JNIEXPORT void JNICALL
SurfaceData_IntersectBounds(SurfaceDataBounds *dst, SurfaceDataBounds *src)
{
int t;
GETMAX(dst->x1, src->x1);
GETMAX(dst->y1, src->y1);
GETMIN(dst->x2, src->x2);
GETMIN(dst->y2, src->y2);
}
JNIEXPORT void JNICALL
SurfaceData_IntersectBoundsXYXY(SurfaceDataBounds *bounds,
jint x1, jint y1, jint x2, jint y2)
{
int t;
GETMAX(bounds->x1, x1);
GETMAX(bounds->y1, y1);
GETMIN(bounds->x2, x2);
GETMIN(bounds->y2, y2);
}
JNIEXPORT void JNICALL
SurfaceData_IntersectBlitBounds(SurfaceDataBounds *src,
SurfaceDataBounds *dst,
jint dx, jint dy)
{
int t;
GETMAX(dst->x1, src->x1 + dx);
GETMAX(dst->y1, src->y1 + dy);
GETMIN(dst->x2, src->x2 + dx);
GETMIN(dst->y2, src->y2 + dy);
GETMAX(src->x1, dst->x1 - dx);
GETMAX(src->y1, dst->y1 - dy);
GETMIN(src->x2, dst->x2 - dx);
GETMIN(src->y2, dst->y2 - dy);
}
void AlignColorSpaceGappedBounded(char *colors,
int readLength,
char *reference,
int referenceLength,
ScoringMatrix *sm,
AlignedEntry *a,
AlignMatrix *matrix,
int32_t position,
char strand,
int32_t maxH,
int32_t maxV)
{
//char *FnName = "AlignColorSpaceGappedBounded";
int i, j;
int alphabetSize=ALPHABET_SIZE;
assert(0 < readLength);
assert(0 < referenceLength);
alphabetSize = AlignColorSpaceGetAlphabetSize(colors, readLength, reference, referenceLength);
AlignColorSpaceInitializeAtStart(colors, matrix, sm, readLength, referenceLength, alphabetSize, COLOR_SPACE_START_NT);
/* Fill in the matrix according to the recursive rules */
for(i=0;i<readLength;i++) { /* read/rows */
/* Get the current color */
for(j=GETMAX(0, i - maxV);
j <= GETMIN(referenceLength-1, referenceLength - (readLength - maxH) + i);
j++) { /* reference/columns */
assert(i-maxV <= j && j <= referenceLength - (readLength - maxH) + i);
AlignColorSpaceFillInCell(colors, readLength, reference, referenceLength, sm, matrix, i, j, colors[i], maxH, maxV, alphabetSize);
}
}
AlignColorSpaceRecoverAlignmentFromMatrix(a, matrix, colors, readLength, reference, referenceLength, 0, 0, readLength - maxV, position, strand, alphabetSize, 0);
}
