From 8a552edf035871b5f30657158edcdef230a70f9d Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 16 Jul 2003 16:26:47 +0000
Subject: [PATCH] updated a few things
---
docs/ensembl_changes_spec.txt | 60 ++++++++++++++++++++++-------------
1 file changed, 38 insertions(+), 22 deletions(-)
diff --git a/docs/ensembl_changes_spec.txt b/docs/ensembl_changes_spec.txt
index 75ae7b7e5b..379af21f33 100644
--- a/docs/ensembl_changes_spec.txt
+++ b/docs/ensembl_changes_spec.txt
@@ -6,7 +6,6 @@ REVISION HISTORY
Graham Mcvicker - July 9, 2003 - Created
-
GOALS
-----
-A cleaner, more intuitive API
@@ -209,10 +208,10 @@ Slice
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 ($clone is a reference to a slice object in
- the clone coordinate system):
+ returning a list of Tile objects it will return a listref of triplets
+ containing a start int, and end int, and a 'to' slice object. The following
+ is an example of how this method would be used ($clone is a reference to a
+ slice object in the clone coordinate system):
my $clone_path = $slice->get_tiling_path('clone');
@@ -254,9 +253,10 @@ RawContig
RawContigAdaptor
----------------
- The RawContigAdaptor is no longer necessary. The RawContigAdaptor is replaced
- by the SliceAdaptor. For backwards compatibility a minimal implementation
- of the RawContigAdaptor can remain which inherits from the SliceAdaptor.
+ The RawContigAdaptor is no longer necessary. The RawContigAdaptor is
+ replaced by the SliceAdaptor. For backwards compatibility a minimal
+ implementation of the RawContigAdaptor can remain which inherits from the
+ SliceAdaptor.
Clone
-----
@@ -438,15 +438,15 @@ Features
transform(coord_system)
-----------------------
Takes a single string specifying the new coord system. If the coord
- system is not valid an exception is thrown. If the coord system is the
- same coord system as the feature is currently in a new feature that is
- a copy of the old one will still be returned. This will also retrieve
- a slice which is the entire span of the region of the coordinate system
- that this feature is being transformed to. For example transforming
- an exon in raw contig coordinates to one in chromosomal coodinates
- will place the exon on a slice of an entire chromosome. If a feature
- spans a boundary in the coordinate system, undef is returned by the
- method instead.
+ system is not valid an exception is thrown. If the coord system is the
+ same coord system as the feature is currently in a new feature that is
+ a copy of the old one will still be returned. This will also retrieve
+ a slice which is the entire span of the region of the coordinate system
+ that this feature is being transformed to. For example transforming
+ an exon in raw contig coordinates to one in chromosomal coodinates
+ will place the exon on a slice of an entire chromosome. If a feature
+ spans a boundary in the coordinate system, undef is returned by the
+ method instead.
translate(slice)
----------------
@@ -490,10 +490,16 @@ AssemblyMapper
do the following:
NTContig -> Contig -> Clone
- This should simply be a matter of offsetting values in a stepwise matter when
- loading the mapper. The mapper will have a table of conversions between the
- NTContig and Clone systems which is constructed by the assembly mapper
- (rather than read directly from the assembly table).
+ In the above example the assembly mapper would have do the following:
+
+ (1) Create a mapper object between the NTContig and Contig region
+ (2) Create a mapper object between the Contig and Clone region
+ (3) Create and return a third mapper constructed from the sets of mappings
+ generated by the intermediate mappers.
+
+ As an intermediate implementation step it would be possible to leave the
+ AssemblyMapper almost as is and to require explicit mappings between all
+ coordinate systems of intereset to be present in the assembly table.
FeatureAdaptors
@@ -558,9 +564,19 @@ Haplotypes
OTHER CONSIDERATIONS
--------------------
+Feature Transfer Accross Assemblies
+-----------------------------------
+ Future assemblies (especially human assemblies) are expected to be small
+ refinements of previous assemblies. Rather then recomputing all of the new
+ genes and features on these assemblies it makes more sense to transfer most
+ features across from the previous assembly, only rebuilding in areas of
+ change. We will supply a mechanism via which features from a previous
+ assembly may be transfered to a new assembly.
+
+
TBD
MHC Regions
Circular Chromosomes
-Multiple Chromosomes
+Multiple Assemblies
--
GitLab