Class: Edlib::Aligner

Inherits:
Object
  • Object
show all
Defined in:
lib/edlib.rb,
ext/edlib/edlibext.c

Instance Method Summary collapse

Constructor Details

#initialize(k: -1,, mode: 'NW', task: 'DISTANCE', additional_equalities: nil) ⇒ Aligner

Returns a new instance of Aligner.



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# File 'lib/edlib.rb', line 7

def initialize(k: -1, mode: 'NW', task: 'DISTANCE', additional_equalities: nil)
  mode = mode.to_s if mode.is_a? Symbol
  task = task.to_s if task.is_a? Symbol
  mode = mode.upcase if mode.is_a? String
  task = task.upcase if task.is_a? String
  initialize_raw(k, mode, task, additional_equalities)
end

Instance Method Details

#additional_equalities ⇒ Object

#additional_equalities=(equalities) ⇒ Object 



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# File 'ext/edlib/edlibext.c', line 329

static VALUE
aligner_set_additional_equalities(VALUE self, VALUE equalities)
{
	EdlibAlignConfig *config = aligner_get_config(self);
	EdlibEqualityPair *eqpairs = aligner_get_equalityPairs(self);
	return set_additional_equalities(config, eqpairs, equalities);
}

#align(query, target, nice: false) ⇒ Object 



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# File 'lib/edlib.rb', line 15

def align(query, target, nice: false)
  if nice
    align_nice(query, target)
  else
    align_raw(query, target)
  end
end

#align_raw(query, target) ⇒ Object 



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# File 'ext/edlib/edlibext.c', line 374

static VALUE
aligner_align(VALUE self, VALUE query, VALUE target)
{
	EdlibAlignConfig *config = aligner_get_config(self);
	if (!config)
	{
		rb_raise(rb_eRuntimeError, "config is NULL");
	}

	EdlibAlignResult result = edlibAlign(
			StringValueCStr(query),
			RSTRING_LEN(query),
			StringValueCStr(target),
			RSTRING_LEN(target),
			*config);

	if (result.status != 0)
	{
		rb_raise(rb_eRuntimeError, "edlibAlign failed");
	}

	VALUE edit_distance = INT2NUM(result.editDistance);
	VALUE alphabet_length = INT2NUM(result.alphabetLength);
	VALUE locations = rb_ary_new();
	VALUE alignment = rb_ary_new();
	VALUE cigar;

	int *el = result.endLocations;
	int *sl = result.startLocations;
	for (int i = 0; i < result.numLocations; i++)
	{
		VALUE ary = rb_ary_new();
		if (sl)
		{
			rb_ary_push(ary, INT2NUM(sl[i]));
		}
		else
		{
			rb_ary_push(ary, Qnil);
		}
		if (el)
		{
			rb_ary_push(ary, INT2NUM(el[i]));
		}
		else
		{
			rb_ary_push(ary, Qnil);
		}
		rb_ary_push(locations, ary);
	}

	for (int i = 0; i < result.alignmentLength; i++)
	{
		rb_ary_push(alignment, UINT2NUM(result.alignment[i]));
	}

	char *ccigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, 1); // EDLIB_CIGAR_EXTENDED
	cigar = rb_str_new2(ccigar);
	free(ccigar);

	VALUE hash = rb_hash_new();
	rb_hash_aset(hash, ID2SYM(rb_intern("edit_distance")), edit_distance);
	rb_hash_aset(hash, ID2SYM(rb_intern("alphabet_length")), alphabet_length);
	rb_hash_aset(hash, ID2SYM(rb_intern("locations")), locations);
	rb_hash_aset(hash, ID2SYM(rb_intern("alignment")), alignment);
	rb_hash_aset(hash, ID2SYM(rb_intern("cigar")), cigar);

	edlibFreeAlignResult(result);

	return hash;
}

#config ⇒ Object 



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# File 'ext/edlib/edlibext.c', line 337

static VALUE
aligner_config_hash(VALUE self)
{
	EdlibAlignConfig *config = aligner_get_config(self);

	VALUE hash = rb_hash_new();

	rb_hash_aset(hash, ID2SYM(rb_intern("k")), get_k(config));
	rb_hash_aset(hash, ID2SYM(rb_intern("mode")), get_mode(config));
	rb_hash_aset(hash, ID2SYM(rb_intern("task")), get_task(config));
	rb_hash_aset(hash, ID2SYM(rb_intern("additional_equalities")), get_additional_equalities(config));

	return hash;
}

#k ⇒ Object

#k= ⇒ Object

#mode ⇒ Object

#mode= ⇒ Object

#task ⇒ Object

#task= ⇒ Object