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#!/usr/bin/env ruby
def gen_access_raw(mode,structvar,pre)
if mode == "bytes"
return "*#{pre}ptr"
elsif mode == "twobit"
return "gt_twobitencoding_char_at_pos(\n" +
" " * 30 + "#{structvar}->twobitencoding,\n" +
" " * 30 + "#{pre}ptr)"
elsif mode == "encseq"
return "gt_encseq_get_encoded_char(#{structvar}->encseq,\n" +
" " * 20 + "#{pre}ptr,\n" +
" " * 20 + "GT_READMODE_FORWARD)"
else
return "gt_sequenceobject_esr_get(#{structvar},#{pre}ptr)"
end
end
def gen_compare(a_mode,b_mode,wildcard,complement)
access_v = gen_access_raw(b_mode,"vseq","v")
splitter = if access_v.length > 10 then ("\n" + " " * 12) else " " end
cmp_expr = (if complement then ("GT_COMPLEMENTBASE(") else "" end) +
"#{access_v}" +
(if complement then ")" else "" end) + ")\n" +
" " * 10 + "break"
if wildcard
return "const GtUchar cu = #{gen_access_raw(a_mode,"useq","u")};\n" +
" " * 8 + "if (cu == GT_WILDCARD ||" + splitter + "cu !=" + splitter +
cmp_expr
else
return "if (#{gen_access_raw(a_mode,"useq","u")} !=" + splitter +
cmp_expr
end
end
def gen_suffix(wildcard)
if wildcard
return "_wildcard"
else
return ""
end
end
def gen_func_name(a_mode,b_mode,wildcard)
return "ft_longest_common_#{a_mode}_#{b_mode}#{gen_suffix(wildcard)}"
end
def gen_ptr_assign(mode,pre,left2right)
if mode == "bytes"
if left2right
return "#{pre}seq->bytesequenceptr + #{pre}seq->offset + #{pre}start; " +
"#{pre}step = 1"
else
return "#{pre}seq->bytesequenceptr + #{pre}seq->offset - #{pre}start; " +
"#{pre}step = -1"
end
else
if left2right
if mode != "encseq_reader"
return "#{pre}seq->offset + #{pre}start; #{pre}step = 1"
else
return "#{pre}start"
end
else
if mode != "encseq_reader"
return "#{pre}seq->offset - #{pre}start; #{pre}step = -1"
else
return "#{pre}start"
end
end
end
end
def gen_ptr_set(mode,pre)
return ["\n if (#{pre}seq->read_seq_left2right)",
"{",
" #{pre}ptr = #{gen_ptr_assign(mode,pre,true)};",
"} else",
"{",
" #{pre}ptr = #{gen_ptr_assign(mode,pre,false)};",
"}"].join("\n ")
end
def gen_minsub(pre)
other = if pre == "u" then "v" else "u" end
return ["\n GtUword minsubstringlength = #{other}start + #{pre}seq->substringlength - #{pre}start;",
"if (#{other}seq->substringlength < minsubstringlength)",
"{",
" minsubstringlength = #{other}seq->substringlength;",
"}"].join("\n ")
end
def gen_minsubstringlength_decl(a_mode,b_mode)
minmatch_decl = ["\n GtUword minsubstringlength = useq->substringlength - ustart;",
"if (vseq->substringlength < useq->insubstringlength)",
"{",
" minsubstringlength = vseq->substringlength - vstart;",
"}"].join("\n ") +
gen_ptr_set(a_mode,"u") +
gen_ptr_set(b_mode,"v")
if a_mode == "encseq_reader"
if b_mode == "encseq_reader"
return "GtUword uptr = ustart, vptr = vstart;" +
gen_minsub("v")
elsif b_mode == "bytes"
return "GtUword uptr = ustart; const GtUchar *vptr; int vstep;" +
gen_minsub("v") +
gen_ptr_set(b_mode,"v")
else
return "GtUword uptr = ustart, vptr; int vstep;" +
gen_minsub("v") +
gen_ptr_set(b_mode,"v")
end
elsif b_mode == "encseq_reader"
if a_mode == "bytes"
return "const GtUchar *uptr; int ustep; GtUword vptr = vstart;" +
gen_minsub("u") +
gen_ptr_set(a_mode,"u")
else
return "GtUword uptr; int ustep; GtUword vptr = vstart;" +
gen_minsub("u") +
gen_ptr_set(a_mode,"u")
end
else
minmatch_decl = [" GtUword minsubstringlength = useq->substringlength - ustart,",
"matchlength = 0;",
"if (vseq->substringlength - vstart < minsubstringlength)",
"{",
" minsubstringlength = vseq->substringlength - vstart;",
"}"].join("\n ") +
gen_ptr_set(a_mode,"u") +
gen_ptr_set(b_mode,"v")
if a_mode == "bytes"
if b_mode == "bytes"
return "const GtUchar *uptr, *vptr; int ustep, vstep;\n" +
minmatch_decl
else
return "const GtUchar *uptr; GtUword vptr; int ustep, vstep;\n" +
minmatch_decl
end
else
if b_mode == "bytes"
return "GtUword uptr; const GtUchar *vptr; int ustep, vstep;\n" +
minmatch_decl
else
return "GtUword uptr, vptr; int ustep, vstep;\n" +
minmatch_decl
end
end
end
end
def gen_ptr_incr(mode,pre)
if mode == "encseq_reader"
return "#{pre}ptr++"
else
return "#{pre}ptr += #{pre}step"
end
end
def gen_matchlength_inc(a_mode,b_mode)
if a_mode == "encseq_reader" or b_mode == "encseq_reader"
return ""
else
return "matchlength++;"
end
end
def gen_smaller(a_mode,b_mode)
if a_mode == "encseq_reader"
return "uptr"
elsif b_mode == "encseq_reader"
return "vptr"
else
return "matchlength"
end
end
def gen_return_matchlength(a_mode,b_mode)
if a_mode == "encseq_reader"
return "uptr - ustart"
elsif b_mode == "encseq_reader"
return "vptr - vstart"
else
return "matchlength"
end
end
def longestcommonfunc(a_mode,b_mode,wildcard)
puts <<EOF
static GtUword #{gen_func_name(a_mode,b_mode,wildcard)}(
GtFtSequenceObject *useq,
GtUword ustart,
GtFtSequenceObject *vseq,
const GtUword vstart)
{
if (ustart < useq->substringlength && vstart < vseq->substringlength)
{
#{gen_minsubstringlength_decl(a_mode,b_mode)}
if (vseq->dir_is_complement)
{
do
{
#{gen_compare(a_mode,b_mode,wildcard,true)};
#{gen_ptr_incr(a_mode,"u")};
#{gen_ptr_incr(b_mode,"v")};#{gen_matchlength_inc(a_mode,b_mode)}
} while (#{gen_smaller(a_mode,b_mode)} < minsubstringlength);
} else
{
do
{
#{gen_compare(a_mode,b_mode,wildcard,false)};
#{gen_ptr_incr(a_mode,"u")};
#{gen_ptr_incr(b_mode,"v")};#{gen_matchlength_inc(a_mode,b_mode)}
} while (#{gen_smaller(a_mode,b_mode)} < minsubstringlength);
}
return #{gen_return_matchlength(a_mode,b_mode)};
}
return 0;
}
EOF
end
first = true
func_list = Array.new()
modes = ["twobit","encseq_reader","encseq","bytes"]
[false,true].each do |wildcard|
modes.each do |a_mode|
modes.each do |b_mode|
if first
first = false
else
puts ""
end
longestcommonfunc(a_mode,b_mode,wildcard)
func_list.push(gen_func_name(a_mode,b_mode,wildcard))
end
end
end
firstwildcard = nil
firstfunc = true
puts "\nGtLongestCommonFunc ft_longest_common_func_tab[] =\n{"
func_list.each_with_index do |func_name,idx|
if firstwildcard.nil? and func_name.match(/_wildcard/)
firstwildcard = idx
end
if firstfunc
firstfunc = false
else
puts ","
end
print " /* #{idx} */ #{func_name}"
end
puts "\n};"
puts "const int ft_longest_common_num_modes = #{modes.length};"
puts "const int ft_longest_common_func_first_wildcard = #{firstwildcard};"
|
