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Topic/phylo orthologs1 #6

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@tomfy tomfy commented Jun 27, 2012

Improvements to ortholog prediction when gene tree
has leaves with species not in species tree.

tomfy added 30 commits May 15, 2012 14:11
@tomfy
Added several species
3648b46
@tomfy
Now has function tests for pre- in- post- order traversals.
a2c36e6
@tomfy
remove some print statements
507b011
@tomfy
add tests for pre- in- post-order traversals
5f8e00c
@tomfy
fix vertical gap calculation
dcaf99a
@tomfy
pre- in- post-order traversals now functional.
01f0af4
@tomfy
Handles (somewhat pathological) 1-leaf case without div by 0 now.
44330ac
@tomfy
handle gene species not in species tree better.
de3cfec
@tomfy
add sub non-speciestree_leafnode_names, other improved handling of ge…
abfe7cc 
…ne species not in species tree.
@tomfy
eliminate parent_hilited argument to recursive_draw.
89bb0d6
@tomfy
Combined phylo.t, phylo_test.t
3513d8a
@tomfy
add species bithash tests
d3bff11
@tomfy
get_standard_species now uses to_standard_format if get_standard_name…
84989d0 
… returns undefined value.
@tomfy
changed 1 comment
87c8232
@tomfy
Deleting phylo_test.t (its tests are in phylo.t)
44de7da
@tomfy
In find_mindl_node decided on path for urec in more sensible way.
416fa10
@tomfy
copy method now also copies attibute 'species_bit_pattern'
6bce192
@tomfy
find_mindl_node now works with a copy of the gene tree,
725551e 
reroots the copy with urec, ...
@tomfy
Now skipping tokens containing only whitespace, in parse.
bb830ab
@tomfy
delete a print statement
bb72fae
@tomfy
delete a print statement.
fa9782e
@tomfy
1) In reset_root_to_point_on_branch, point to reset root to is specified
b50f653 
by giving a node and a distance above it. If the node is already the
root, then now it skips rerooting.
2) In find_mindl_node, decircularize $gene_tree_copy to avoid mem leak.
@tomfy
Handles the case of <2 leave left after pruning those
15fd336 
not in species tree (in find_mindl_node).
@tomfy
Initial commit. Class to analyze alignments for orthology.
46c1987
@tomfy
Initial commit. Class to get overlap from alignment,
7ad1d8c 
including getting bootstrap resampled overlaps.
@tomfy
dir deleted
4db4d30
@tomfy
Module for translating seqence ids to species.
fd733c8
@tomfy
For running MrBayes. Initial commit in cxgn-corelibs
ceea2b4
@tomfy
Tests to go with Orthologger module.
95d01dd
@tomfy
Remove extraneous printing in test.
d9833d0
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