some POD for NameHandler

lib/NameHandler.pm

@@ -1,3 +1,26 @@
+=head1 NAME
+
+NameHandler - create JSON indices of feature names
+
+=head1 SYNOPSIS
+
+  # instantiate with a callback that gives the directory to use for a
+  # given reference sequence
+  my $nameHandler = NameHandler->new(
+     sub { "$trackDir/" . $_[0] . "/" . $track->{"track"}; };
+  );
+
+  for my $name ( @feature_names ) {
+      $nameHandler->addName( $name );
+  }
+
+  # write out the finished names index
+  $nameHandler->finish;
+
+=head1 METHODS
+
+=cut
+
 package NameHandler;
 
 use strict;
@@ -16,6 +39,14 @@ our $chromIndex = 3;
 
 my $nameFile = "names.json";
 
+=head1 new( \&directory_callback )
+
+Make a new NameHandler.  Takes a subroutine reference that should take
+a reference sequence name as an argument and return the path to the
+directory that should contain the name index we generate.
+
+=cut
+
 sub new {
     my ($class, $trackDirForChrom) = @_;
 
@@ -28,6 +59,13 @@ sub new {
     return $self;
 }
 
+=head1 addName( \@name_record )
+
+Name record (an arrayref) to add to the names index.  Generated by the
+BioperlFlattener.
+
+=cut
+
 sub addName {
     my ($self, $nameArr) = @_;
     my $chrom = $nameArr->[$chromIndex];
@@ -47,6 +85,14 @@ sub addName {
         or die "couldn't write to file for $chrom: $!";
 }
 
+=head1 newChrom( $refSeqName )
+
+Given the name of the reference sequence, returns a filehandle to the
+proper name index file.  Makes a new directory to hold the file if
+necessary.
+
+=cut
+
 sub newChrom {
     my ($self, $chrom) = @_;
     my $chromDir = $self->{trackDirForChrom}->($chrom);
@@ -60,6 +106,12 @@ sub newChrom {
     return $fh;
 }
 
+=head1 finish
+
+Finalize and flush to disk any currently open name index.
+
+=cut
+
 sub finish {
     my ($self) = @_;
     foreach my $chrom (keys %{$self->{nameFiles}}) {