Add automatic garbage collection on ApatPattern

pkg/obiapat/pattern.go

@@ -8,6 +8,7 @@ package obiapat
 import "C"
 import (
 	"errors"
+	"runtime"
 	"unsafe"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@@ -17,10 +18,14 @@ var _MaxPatLen = int(C.MAX_PAT_LEN)
 
 // ApatPattern stores a regular pattern usable by the
 // Apat algorithm functions and methods
-type ApatPattern struct {
+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 {
@@ -58,15 +63,22 @@ func MakeApatPattern(pattern string, errormax int) (ApatPattern, error) {
 	var errno C.int32_t
 	var errmsg *C.char
 
-	ap := C.buildPattern(cpattern, cerrormax, &errno, &errmsg)
+	apc := C.buildPattern(cpattern, cerrormax, &errno, &errmsg)
 
-	if ap == nil {
+	if apc == nil {
 		message := C.GoString(errmsg)
 		C.free(unsafe.Pointer(errmsg))
 		return NilApatPattern, errors.New(message)
 	}
 
-	return ApatPattern{pointer: ap}, nil
+	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
@@ -75,38 +87,56 @@ func MakeApatPattern(pattern string, errormax int) (ApatPattern, error) {
 func (pattern ApatPattern) ReverseComplement() (ApatPattern, error) {
 	var errno C.int32_t
 	var errmsg *C.char
-	ap := C.complementPattern((*C.Pattern)(pattern.pointer), &errno, &errmsg)
+	apc := C.complementPattern((*C.Pattern)(pattern.pointer.pointer), &errno, &errmsg)
 
-	if ap == nil {
+	if apc == nil {
 		message := C.GoString(errmsg)
 		C.free(unsafe.Pointer(errmsg))
 		return ApatPattern{nil}, errors.New(message)
 	}
 
-	return ApatPattern{pointer: ap}, nil
+	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.cpat)
+	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.patlen)
+	return int(pattern.pointer.pointer.patlen)
 }
 
-// Free method ensure that the C structure wrapped is
-// desallocated
+// 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() {
-	C.free(unsafe.Pointer(pattern.pointer))
+	// log.Printf("Free called on %s\n", C.GoString(pattern.pointer.pointer.cpat))
+	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))
+	C.PrintDebugPattern(C.PatternPtr(pattern.pointer.pointer))
 }
 
 // MakeApatSequence casts an obiseq.BioSequence to an ApatSequence.
@@ -197,7 +227,7 @@ func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, limits ...int) (l
 	}
 
 	nhits := int(C.ManberAll(sequence.pointer,
-		pattern.pointer,
+		pattern.pointer.pointer,
 		0,
 		C.int32_t(begin),
 		C.int32_t(length+C.MAX_PAT_LEN)))
@@ -208,7 +238,7 @@ func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, limits ...int) (l
 
 	stktmp := (*[1 << 30]int32)(unsafe.Pointer(sequence.pointer.hitpos[0].val))
 	errtmp := (*[1 << 30]int32)(unsafe.Pointer(sequence.pointer.hiterr[0].val))
-	patlen := int(pattern.pointer.patlen)
+	patlen := int(pattern.pointer.pointer.patlen)
 
 	for i := 0; i < nhits; i++ {
 		start := int(stktmp[i])