Code

Topic/phylo orthologs1#6

Code

Open

tomfy wants to merge 43 commits intomastersolgenomics/cxgn-corelibs:masterfrom topic/phylo_orthologs1solgenomics/cxgn-corelibs:topic/phylo_orthologs1Copy head branch name to clipboard

+4,035-2,666

Commits

Commits on May 15, 2012

• Added several species

  tomfy

  committed
  3648b46

Commits on May 16, 2012

• Now has function tests for pre- in- post- order traversals.

  tomfy

  committed
  a2c36e6

Commits on Jun 6, 2012

• remove some print statements

  tomfy

  committed
  507b011

• add tests for pre- in- post-order traversals

  tomfy

  committed
  5f8e00c

• fix vertical gap calculation

  tomfy

  committed
  dcaf99a

• pre- in- post-order traversals now functional.

  tomfy

  committed
  01f0af4

Commits on Jun 7, 2012

• Handles (somewhat pathological) 1-leaf case without div by 0 now.

  tomfy

  committed
  44330ac

Commits on Jun 13, 2012

• handle gene species not in species tree better.

  tomfy

  committed
  de3cfec

• add sub non-speciestree_leafnode_names, other improved handling of gene species not in species tree.

  tomfy

  committed
  abfe7cc

Commits on Jun 18, 2012

• eliminate parent_hilited argument to recursive_draw.

  tomfy

  committed
  89bb0d6

Commits on Jun 20, 2012

• Combined phylo.t, phylo_test.t

  tomfy

  committed
  3513d8a

Commits on Jun 26, 2012

• add species bithash tests

  tomfy

  committed
  d3bff11

• get_standard_species now uses to_standard_format if get_standard_name returns undefined value.

  tomfy

  committed
  84989d0

• changed 1 comment

  tomfy

  committed
  87c8232

• Deleting phylo_test.t (its tests are in phylo.t)

  tomfy

  committed
  44de7da

Commits on Jul 2, 2012

• In find_mindl_node decided on path for urec in more sensible way.

  tomfy

  committed
  416fa10

Commits on Jul 10, 2012

• copy method now also copies attibute 'species_bit_pattern'

  tomfy

  committed
  6bce192

• find_mindl_node now works with a copy of the gene tree,

  Show description for 725551e
  tomfy

  committed
  725551e

• Now skipping tokens containing only whitespace, in parse.

  tomfy

  committed
  bb830ab

Commits on Jul 12, 2012

• delete a print statement

  tomfy

  committed
  bb72fae

• delete a print statement.

  tomfy

  committed
  fa9782e

• 1) In reset_root_to_point_on_branch, point to reset root to is specified

  Show description for b50f653
  tomfy

  committed
  b50f653

Commits on Jul 13, 2012

• Handles the case of <2 leave left after pruning those

  Show description for 15fd336
  tomfy

  committed
  15fd336

• Initial commit. Class to analyze alignments for orthology.

  tomfy

  committed
  46c1987

• Initial commit. Class to get overlap from alignment,

  Show description for 7ad1d8c
  tomfy

  committed
  7ad1d8c

Commits on Jul 16, 2012

• dir deleted

  tomfy

  committed
  4db4d30

Commits on Jul 17, 2012

• Module for translating seqence ids to species.

  tomfy

  committed
  fd733c8

• For running MrBayes. Initial commit in cxgn-corelibs

  tomfy

  committed
  ceea2b4

• Tests to go with Orthologger module.

  tomfy

  committed
  95d01dd

• Remove extraneous printing in test.

  tomfy

  committed
  d9833d0

• improve pod for RF_distance

  tomfy

  committed
  7183d51

Commits on Jul 19, 2012

• Orthologger -> CXGN::Phylo::Orthologger

  tomfy

  committed
  ba8bdf0

• package name Orthologger -> CXGN::Phylo::Orthologger

  tomfy

  committed
  372e162

• Now uses trees id_taxon_map to get species from seq id.

  tomfy

  committed
  1adbf70

• package name Orthologger -> CXGN::Phylo::Orthologger

  tomfy

  committed
  f4424dd

• added IdTaxonMap.

  tomfy

  committed
  bb714d9

Commits on Jul 20, 2012

• use Math::BigInt for species bit patterns; add collapsing after each node deletion to prune_leaves

  tomfy

  committed
  5454279

• add a comment

  tomfy

  committed
  2e72829

Commits on Aug 2, 2012

• ortholog_result_string now calls Tree::leaf_ortholog_table

  tomfy

  committed
  cdb9e6b

• Calls leaf_ortholog_table (sub name changed in Tree)

  tomfy

  committed
  bcd5675

• sub leaf_ortholog_table added.

  tomfy

  committed
  d5efa40

Commits on Dec 5, 2012

• test

  tomfy

  committed
  ef1c456

• deleted.

  tomfy

  committed
  39f0173