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root_node.loc_idx fixed
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@bver
bver committed May 11, 2012
1 parent 66cca54 commit 8772511
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Showing 2 changed files with 91 additions and 7 deletions.
14 changes: 8 additions & 6 deletions lib/mutation_simplify.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -97,22 +97,24 @@ def match_patterns( track_reloc, patterns, node_idx )

def replace( genome, ptm, patterns, replacement, track_reloc )
args = exp_args( track_reloc, patterns, ptm )

root_node = track_reloc[ptm.first]
res = genome[0 ... root_node.from].clone
replacement.each do |idx|

replacement.each_with_index do |idx,i|
if idx.kind_of? Expansion
res << 0 if @mapper_type == 'DepthLocus' # TODO: different Codon types?
res << (i==0 ? root_node.loc_idx : 0) if @mapper_type == 'DepthLocus' # TODO: different Codon types?
if idx.alt_idx.respond_to? 'call'
out = idx.alt_idx.call args
return genome.clone if out.nil?
res << text2alt_idx( idx.symbol, out )
else
res << idx.alt_idx
end
else
else # subtree
node = track_reloc[ ptm[idx] ]
res.concat genome[node.from .. node.to]
subtree = genome[node.from .. node.to].clone
subtree[0] = root_node.loc_idx if @mapper_type == 'DepthLocus' and i==0
res.concat subtree
end
end

Expand Down Expand Up @@ -162,7 +164,7 @@ def text2alt_idx( symbol, text, hash=@grammar_texts )
found = hash[symbol]
raise "MutationSimplify: altidx for symbol '#{symbol}' not found" if found.nil?
res = found[text]
raise "MutationSimplify: altidx for RuleAlt '#{text}' not found" if res.nil?
raise "MutationSimplify: altidx for RuleAlt '#{text}' (symbol '#{symbol}') not found" if res.nil?
res
end

Expand Down
84 changes: 83 additions & 1 deletion test/tc_mutation_simplify.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -705,7 +705,7 @@ def test_alt_idx_text_grammar_conversions
assert_equal( 2, s.text2alt_idx( 'op', '/' ) )

exception = assert_raise( RuntimeError ) { s.text2alt_idx( 'expr', 'unknown' ) }
assert_equal( "MutationSimplify: altidx for RuleAlt 'unknown' not found", exception.message )
assert_equal( "MutationSimplify: altidx for RuleAlt 'unknown' (symbol 'expr') not found", exception.message )

exception = assert_raise( RuntimeError ) { s.text2alt_idx( 'unknown', 'irrelevant' ) }
assert_equal( "MutationSimplify: altidx for symbol 'unknown' not found", exception.message )
Expand Down Expand Up @@ -1125,5 +1125,87 @@ def test_parse_yaml
assert_equal( "7", replacement[2].alt_idx.call(input) )
end

def test_mult_by_two_bugfix
#[38,219, 206,216, 239,178, 117,33, 251,35, 234,145, 244,104, 141,199, 190,132]
#SIN(COS((y+y)))
#0. expr genome:0..17 parent: locus:0 expansion:'<fn1arg> "(" <expr> ")"' 38,219,
#1. fn1arg genome:2..3 parent:0 locus:0 expansion:'"SIN"' 206,216,
#2. expr genome:4..17 parent:0 locus:0 expansion:'<expr>' 239,178,
#3. expr genome:6..17 parent:2 locus:0 expansion:'<fn1arg> "(" <expr> ")"' 117,33,
#4. expr genome:8..15 parent:3 locus:1 expansion:'"(" <expr> <op> <expr> ")"' 251,35,
#5. expr genome:10..11 parent:4 locus:0 expansion:'"y"' 234,145,
#6. op genome:12..13 parent:4 locus:0 expansion:'"+"' 244,104,
#7. expr genome:14..15 parent:4 locus:0 expansion:'"y"' 141,199,
#8. fn1arg genome:16..17 parent:3 locus:0 expansion:'"COS"' 190,132
#
#"#<struct Struct::TrackNode symbol=\"expr\", from=0, to=17, back=nil, alt_idx=3, loc_idx=0>" '<fn1arg> "(" <expr> ")"'
#"#<struct Struct::TrackNode symbol=\"fn1arg\", from=2, to=3, back=0, alt_idx=1, loc_idx=0>" '"SIN"'
#"#<struct Struct::TrackNode symbol=\"expr\", from=4, to=17, back=0, alt_idx=4, loc_idx=1>" '<expr>'
#"#<struct Struct::TrackNode symbol=\"expr\", from=6, to=17, back=2, alt_idx=3, loc_idx=0>" '<fn1arg> "(" <expr> ")"'
#"#<struct Struct::TrackNode symbol=\"expr\", from=8, to=15, back=3, alt_idx=5, loc_idx=1>" '"(" <expr> <op> <expr> ")"' root_node
#"#<struct Struct::TrackNode symbol=\"expr\", from=10, to=11, back=4, alt_idx=1, loc_idx=0>" '"y"'
#"#<struct Struct::TrackNode symbol=\"op\", from=12, to=13, back=4, alt_idx=0, loc_idx=1>" '"+"'
#"#<struct Struct::TrackNode symbol=\"expr\", from=14, to=15, back=4, alt_idx=1, loc_idx=2>" '"y"'
#"#<struct Struct::TrackNode symbol=\"fn1arg\", from=16, to=17, back=3, alt_idx=2, loc_idx=0>" '"COS"'
#

#[38,219, 206,216, 239,178, 117,33, 0, 5, 0,2, 0,2, 0,0, 0,3, 234,145, 190,132] !!! loc=0 and should be 1
#SIN(ABS(2.0))
#0. expr genome:0..15 parent: locus:0 expansion:'<fn1arg> "(" <expr> ")"' 38,219,
#1. fn1arg genome:2..3 parent:0 locus:0 expansion:'"SIN"' 206,216,
#2. expr genome:4..15 parent:0 locus:0 expansion:'<expr>' 239,178,
#3. expr genome:6..15 parent:2 locus:0 expansion:'<fn1arg> "(" <expr> ")"' 117,33,
#4. fn1arg genome:8..9 parent:3 locus:0 expansion:'"ABS"' 0,5,
#5. expr genome:10..15 parent:3 locus:0 expansion:'<_digit> "." <_digit>' 0,2,
#6. _digit genome:12..13 parent:5 locus:0 expansion:'"2"' 0,2,
#7. _digit genome:14..15 parent:5 locus:0 expansion:'"0"' 0,0,
# 234,145,
# 190,132
#
#pattern:
#- expr.main = "(" expr.same op.plus expr.same ")"
#- expr.same
#- op.plus = "+"
#- expr.same
#replacement:
#- expr = "(" expr op expr ")"
#- expr = digit "." digit
#- digit = "2"
#- digit = "0"
#- op = "*"
#- expr.same

s = MutationSimplify.new @grammar
s.mapper_type = 'DepthLocus'
s.filename = 'test/data/simplify_bug.yaml'

m = Mapper::DepthLocus.new @grammar
m.track_support_on = true

# 1st case (expansion)
genotype_src1 = [38,219, 206,216, 239,178, 117,33, 251,35, 234,145, 244,104, 141,199, 190,132]
assert_equal( 'SIN(COS((y+y)))', m.phenotype( genotype_src1 ) )
track_src1 = m.track_support

track_reloc = s.reloc(track_src1)
ptm = s.match(s.reloc(track_src1), s.rules.first.match )
#[4, 5, 6, 7]
assert_equal( [[1, 3]], s.rules.first.equals )
#[[1, 3]] -> ptm -> 5,7
assert( s.nodes_equal( track_reloc, 5, 7 ) )

# mutant = s.mutation( genotype_src1, track_src1 )
# assert_equal( 'SIN(COS((2.0*y)))', m.phenotype( mutant ) ) # simplified

# 2nd case (subtree)
genotype_src2 = [0,3, 1,5, 0,0, 0,0, 0,2, 0,0, 1,0, 0,2]
assert_equal( 'COS((x+0.0))', m.phenotype( genotype_src2 ) )
track_src2 = m.track_support

mutant = s.mutation( genotype_src2, track_src2 )
assert_equal( 'COS(x)', m.phenotype( mutant ) ) # simplified

end

end

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