@
+package Transcript;
+use strict;
+use Carp;
+use Data::Dumper;
+
+# we are going to use a light weight Transcript model here 
+my @Transcript_slots;
+BEGIN {
+	@Transcript_slots = qw(NAME REFSEQ_ID CHR START END STRAND CDS_START CDS_END EXONS TYPE);
+}
+use enum @Transcript_slots;
+
+my %attribute = (
+    name         => NAME,
+    refseq_id    => REFSEQ_ID,
+	chr			 => CHR,
+    start        => START,
+    end          => END,
+	strand		 => STRAND,
+    cds_start    => CDS_START,
+	cds_end      => CDS_END,
+	exons        => EXONS,
+	type		 => TYPE,
+);
+
+#using an array instead of a hash for the node
+sub _accessor {
+    my $index = shift;
+    return sub {
+        my $self = shift;
+        return undef unless $self;
+        if (@_) {
+          $self->[$index] = shift;
+        }
+        return $self->[$index];
+    };
+}
+
+while(my($at, $idx) = each %attribute) {
+    no strict 'refs';
+    *$at = _accessor($idx);
+}
+
+sub new {
+    my $class = shift;
+    my $obj = [];
+
+    if (@_) {
+		my %arg = @_;
+        $obj->[NAME]      = $arg{-NAME}      if($arg{-NAME});
+		$obj->[REFSEQ_ID] = $arg{-REFSEQ_ID} if($arg{-REFSEQ_ID});
+		$obj->[CHR]       = $arg{-CHR}       if($arg{-CHR});
+		$obj->[START]     = $arg{-START}     if($arg{-START});
+		$obj->[END]       = $arg{-END}       if($arg{-END});
+		$obj->[STRAND]    = $arg{-STRAND}    if($arg{-STRAND});
+		$obj->[CDS_START] = $arg{-CDS_START} if($arg{-CDS_START});
+		$obj->[CDS_END]   = $arg{-CDS_END}   if($arg{-CDS_END});
+		$obj->[EXONS]     = $arg{-EXONS}     if($arg{-EXONS});
+		$obj->[TYPE]      = $arg{-TYPE}      if($arg{-TYPE});
+    }
+    return bless $obj, $class;
+}
+
+sub get_start {
+	my ($self, $pos, $ext) = @_;
+	my @tmp;
+	foreach my $e( @{$self->[EXONS]} ) {
+		if($e->[1] < $pos) {
+			push @tmp, $e;
+			next;
+		}
+		last;
+	}
+	my $len = 0;
+	while(scalar @tmp > 0) {
+		my $e = pop @tmp;
+		if($e->[1] >= $pos) {
+			my $l = $pos - $e->[0];
+			if($l + $len < $ext) {
+				$len = $l;
+				next;
+			}
+			return $pos - $ext;
+		}
+		if($e->[1] - $e->[0] + 1 + $len < $ext) {
+			$len += ($e->[1] - $e->[0] + 1);
+			next;
+		}
+		return ($e->[1] - $ext + $len);
+	}
+	return $self->start;
+}
+
+sub get_end {
+	my ($self, $pos, $ext) = @_;
+	my @tmp = @{$self->[EXONS]};
+	my $len = 0;
+	while(scalar @tmp > 0) {
+		my $e = shift @tmp;
+		next if($e->[1] < $pos);
+		if($e->[0] <= $pos ) {
+			return $pos + $ext if($e->[1] - $pos >= $ext);
+			$len = $e->[1] - $pos;
+			next;
+		}
+		if($e->[1] - $e->[0] + 1 + $len < $ext) {
+			$len += ($e->[1] - $e->[0] + 1);
+			next;
+		}
+		return ($e->[0] + $ext - $len);
+	}
+	return $self->end;
+}
+
+sub overlap {
+	my $self = shift;
+	my $range = shift;
+	croak "Range must be a ref of array" unless(ref($range) eq 'ARRAY');
+
+	foreach my $e ( @{$self->[EXONS]} ) {
+		return 1 if($e->[0] <= $range->[1] && $e->[1] >= $range->[0]);
+	}
+	return;
+}
+
+1;