obitools4/pkg/obiapat/pattern.go

package obiapat

/*
#cgo CFLAGS: -g -Wall
#include <stdlib.h>
#include "obiapat.h"
*/
import "C"
import (
	"errors"
	"runtime"
	"unsafe"

	log "github.com/sirupsen/logrus"

	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)

var _MaxPatLen = int(C.MAX_PAT_LEN)

// var _AllocatedApaSequences = int64(0)
var _AllocatedApaPattern = 0

// ApatPattern stores a regular pattern usable by the
// Apat algorithm functions and methods
type _ApatPattern struct {
	pointer *C.Pattern
}

type ApatPattern struct {
	pointer *_ApatPattern
}

// ApatSequence stores sequence in structure usable by the
// Apat algorithm functions and methods
type _ApatSequence struct {
	pointer *C.Seq
}

type ApatSequence struct {
	pointer *_ApatSequence
}

// NilApatPattern is the nil instance of the BuildAlignArena
// type.
var NilApatPattern = ApatPattern{nil}

// NilApatSequence is the nil instance of the ApatSequence
// type.
var NilApatSequence = ApatSequence{nil}

// MakeApatPattern builds a new ApatPattern.
// The created object wrap a C allocated structure.
// Do not forget to free it when it is no more needed
// to forbid memory leaks using the Free methode of the
// ApatPattern.
// The pattern is a short DNA sequence (up to 64 symboles).
// Ambiguities can be represented or using UIPAC symboles,
// or using the [...] classical in regular pattern grammar.
// For example, the ambiguity A/T can be indicated using W
// or [AT]. A nucleotide can be negated by preceding it with
// a '!'. The APAT algorithm allows for error during the
// matching process. The maximum number of tolerated error
// is indicated at the construction of the pattern using
// the errormax parameter. Some positions can be marked as not
// allowed for mismatches. They have to be signaled using a '#'
// sign after the corresponding nucleotide.
func MakeApatPattern(pattern string, errormax int) (ApatPattern, error) {
	cpattern := C.CString(pattern)
	defer C.free(unsafe.Pointer(cpattern))
	cerrormax := C.int32_t(errormax)
	var errno C.int32_t
	var errmsg *C.char

	apc := C.buildPattern(cpattern, cerrormax, &errno, &errmsg)

	if apc == nil {
		message := C.GoString(errmsg)
		C.free(unsafe.Pointer(errmsg))
		return NilApatPattern, errors.New(message)
	}

	ap := _ApatPattern{apc}

	runtime.SetFinalizer(&ap, func(p *_ApatPattern) {
		// log.Printf("Finaliser called on %s\n", C.GoString(p.pointer.cpat))
		C.free(unsafe.Pointer(p.pointer))
	})

	return ApatPattern{pointer: &ap}, nil
}

// ReverseComplement method builds a new ApatPattern
// matching the reverse complemented sequence of the original
// pattern.
func (pattern ApatPattern) ReverseComplement() (ApatPattern, error) {
	var errno C.int32_t
	var errmsg *C.char
	apc := C.complementPattern((*C.Pattern)(pattern.pointer.pointer), &errno, &errmsg)

	if apc == nil {
		message := C.GoString(errmsg)
		C.free(unsafe.Pointer(errmsg))
		return ApatPattern{nil}, errors.New(message)
	}

	ap := _ApatPattern{apc}

	runtime.SetFinalizer(&ap, func(p *_ApatPattern) {
		// log.Printf("Finaliser called on %s\n", C.GoString(p.pointer.cpat))
		C.free(unsafe.Pointer(p.pointer))
	})

	return ApatPattern{pointer: &ap}, nil
}

// String method casts the ApatPattern to a Go String.
func (pattern ApatPattern) String() string {
	return C.GoString(pattern.pointer.pointer.cpat)
}

// Length method returns the length of the matched pattern.
func (pattern ApatPattern) Length() int {
	return int(pattern.pointer.pointer.patlen)
}

// Release the C allocated memory of an ApatPattern instance.
//
// Thee method ensurse that the C structure wrapped in
// an ApatPattern instance is released. Normally this
// action is taken in charge by a finalizer and the call
// to the Free meethod is not mandatory. Nevertheless,
// If you choose to call this method, it will disconnect
// the finalizer associated to the ApatPattern instance
// to avoid double freeing.
func (pattern ApatPattern) Free() {
	// log.Printf("Free called on %s\n", C.GoString(pattern.pointer.pointer.cpat))
	if pattern.pointer != nil {
		C.free(unsafe.Pointer(pattern.pointer.pointer))
		runtime.SetFinalizer(pattern.pointer, nil)

		pattern.pointer = nil
	}
}

// Print method prints the ApatPattern to the standard output.
// This is mainly a debug method.
func (pattern ApatPattern) Print() {
	C.PrintDebugPattern(C.PatternPtr(pattern.pointer.pointer))
}

// MakeApatSequence casts an obiseq.BioSequence to an ApatSequence.
// The circular parameter indicates the topology of the sequence.
// if sequence is circular (ciruclar = true), the match can occurs
// at the junction. To limit memory allocation, it is possible to provide
// an already allocated ApatSequence to recycle its allocated memory.
// The provided sequence is no more usable after the call.
func MakeApatSequence(sequence *obiseq.BioSequence, circular bool, recycle ...ApatSequence) (ApatSequence, error) {
	var errno C.int32_t
	var errmsg *C.char
	var p unsafe.Pointer
	seqlen := sequence.Length()

	ic := 0
	if circular {
		ic = 1
	}

	var out *C.Seq

	if len(recycle) > 0 {
		out = recycle[0].pointer.pointer
		if (int(out.seqlen) < seqlen || int(out.seqlen) > 5*seqlen) && out.cseq != nil {
			C.free(unsafe.Pointer(out.cseq))
			out.cseq = nil
		}
	} else {
		out = nil
	}

	if out == nil || out.cseq == nil {

		p = C.malloc(C.size_t(seqlen) + 1)
		// if p != nil {
		// 	// atomic.AddInt64(&_AllocatedApaSequences, 1)
		// }
	} else {
		p = unsafe.Pointer(out.cseq)
	}

	if p == nil {
		log.Panicln("Cannot allocate memory chunk for Cseq Apat sequecence")
	}

	// copy the data into the buffer, by converting it to a Go array
	cBuf := (*[1 << 31]byte)(p)
	copy(cBuf[:], sequence.Sequence())
	cBuf[sequence.Length()] = 0

	pseqc := C.new_apatseq((*C.char)(p), C.int32_t(ic), C.int32_t(seqlen),
		(*C.Seq)(out),
		&errno, &errmsg)

	if pseqc == nil {
		message := C.GoString(errmsg)
		C.free(unsafe.Pointer(errmsg))
		if p != nil {
			C.free(p)
			// atomic.AddInt64(&_AllocatedApaSequences, -1)
		}
		return NilApatSequence, errors.New(message)
	}

	if out == nil {
		// log.Printf("Make ApatSeq called on %p -> %p\n", out, pseqc)
		seq := _ApatSequence{pointer: pseqc}

		runtime.SetFinalizer(&seq, func(apat_p *_ApatSequence) {
			var errno C.int32_t
			var errmsg *C.char
			// log.Printf("Finaliser called on %p\n", apat_p.pointer)

			if apat_p != nil && apat_p.pointer != nil {
				if apat_p.pointer.cseq != nil {
					C.free(unsafe.Pointer(apat_p.pointer.cseq))
					apat_p.pointer.cseq = nil
					// atomic.AddInt64(&_AllocatedApaSequences, -1)
				}
				C.delete_apatseq(apat_p.pointer, &errno, &errmsg)
			}
		})

		return ApatSequence{&seq}, nil
	}

	recycle[0].pointer.pointer = pseqc

	//log.Println(C.GoString(pseq.cseq))

	return ApatSequence{recycle[0].pointer}, nil
}

// Length method returns the length of the ApatSequence.
func (sequence ApatSequence) Length() int {
	return int(sequence.pointer.pointer.seqlen)
}

// Free method ensure that the C structure wrapped is
// desallocated
func (sequence ApatSequence) Free() {
	var errno C.int32_t
	var errmsg *C.char

	// log.Printf("Free called on %p\n", sequence.pointer.pointer)

	if sequence.pointer != nil && sequence.pointer.pointer != nil {

		if sequence.pointer.pointer.cseq != nil {
			C.free(unsafe.Pointer(sequence.pointer.pointer.cseq))
			sequence.pointer.pointer.cseq = nil
			// atomic.AddInt64(&_AllocatedApaSequences, -1)
		}

		C.delete_apatseq(sequence.pointer.pointer,
			&errno, &errmsg)

		runtime.SetFinalizer(sequence.pointer, nil)

		sequence.pointer = nil
	}
}

// FindAllIndex methood returns the position of every occurrences of the
// pattern on the provided sequences. The search can be limited
// to a portion of the sequence by adding one or two integer parameters
// when calling the FindAllIndex method. The fisrt optional argument indicates
// the starting point of the search. The first nucleotide of the sequence is
// indexed as 0. The second optional argument indicates the length of the region
// where the pattern is looked for.
// The FindAllIndex methood returns return a slice of [3]int. The two firsts
// values of the [3]int indicate respectively the start and the end position of
// the match. Following the GO convention the end position is not included in the
// match. The third value indicates the number of error detected for this occurrence.
func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, limits ...int) (loc [][3]int) {
	begin := 0
	length := sequence.Length()

	if len(limits) > 0 {
		begin = limits[0]
	}

	if len(limits) > 1 {
		length = limits[1]
	}

	nhits := int(C.ManberAll(sequence.pointer.pointer,
		pattern.pointer.pointer,
		0,
		C.int32_t(begin),
		C.int32_t(length+C.MAX_PAT_LEN)))

	if nhits == 0 {
		return nil
	}

	stktmp := (*[1 << 30]int32)(unsafe.Pointer(sequence.pointer.pointer.hitpos[0].val))
	errtmp := (*[1 << 30]int32)(unsafe.Pointer(sequence.pointer.pointer.hiterr[0].val))
	patlen := int(pattern.pointer.pointer.patlen)

	for i := 0; i < nhits; i++ {
		start := int(stktmp[i])
		err := int(errtmp[i])

		loc = append(loc, [3]int{start, start + patlen, err})
	}

	return loc
}

// func AllocatedApaSequences() int {
// 	return int(_AllocatedApaSequences)
// }