From 4cf0697b692bfd0a080b99ef2945ba162c052e38 Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Wed, 9 Jul 2003 13:35:12 +0000
Subject: [PATCH] get_tiling_path description added
---
docs/ensembl_changes_spec.txt | 28 +++++++++++++++++++---------
1 file changed, 19 insertions(+), 9 deletions(-)
diff --git a/docs/ensembl_changes_spec.txt b/docs/ensembl_changes_spec.txt
index 90bf7cd4d3..eb77b09560 100644
--- a/docs/ensembl_changes_spec.txt
+++ b/docs/ensembl_changes_spec.txt
@@ -223,16 +223,26 @@ Slice
The concept of an 'empty' slice will no longer exist.
- Should we remove all of the get_all_FeatureTypeX methods from Slice? These
- methods are not strictly needed and they are annoying because they result in
- a duplication of coding effort. Everytime a new feature is added, a new
- feature adaptor needs to be added AND a new method needs to be added to the
- slice. Would it not make everything simpler if features could still be
- fetched by slice from adaptors but not from slices as well? This also
- results in slices being smaller objects and makes the code more distributed.
- *probably can't get away with this change since much code depends on it,
- and it is not a huge flaw in the design anyway
+ The get_tiling_path method will have to be implemented differently for the
+ new system. It will take a coord_system string as an argument and rather than
+ returning a list of Tile objects it will return a listref of triplets containing
+ a start int, and end int, and a 'to' slice object. The following is an example
+ of how this method would be used ($clone is a reference to a slice object in
+ the clone coordinate system):
+
+ my $clone_path = $slice->get_tiling_path('clone');
+
+ foreach my $tile (@$clone_path) {
+ my ($start, $end, $clone) = @$tile;
+ print $slice->frag_name, ':', $start, '-', $end , ' -> ',
+ $clone->frag_name, ':', $clone->start, '-', $clone->end,
+ $clone->strand, "\n";
+ }
+
+Tile
+----
+ The tile object will no longer be necessary.
SliceAdaptor
--
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