virtual void onSizeChange() {
this->INHERITED::onSizeChange();
fNext->setSize(this->width(), this->height());
fPrev->setSize(this->width(), this->height());
SkScalar lr = 0, ud = 0;
if (fAnimationDirection & (kLeftDirection|kULDirection|kDLDirection))
lr = this->width();
if (fAnimationDirection & (kRightDirection|kURDirection|kDRDirection))
lr = -this->width();
if (fAnimationDirection & (kUpDirection|kULDirection|kURDirection))
ud = this->height();
if (fAnimationDirection & (kDownDirection|kDLDirection|kDRDirection))
ud = -this->height();
fBegin[kPrevX] = fBegin[kPrevY] = 0;
fBegin[kNextX] = lr;
fBegin[kNextY] = ud;
fNext->setLocX(lr);
fNext->setLocY(ud);
if (is_transition(fPrev))
lr = ud = 0;
fEnd[kPrevX] = -lr;
fEnd[kPrevY] = -ud;
fEnd[kNextX] = fEnd[kNextY] = 0;
SkScalar blend[] = { SkFloatToScalar(0.8f), SkFloatToScalar(0.0f),
SkFloatToScalar(0.0f), SK_Scalar1 };
fInterp.setKeyFrame(0, SkTime::GetMSecs(), fBegin, blend);
fInterp.setKeyFrame(1, SkTime::GetMSecs()+kDurationMS, fEnd, blend);
}
/**
* ir_rc6_decode() - Decode one RC6 pulse or space
* @dev: the struct rc_dev descriptor of the device
* @ev: the struct ir_raw_event descriptor of the pulse/space
*
* This function returns -EINVAL if the pulse violates the state machine
*/
static int ir_rc6_decode(struct rc_dev *dev, struct ir_raw_event ev)
{
struct rc6_dec *data = &dev->raw->rc6;
u32 scancode;
u8 toggle;
enum rc_proto protocol;
if (!is_timing_event(ev)) {
if (ev.reset)
data->state = STATE_INACTIVE;
return 0;
}
if (!geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
goto out;
again:
IR_dprintk(2, "RC6 decode started at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
if (!geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!ev.pulse)
break;
/* Note: larger margin on first pulse since each RC6_UNIT
is quite short and some hardware takes some time to
adjust to the signal */
if (!eq_margin(ev.duration, RC6_PREFIX_PULSE, RC6_UNIT))
break;
data->state = STATE_PREFIX_SPACE;
data->count = 0;
return 0;
case STATE_PREFIX_SPACE:
if (ev.pulse)
break;
if (!eq_margin(ev.duration, RC6_PREFIX_SPACE, RC6_UNIT / 2))
break;
data->state = STATE_HEADER_BIT_START;
data->header = 0;
return 0;
case STATE_HEADER_BIT_START:
if (!eq_margin(ev.duration, RC6_BIT_START, RC6_UNIT / 2))
break;
data->header <<= 1;
if (ev.pulse)
data->header |= 1;
data->count++;
data->state = STATE_HEADER_BIT_END;
return 0;
case STATE_HEADER_BIT_END:
if (!is_transition(&ev, &dev->raw->prev_ev))
break;
if (data->count == RC6_HEADER_NBITS)
data->state = STATE_TOGGLE_START;
else
data->state = STATE_HEADER_BIT_START;
decrease_duration(&ev, RC6_BIT_END);
goto again;
case STATE_TOGGLE_START:
if (!eq_margin(ev.duration, RC6_TOGGLE_START, RC6_UNIT / 2))
break;
data->toggle = ev.pulse;
data->state = STATE_TOGGLE_END;
return 0;
case STATE_TOGGLE_END:
if (!is_transition(&ev, &dev->raw->prev_ev) ||
!geq_margin(ev.duration, RC6_TOGGLE_END, RC6_UNIT / 2))
break;
if (!(data->header & RC6_STARTBIT_MASK)) {
IR_dprintk(1, "RC6 invalid start bit\n");
break;
}
data->state = STATE_BODY_BIT_START;
decrease_duration(&ev, RC6_TOGGLE_END);
data->count = 0;
data->body = 0;
switch (rc6_mode(data)) {
case RC6_MODE_0:
data->wanted_bits = RC6_0_NBITS;
break;
case RC6_MODE_6A:
data->wanted_bits = RC6_6A_NBITS;
break;
default:
IR_dprintk(1, "RC6 unknown mode\n");
goto out;
}
goto again;
case STATE_BODY_BIT_START:
if (eq_margin(ev.duration, RC6_BIT_START, RC6_UNIT / 2)) {
/* Discard LSB's that won't fit in data->body */
if (data->count++ < CHAR_BIT * sizeof data->body) {
data->body <<= 1;
if (ev.pulse)
data->body |= 1;
}
data->state = STATE_BODY_BIT_END;
return 0;
} else if (RC6_MODE_6A == rc6_mode(data) && !ev.pulse &&
geq_margin(ev.duration, RC6_SUFFIX_SPACE, RC6_UNIT / 2)) {
data->state = STATE_FINISHED;
goto again;
}
break;
case STATE_BODY_BIT_END:
if (!is_transition(&ev, &dev->raw->prev_ev))
break;
if (data->count == data->wanted_bits)
data->state = STATE_FINISHED;
else
data->state = STATE_BODY_BIT_START;
decrease_duration(&ev, RC6_BIT_END);
goto again;
case STATE_FINISHED:
if (ev.pulse)
break;
switch (rc6_mode(data)) {
case RC6_MODE_0:
scancode = data->body;
toggle = data->toggle;
protocol = RC_PROTO_RC6_0;
IR_dprintk(1, "RC6(0) scancode 0x%04x (toggle: %u)\n",
scancode, toggle);
break;
case RC6_MODE_6A:
if (data->count > CHAR_BIT * sizeof data->body) {
IR_dprintk(1, "RC6 too many (%u) data bits\n",
data->count);
goto out;
}
scancode = data->body;
switch (data->count) {
case 20:
protocol = RC_PROTO_RC6_6A_20;
toggle = 0;
break;
case 24:
protocol = RC_PROTO_RC6_6A_24;
toggle = 0;
break;
case 32:
if ((scancode & RC6_6A_LCC_MASK) == RC6_6A_MCE_CC) {
protocol = RC_PROTO_RC6_MCE;
toggle = !!(scancode & RC6_6A_MCE_TOGGLE_MASK);
scancode &= ~RC6_6A_MCE_TOGGLE_MASK;
} else {
protocol = RC_PROTO_RC6_6A_32;
toggle = 0;
}
break;
default:
IR_dprintk(1, "RC6(6A) unsupported length\n");
goto out;
}
IR_dprintk(1, "RC6(6A) proto 0x%04x, scancode 0x%08x (toggle: %u)\n",
protocol, scancode, toggle);
break;
default:
IR_dprintk(1, "RC6 unknown mode\n");
goto out;
}
rc_keydown(dev, protocol, scancode, toggle);
data->state = STATE_INACTIVE;
return 0;
}
out:
IR_dprintk(1, "RC6 decode failed at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
data->state = STATE_INACTIVE;
return -EINVAL;
}
/**
* ir_rc5_decode() - Decode one RC-5 pulse or space
* @dev: the struct rc_dev descriptor of the device
* @ev: the struct ir_raw_event descriptor of the pulse/space
*
* This function returns -EINVAL if the pulse violates the state machine
*/
static int ir_rc5_decode(struct rc_dev *dev, struct ir_raw_event ev)
{
struct rc5_dec *data = &dev->raw->rc5;
u8 toggle;
u32 scancode;
if (!(dev->raw->enabled_protocols & RC_TYPE_RC5))
return 0;
if (!is_timing_event(ev)) {
if (ev.reset)
data->state = STATE_INACTIVE;
return 0;
}
if (!geq_margin(ev.duration, RC5_UNIT, RC5_UNIT / 2))
goto out;
again:
IR_dprintk(2, "RC5(x) decode started at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
if (!geq_margin(ev.duration, RC5_UNIT, RC5_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!ev.pulse)
break;
data->state = STATE_BIT_START;
data->count = 1;
/* We just need enough bits to get to STATE_CHECK_RC5X */
data->wanted_bits = RC5X_NBITS;
decrease_duration(&ev, RC5_BIT_START);
goto again;
case STATE_BIT_START:
if (!eq_margin(ev.duration, RC5_BIT_START, RC5_UNIT / 2))
break;
data->bits <<= 1;
if (!ev.pulse)
data->bits |= 1;
data->count++;
data->state = STATE_BIT_END;
return 0;
case STATE_BIT_END:
if (!is_transition(&ev, &dev->raw->prev_ev))
break;
if (data->count == data->wanted_bits)
data->state = STATE_FINISHED;
else if (data->count == CHECK_RC5X_NBITS)
data->state = STATE_CHECK_RC5X;
else
data->state = STATE_BIT_START;
decrease_duration(&ev, RC5_BIT_END);
goto again;
case STATE_CHECK_RC5X:
if (!ev.pulse && geq_margin(ev.duration, RC5X_SPACE, RC5_UNIT / 2)) {
/* RC5X */
data->wanted_bits = RC5X_NBITS;
decrease_duration(&ev, RC5X_SPACE);
} else {
/* RC5 */
data->wanted_bits = RC5_NBITS;
}
data->state = STATE_BIT_START;
goto again;
case STATE_FINISHED:
if (ev.pulse)
break;
if (data->wanted_bits == RC5X_NBITS) {
/* RC5X */
u8 xdata, command, system;
xdata = (data->bits & 0x0003F) >> 0;
command = (data->bits & 0x00FC0) >> 6;
system = (data->bits & 0x1F000) >> 12;
toggle = (data->bits & 0x20000) ? 1 : 0;
command += (data->bits & 0x01000) ? 0 : 0x40;
scancode = system << 16 | command << 8 | xdata;
IR_dprintk(1, "RC5X scancode 0x%06x (toggle: %u)\n",
scancode, toggle);
} else {
/**
* ir_rc6_decode() - Decode one RC6 pulse or space
* @input_dev: the struct input_dev descriptor of the device
* @ev: the struct ir_raw_event descriptor of the pulse/space
*
* This function returns -EINVAL if the pulse violates the state machine
*/
static int ir_rc6_decode(struct input_dev *input_dev, struct ir_raw_event ev)
{
struct ir_input_dev *ir_dev = input_get_drvdata(input_dev);
struct rc6_dec *data = &ir_dev->raw->rc6;
u32 scancode;
u8 toggle;
if (!(ir_dev->raw->enabled_protocols & IR_TYPE_RC6))
return 0;
if (IS_RESET(ev)) {
data->state = STATE_INACTIVE;
return 0;
}
if (!geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
goto out;
again:
IR_dprintk(2, "RC6 decode started at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
if (!geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!ev.pulse)
break;
/* Note: larger margin on first pulse since each RC6_UNIT
is quite short and some hardware takes some time to
adjust to the signal */
if (!eq_margin(ev.duration, RC6_PREFIX_PULSE, RC6_UNIT))
break;
data->state = STATE_PREFIX_SPACE;
data->count = 0;
return 0;
case STATE_PREFIX_SPACE:
if (ev.pulse)
break;
if (!eq_margin(ev.duration, RC6_PREFIX_SPACE, RC6_UNIT / 2))
break;
data->state = STATE_HEADER_BIT_START;
return 0;
case STATE_HEADER_BIT_START:
if (!eq_margin(ev.duration, RC6_BIT_START, RC6_UNIT / 2))
break;
data->header <<= 1;
if (ev.pulse)
data->header |= 1;
data->count++;
data->state = STATE_HEADER_BIT_END;
return 0;
case STATE_HEADER_BIT_END:
if (!is_transition(&ev, &ir_dev->raw->prev_ev))
break;
if (data->count == RC6_HEADER_NBITS)
data->state = STATE_TOGGLE_START;
else
data->state = STATE_HEADER_BIT_START;
decrease_duration(&ev, RC6_BIT_END);
goto again;
case STATE_TOGGLE_START:
if (!eq_margin(ev.duration, RC6_TOGGLE_START, RC6_UNIT / 2))
break;
data->toggle = ev.pulse;
data->state = STATE_TOGGLE_END;
return 0;
case STATE_TOGGLE_END:
if (!is_transition(&ev, &ir_dev->raw->prev_ev) ||
!geq_margin(ev.duration, RC6_TOGGLE_END, RC6_UNIT / 2))
break;
if (!(data->header & RC6_STARTBIT_MASK)) {
IR_dprintk(1, "RC6 invalid start bit\n");
break;
}
data->state = STATE_BODY_BIT_START;
decrease_duration(&ev, RC6_TOGGLE_END);
data->count = 0;
switch (rc6_mode(data)) {
case RC6_MODE_0:
data->wanted_bits = RC6_0_NBITS;
break;
case RC6_MODE_6A:
/* This might look weird, but we basically
check the value of the first body bit to
determine the number of bits in mode 6A */
if ((!ev.pulse && !geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2)) ||
geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
data->wanted_bits = RC6_6A_LARGE_NBITS;
else
data->wanted_bits = RC6_6A_SMALL_NBITS;
break;
default:
IR_dprintk(1, "RC6 unknown mode\n");
goto out;
}
goto again;
case STATE_BODY_BIT_START:
if (!eq_margin(ev.duration, RC6_BIT_START, RC6_UNIT / 2))
break;
data->body <<= 1;
if (ev.pulse)
data->body |= 1;
data->count++;
data->state = STATE_BODY_BIT_END;
return 0;
case STATE_BODY_BIT_END:
if (!is_transition(&ev, &ir_dev->raw->prev_ev))
break;
if (data->count == data->wanted_bits)
data->state = STATE_FINISHED;
else
data->state = STATE_BODY_BIT_START;
decrease_duration(&ev, RC6_BIT_END);
goto again;
case STATE_FINISHED:
if (ev.pulse)
break;
switch (rc6_mode(data)) {
case RC6_MODE_0:
scancode = data->body & 0xffff;
toggle = data->toggle;
IR_dprintk(1, "RC6(0) scancode 0x%04x (toggle: %u)\n",
scancode, toggle);
break;
case RC6_MODE_6A:
if (data->wanted_bits == RC6_6A_LARGE_NBITS) {
toggle = data->body & RC6_6A_MCE_TOGGLE_MASK ? 1 : 0;
scancode = data->body & ~RC6_6A_MCE_TOGGLE_MASK;
} else {
toggle = 0;
scancode = data->body & 0xffffff;
}
IR_dprintk(1, "RC6(6A) scancode 0x%08x (toggle: %u)\n",
scancode, toggle);
break;
default:
IR_dprintk(1, "RC6 unknown mode\n");
goto out;
}
ir_keydown(input_dev, scancode, toggle);
data->state = STATE_INACTIVE;
return 0;
}
out:
IR_dprintk(1, "RC6 decode failed at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
data->state = STATE_INACTIVE;
return -EINVAL;
}
/**
* ir_rc5_decode() - Decode one RC-5 pulse or space
* @dev: the struct rc_dev descriptor of the device
* @ev: the struct ir_raw_event descriptor of the pulse/space
*
* This function returns -EINVAL if the pulse violates the state machine
*/
static int ir_rc5_decode(struct rc_dev *dev, struct ir_raw_event ev)
{
struct rc5_dec *data = &dev->raw->rc5;
u8 toggle;
u32 scancode;
enum rc_type protocol;
if (!is_timing_event(ev)) {
if (ev.reset)
data->state = STATE_INACTIVE;
return 0;
}
if (!geq_margin(ev.duration, RC5_UNIT, RC5_UNIT / 2))
goto out;
again:
IR_dprintk(2, "RC5(x/sz) decode started at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
if (!geq_margin(ev.duration, RC5_UNIT, RC5_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!ev.pulse)
break;
data->state = STATE_BIT_START;
data->count = 1;
decrease_duration(&ev, RC5_BIT_START);
goto again;
case STATE_BIT_START:
if (!ev.pulse && geq_margin(ev.duration, RC5_TRAILER, RC5_UNIT / 2)) {
data->state = STATE_FINISHED;
goto again;
}
if (!eq_margin(ev.duration, RC5_BIT_START, RC5_UNIT / 2))
break;
data->bits <<= 1;
if (!ev.pulse)
data->bits |= 1;
data->count++;
data->state = STATE_BIT_END;
return 0;
case STATE_BIT_END:
if (!is_transition(&ev, &dev->raw->prev_ev))
break;
if (data->count == CHECK_RC5X_NBITS)
data->state = STATE_CHECK_RC5X;
else
data->state = STATE_BIT_START;
decrease_duration(&ev, RC5_BIT_END);
goto again;
case STATE_CHECK_RC5X:
if (!ev.pulse && geq_margin(ev.duration, RC5X_SPACE, RC5_UNIT / 2)) {
data->is_rc5x = true;
decrease_duration(&ev, RC5X_SPACE);
} else
data->is_rc5x = false;
data->state = STATE_BIT_START;
goto again;
case STATE_FINISHED:
if (ev.pulse)
break;
if (data->is_rc5x && data->count == RC5X_NBITS) {
/* RC5X */
u8 xdata, command, system;
if (!(dev->enabled_protocols & RC_BIT_RC5X)) {
data->state = STATE_INACTIVE;
return 0;
}
xdata = (data->bits & 0x0003F) >> 0;
command = (data->bits & 0x00FC0) >> 6;
system = (data->bits & 0x1F000) >> 12;
toggle = (data->bits & 0x20000) ? 1 : 0;
command += (data->bits & 0x01000) ? 0 : 0x40;
scancode = system << 16 | command << 8 | xdata;
protocol = RC_TYPE_RC5X;
} else if (!data->is_rc5x && data->count == RC5_NBITS) {
void init_params_R1 (BNTree *bntree) {
int i, j;
int dimer_pair_num = 0;
int param_idx = 0;
int types[] = {0, 1, 2, 3, 16, 17,
4, 5, 6, 7, 16, 17,
8, 9, 10, 11, 16, 17,
12, 13, 14, 15, 16, 17,
18, 18, 18, 18, 19, 20,
21, 21, 21, 21, 22, 23};
for (i=0; i<36; i++) {
for (j=0; j<36; j++) {
int type1 = types[i];
int type2 = types[j];
int char1 = i / 6;
int char2 = i % 6;
int char3 = j / 6;
int char4 = j % 6;
if (i == j) continue;
if (type1 < 16 && type2 < 16) { /* base dimer to base dimer substitution */
if (i > j) continue; /* already took care of these */
param_idx = dimer_pair_num++;
bntree->param_map[i][j] = param_idx;
bntree->param_map[j][i] = param_idx;
bntree->weight_idx[i][j] = j;
bntree->weight_idx[j][i] = i;
}
else if (type1 == type2 && (char1 != char3 || char2 != char4)) {
/* mutation in a gap pattern base with no change in pattern */
if (type1 == 16) {
if (is_transition (char1, char3))
param_idx = 192;
else
param_idx = 193;
}
else if (type1 == 17) {
if (is_transition (char1, char3))
param_idx = 194;
else
param_idx = 195;
}
else if (type1 == 18) {
if (is_transition (char2, char4))
param_idx = 196;
else
param_idx = 197;
}
else if (type1 == 21) {
if (is_transition (char2, char4))
param_idx = 198;
else
param_idx = 199;
}
bntree->param_map[i][j] = param_idx;
bntree->weight_idx[i][j] = -1;
}
else { /* gap pattern to different gap pattern */
param_idx = 120 + 8 * int_max(type1 - 15, 0) + int_max(type2 - 15, 0);
if (type1 < type2)
param_idx--;
bntree->param_map[i][j] = param_idx;
if (type2 < 16)
bntree->weight_idx[i][j] = j;
else
bntree->weight_idx[i][j] = -1;
}
}
}
/* self substitutions */
for (i=0; i<36; i++) {
bntree->param_map[i][i] = 200 + i;
bntree->weight_idx[i][i] = -1;
}
assert (dimer_pair_num == 120);
}
static int ir_rc6_decode(struct rc6_ir *data, struct ir_signal signal,
struct ir_protocol *ip)
{
int i;
i = ip->priv;
if (i >= MAX_RC6_INFR_NR)
goto out;
if (!geq_margin(signal.duration, RC6_UNIT, RC6_UNIT / 2))
goto out;
again:
hiir_debug("RC6 decode started at state %i (%uus %s) "
"count %d header 0x%x bits 0x%llx, count:%d\n",
data->state, signal.duration, TO_STR(signal.pulse),
data->count, data->header, data->bits, data->count);
if (!geq_margin(signal.duration, RC6_UNIT, RC6_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!signal.pulse)
break;
if (!eq_margin(signal.duration, RC6_PREFIX_PULSE, RC6_UNIT))
break;
data->state = STATE_PREFIX_SPACE;
data->bits = 0;
data->count = 0;
data->header = 0;
memset(&data->this_key, 0, sizeof(struct key_attr));
return 0;
case STATE_PREFIX_SPACE:
if (signal.pulse)
break;
if (!eq_margin(signal.duration, RC6_PREFIX_SPACE,
RC6_UNIT / 2))
break;
data->state = STATE_HEADER_BIT_START;
return 0;
case STATE_HEADER_BIT_START:
if (!eq_margin(signal.duration, RC6_BIT_START,
RC6_UNIT / 2))
break;
data->header <<= 1;
if (signal.pulse)
data->header |= 1;
data->count++;
data->state = STATE_HEADER_BIT_END;
return 0;
case STATE_HEADER_BIT_END:
if (!is_transition(&signal, &data->prev_signal))
break;
if (data->count == RC6_HEADER_NBITS)
data->state = STATE_TOGGLE_START;
else
data->state = STATE_HEADER_BIT_START;
decrease_duration(&signal, RC6_BIT_END);
goto again;
case STATE_TOGGLE_START:
if (!eq_margin(signal.duration, RC6_TOGGLE_START, RC6_UNIT / 2))
break;
data->state = STATE_TOGGLE_END;
return 0;
case STATE_TOGGLE_END:
if (!is_transition(&signal, &data->prev_signal)
|| !geq_margin(signal.duration, RC6_TOGGLE_END,
RC6_UNIT / 2))
break;
data->state = STATE_BIT_START;
decrease_duration(&signal, RC6_TOGGLE_END);
data->count = 0;
goto again;
case STATE_BIT_START:
if (!eq_margin(signal.duration, RC6_BIT_START, RC6_UNIT / 2))
break;
data->bits <<= 1;
if (signal.pulse)
data->bits |= 1;
data->count++;
data->state = STATE_BIT_END;
return 0;
case STATE_BIT_END:
if (!is_transition(&signal, &data->prev_signal))
break;
if (data->count == ip->attr.wanna_bits) {
data->scancode = data->bits;
data->this_key.lower = (data->scancode & (~RC6_TOGGLE_MASK));
data->this_key.upper = 0;
data->state = STATE_FINISHED;
return 0;
} else
data->state = STATE_BIT_START;
decrease_duration(&signal, RC6_BIT_END);
goto again;
case STATE_FINISHED:
if (signal.pulse)
break;
data->state = STATE_INACTIVE;
return 0;
}
out:
hiir_info("RC6 decode failed at state %i (%uus %s), bits received:%d\n",
data->state, signal.duration, TO_STR(signal.pulse), data->count);
data->state = STATE_INACTIVE;
return -EINVAL;
}
/**
* ir_rc5_sz_decode() - Decode one RC-5 Streamzap pulse or space
* @input_dev: the struct input_dev descriptor of the device
* @ev: the struct ir_raw_event descriptor of the pulse/space
*
* This function returns -EINVAL if the pulse violates the state machine
*/
static int ir_rc5_sz_decode(struct input_dev *input_dev, struct ir_raw_event ev)
{
struct ir_input_dev *ir_dev = input_get_drvdata(input_dev);
struct rc5_sz_dec *data = &ir_dev->raw->rc5_sz;
u8 toggle, command, system;
u32 scancode;
if (!(ir_dev->raw->enabled_protocols & IR_TYPE_RC5_SZ))
return 0;
if (!is_timing_event(ev)) {
if (ev.reset)
data->state = STATE_INACTIVE;
return 0;
}
if (!geq_margin(ev.duration, RC5_UNIT, RC5_UNIT / 2))
goto out;
again:
IR_dprintk(2, "RC5-sz decode started at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
if (!geq_margin(ev.duration, RC5_UNIT, RC5_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!ev.pulse)
break;
data->state = STATE_BIT_START;
data->count = 1;
data->wanted_bits = RC5_SZ_NBITS;
decrease_duration(&ev, RC5_BIT_START);
goto again;
case STATE_BIT_START:
if (!eq_margin(ev.duration, RC5_BIT_START, RC5_UNIT / 2))
break;
data->bits <<= 1;
if (!ev.pulse)
data->bits |= 1;
data->count++;
data->state = STATE_BIT_END;
return 0;
case STATE_BIT_END:
if (!is_transition(&ev, &ir_dev->raw->prev_ev))
break;
if (data->count == data->wanted_bits)
data->state = STATE_FINISHED;
else
data->state = STATE_BIT_START;
decrease_duration(&ev, RC5_BIT_END);
goto again;
case STATE_FINISHED:
if (ev.pulse)
break;
/* RC5-sz */
command = (data->bits & 0x0003F) >> 0;
system = (data->bits & 0x02FC0) >> 6;
toggle = (data->bits & 0x01000) ? 1 : 0;
scancode = system << 6 | command;
IR_dprintk(1, "RC5-sz scancode 0x%04x (toggle: %u)\n",
scancode, toggle);
ir_keydown(input_dev, scancode, toggle);
data->state = STATE_INACTIVE;
return 0;
}
out:
IR_dprintk(1, "RC5-sz decode failed at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
data->state = STATE_INACTIVE;
return -EINVAL;
}
static int ir_rc6_decode(struct rc_dev *dev, struct ir_raw_event ev)
{
struct rc6_dec *data = &dev->raw->rc6;
u32 scancode;
u8 toggle;
if (!(dev->raw->enabled_protocols & RC_TYPE_RC6))
return 0;
if (!is_timing_event(ev)) {
if (ev.reset)
data->state = STATE_INACTIVE;
return 0;
}
if (!geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
goto out;
again:
IR_dprintk(2, "RC6 decode started at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
if (!geq_margin(ev.duration, RC6_UNIT, RC6_UNIT / 2))
return 0;
switch (data->state) {
case STATE_INACTIVE:
if (!ev.pulse)
break;
if (!eq_margin(ev.duration, RC6_PREFIX_PULSE, RC6_UNIT))
break;
data->state = STATE_PREFIX_SPACE;
data->count = 0;
return 0;
case STATE_PREFIX_SPACE:
if (ev.pulse)
break;
if (!eq_margin(ev.duration, RC6_PREFIX_SPACE, RC6_UNIT / 2))
break;
data->state = STATE_HEADER_BIT_START;
data->header = 0;
return 0;
case STATE_HEADER_BIT_START:
if (!eq_margin(ev.duration, RC6_BIT_START, RC6_UNIT / 2))
break;
data->header <<= 1;
if (ev.pulse)
data->header |= 1;
data->count++;
data->state = STATE_HEADER_BIT_END;
return 0;
case STATE_HEADER_BIT_END:
if (!is_transition(&ev, &dev->raw->prev_ev))
break;
if (data->count == RC6_HEADER_NBITS)
data->state = STATE_TOGGLE_START;
else
data->state = STATE_HEADER_BIT_START;
decrease_duration(&ev, RC6_BIT_END);
goto again;
case STATE_TOGGLE_START:
if (!eq_margin(ev.duration, RC6_TOGGLE_START, RC6_UNIT / 2))
break;
data->toggle = ev.pulse;
data->state = STATE_TOGGLE_END;
return 0;
case STATE_TOGGLE_END:
if (!is_transition(&ev, &dev->raw->prev_ev) ||
!geq_margin(ev.duration, RC6_TOGGLE_END, RC6_UNIT / 2))
break;
if (!(data->header & RC6_STARTBIT_MASK)) {
IR_dprintk(1, "RC6 invalid start bit\n");
break;
}
data->state = STATE_BODY_BIT_START;
decrease_duration(&ev, RC6_TOGGLE_END);
data->count = 0;
data->body = 0;
switch (rc6_mode(data)) {
case RC6_MODE_0:
data->wanted_bits = RC6_0_NBITS;
break;
case RC6_MODE_6A:
data->wanted_bits = RC6_6A_NBITS;
break;
default:
IR_dprintk(1, "RC6 unknown mode\n");
goto out;
}
goto again;
case STATE_BODY_BIT_START:
if (eq_margin(ev.duration, RC6_BIT_START, RC6_UNIT / 2)) {
if (data->count++ < CHAR_BIT * sizeof data->body) {
data->body <<= 1;
if (ev.pulse)
data->body |= 1;
}
data->state = STATE_BODY_BIT_END;
return 0;
} else if (RC6_MODE_6A == rc6_mode(data) && !ev.pulse &&
geq_margin(ev.duration, RC6_SUFFIX_SPACE, RC6_UNIT / 2)) {
data->state = STATE_FINISHED;
goto again;
}
break;
case STATE_BODY_BIT_END:
if (!is_transition(&ev, &dev->raw->prev_ev))
break;
if (data->count == data->wanted_bits)
data->state = STATE_FINISHED;
else
data->state = STATE_BODY_BIT_START;
decrease_duration(&ev, RC6_BIT_END);
goto again;
case STATE_FINISHED:
if (ev.pulse)
break;
switch (rc6_mode(data)) {
case RC6_MODE_0:
scancode = data->body;
toggle = data->toggle;
IR_dprintk(1, "RC6(0) scancode 0x%04x (toggle: %u)\n",
scancode, toggle);
break;
case RC6_MODE_6A:
if (data->count > CHAR_BIT * sizeof data->body) {
IR_dprintk(1, "RC6 too many (%u) data bits\n",
data->count);
goto out;
}
scancode = data->body;
if (data->count == RC6_6A_32_NBITS &&
(scancode & RC6_6A_LCC_MASK) == RC6_6A_MCE_CC) {
toggle = (scancode & RC6_6A_MCE_TOGGLE_MASK) ? 1 : 0;
scancode &= ~RC6_6A_MCE_TOGGLE_MASK;
} else {
toggle = 0;
}
IR_dprintk(1, "RC6(6A) scancode 0x%08x (toggle: %u)\n",
scancode, toggle);
break;
default:
IR_dprintk(1, "RC6 unknown mode\n");
goto out;
}
rc_keydown(dev, scancode, toggle);
data->state = STATE_INACTIVE;
return 0;
}
out:
IR_dprintk(1, "RC6 decode failed at state %i (%uus %s)\n",
data->state, TO_US(ev.duration), TO_STR(ev.pulse));
data->state = STATE_INACTIVE;
return -EINVAL;
}
int main(int argc, char* argv[]) {
FILE* F;
TreeModel *model;
int i, j, k, alph_size, nstates, do_eqfreqs = 0, exch_mode = 0,
list_mode = 0, latex_mode = 0, suppress_diag = 0, ti_tv = 0,
scientific_mode = 0,
induced_aa = 0, do_stop_codons = 0, do_zeroes = 0, symmetric = 0,
context_ti_tv = 0, all_branches = 0;
int startcol, endcol, ncols, branch_no = 0, matrix_idx = 0;
/* int aa_inv[256]; */
double t = -1, total_ti = 0, total_tv = 0, rho_s = 0, cpg_ti = 0,
cpg_tv = 0, non_cpg_ti = 0, non_cpg_tv = 0, cpg_eqfreq = 0;
char *rate_format_string = "%8.6f";
MarkovMatrix *M;
char c;
char tuple[5], tuple2[5]; /* , aa_alph[50]; */
char *subst_mat_fname = NULL, *subst_score_fname = NULL,
*subst_mat_fname_paml = NULL, *order1_mod_fname = NULL;
Matrix *subst_mat = NULL;
List *matrix_list = lst_new_ptr(20), *traversal = NULL;
while ((c = (char)getopt(argc, argv, "t:fedlLiM:N:A:B:aszSECh")) != -1) {
switch(c) {
case 't':
if (optarg[0] == 'A') all_branches = 1;
else t = get_arg_dbl_bounds(optarg, 0, INFTY);
break;
case 'f':
do_eqfreqs = 1;
break;
case 'e':
exch_mode = 1;
break;
case 'd':
suppress_diag = 1;
break;
case 'l':
list_mode = 1;
break;
case 'L':
latex_mode = 1;
break;
case 'i':
ti_tv = 1;
break;
case 'M':
subst_mat_fname = optarg;
induced_aa = 1;
break;
case 'N':
subst_mat_fname_paml = optarg;
induced_aa = 1;
break;
case 'A':
subst_score_fname = optarg;
break;
case 'B':
order1_mod_fname = optarg;
break;
case 'a':
induced_aa = 1;
do_zeroes = 1;
break;
case 's':
do_stop_codons = 1;
break;
case 'z':
do_zeroes = 1;
break;
case 'S':
symmetric = 1;
break;
case 'E':
scientific_mode = 1;
rate_format_string = "%13.6e";
break;
case 'C':
context_ti_tv = 1;
break;
case 'h':
print_usage();
exit(0);
case '?':
die("Unrecognized option. Try \"display_rate_matrix -h\" for help.\n");
}
}
set_seed(-1);
if ((t >= 0 && exch_mode) || (latex_mode && list_mode) ||
((ti_tv || subst_mat_fname != NULL || subst_score_fname != NULL ||
subst_mat_fname_paml != NULL || scientific_mode) && !list_mode) ||
(subst_mat_fname != NULL && subst_score_fname != NULL) ||
(subst_score_fname != NULL && subst_mat_fname_paml != NULL) ||
(subst_mat_fname != NULL && subst_mat_fname_paml != NULL) ||
optind != argc - 1) {
die("ERROR: missing required arguments or illegal combination of arguments.\nTry \"display_rate_matrix -h\" for help.\n");
}
F = phast_fopen(argv[optind], "r");
model = tm_new_from_file(F, 1);
if (context_ti_tv) {
/* this option requires completely different handling from the others */
if (model->order != 2) {
die("ERROR: -C requires a model of order 3.\n");
}
do_context_dependent_ti_tv(model);
exit(0);
}
if (induced_aa) {
TreeModel *aa_model = tm_induced_aa(model);
char *codon_to_aa = get_codon_mapping(model->rate_matrix->states);
/* before freeing model, grab the expected rate of synonymous
subst, rho_s */
for (i = 0; i < model->rate_matrix->size; i++)
for (j = 0; j < model->rate_matrix->size; j++)
if (i != j && codon_to_aa[i] == codon_to_aa[j])
rho_s += mm_get(model->rate_matrix, i, j) *
vec_get(model->backgd_freqs, i);
sfree(codon_to_aa);
tm_free(model);
model = aa_model;
}
if (all_branches) {
traversal = tr_inorder(model->tree);
for (matrix_idx = 0; matrix_idx < lst_size(traversal); matrix_idx++) {
TreeNode *n = lst_get_ptr(traversal, matrix_idx);
if (n->parent == NULL) { lst_push_ptr(matrix_list, NULL); continue; }
M = mm_new(model->rate_matrix->size, model->rate_matrix->states, DISCRETE);
mm_exp(M, model->rate_matrix, n->dparent);
lst_push_ptr(matrix_list, M);
}
}
else if (t >= 0) {
M = mm_new(model->rate_matrix->size, model->rate_matrix->states, DISCRETE);
mm_exp(M, model->rate_matrix, t);
lst_push_ptr(matrix_list, M);
}
else
lst_push_ptr(matrix_list, model->rate_matrix);
alph_size = (int)strlen(model->rate_matrix->states);
nstates = model->rate_matrix->size;
if (subst_mat_fname != NULL) {
if ((F = fopen(subst_mat_fname, "r")) == NULL) {
die("ERROR: Can't open %s.\n", subst_mat_fname);
}
subst_mat = read_subst_mat(F, AA_ALPHABET);
}
else if (subst_mat_fname_paml != NULL) {
if ((F = fopen(subst_mat_fname_paml, "r")) == NULL) {
die("ERROR: Can't open %s.\n", subst_mat_fname_paml);
}
subst_mat = read_paml_matrix(F, AA_ALPHABET);
}
else if (subst_score_fname != NULL) {
if ((F = fopen(subst_score_fname, "r")) == NULL) {
die("ERROR: Can't open %s.\n", subst_score_fname);
}
subst_mat = read_subst_scores(model, F);
}
else if (order1_mod_fname != NULL) {
if ((F = fopen(order1_mod_fname, "r")) == NULL) {
die("ERROR: Can't open %s.\n", order1_mod_fname);
}
subst_mat = unproject_rates(model, tm_new_from_file(F, 1));
}
/* loop through matrices to print */
for (matrix_idx = 0; matrix_idx < lst_size(matrix_list); matrix_idx++) {
M = lst_get_ptr(matrix_list, matrix_idx);
if (all_branches) {
if (M == NULL) continue; /* root */
printf("BRANCH %d (t = %.6f)\n", ++branch_no,
((TreeNode*)lst_get_ptr(traversal, matrix_idx))->dparent);
}
/* print no more than 16 columns at a time (except with -a) */
ncols = (induced_aa ? nstates : 16);
for (startcol = 0; startcol < nstates; startcol += ncols) {
endcol = min(nstates, startcol+ncols);
/* table header */
if (! list_mode) {
if (latex_mode) {
printf("\\begin{tabular}{|c|");
for (i = startcol; i < endcol; i++) printf("r");
printf("|}\n\\hline\n");
}
printf("%-5s ", "");
if (latex_mode) printf("& ");
for (i = startcol; i < endcol; i++) {
get_state_tuple(model, tuple, i);
if (latex_mode) {
printf("{\\bf %s}", tuple);
if (i < endcol-1) printf("& ");
}
else printf("%8s ", tuple);
}
if (latex_mode) printf("\\\\\n\\hline\n");
else printf("\n");
}
/* table or list contents */
for (i = 0; i < nstates; i++) {
if (induced_aa && AA_ALPHABET[i] == '$' && !do_stop_codons) continue;
get_state_tuple(model, tuple, i);
/* get total eq freq of tuples containing CpG dinucs */
for (k = 0; k < model->order; k++) {
if (tuple[k] == 'C' && tuple[k+1] == 'G') {
cpg_eqfreq += vec_get(model->backgd_freqs, i);
/* printf("***CPG***"); */
break;
}
}
if (latex_mode) printf("{\\bf %s}& ", tuple);
else if (!list_mode) printf("%-5s ", tuple);
for (j = startcol; j < endcol; j++) {
if (induced_aa && AA_ALPHABET[j] == '$' && !do_stop_codons) continue;
if (latex_mode) printf("$");
if (list_mode) {
if (symmetric && j <= i) continue;
else if ((t < 0 && ! all_branches)
&& (i == j || (!do_zeroes && mm_get(M, i, j) == 0)))
continue;
get_state_tuple(model, tuple2, j);
printf("%-5s %-5s ", tuple, tuple2);
}
if (i == j && suppress_diag && !list_mode) printf("%-7s", "-");
else {
/* get rate or probability */
double val = exch_mode == 0 ? mm_get(M, i, j) :
safediv(mm_get(M, i, j), vec_get(model->backgd_freqs,j));
/* print value in format %8.6f or %13.6e */
printf(rate_format_string, val);
printf(" ");
}
if (latex_mode) {
printf("$");
if (j < endcol-1) printf("& ");
}
else if (list_mode) {
int ti, is_cpg;
if (ti_tv) {
ti = -1;
is_cpg = 0;
for (k = 0; k <= model->order; k++) {
int dig_i = (i % int_pow(alph_size, k+1)) / int_pow(alph_size, k);
int dig_j = (j % int_pow(alph_size, k+1)) / int_pow(alph_size, k);
char next_char = '\0', prev_char = '\0';
if (dig_i != dig_j) {
ti = is_transition(M->states[dig_i], M->states[dig_j]);
if (k != model->order)
prev_char = M->states[(i % int_pow(alph_size, k+2)) /
int_pow(alph_size, k+1)];
if (k != 0)
next_char = M->states[(i % int_pow(alph_size, k)) /
int_pow(alph_size, k-1)];
if ((M->states[dig_i] == 'C' && next_char == 'G') ||
(M->states[dig_i] == 'G' && prev_char == 'C'))
is_cpg = 1;
}
}
if (ti == -1)
die("ERROR ti=-1\n");
printf("%5s ", ti ? "ti" : "tv");
/* printf("%5s ", is_cpg ? "CPG" : "-"); */
if (ti) {
total_ti += mm_get(M, i, j) *
vec_get(model->backgd_freqs, i);
if (is_cpg)
cpg_ti += mm_get(M, i, j) *
vec_get(model->backgd_freqs, i);
else non_cpg_ti += mm_get(M, i, j) *
vec_get(model->backgd_freqs, i);
}
else {
total_tv += mm_get(M, i, j) *
vec_get(model->backgd_freqs, i);
if (is_cpg)
cpg_tv += mm_get(M, i, j) *
vec_get(model->backgd_freqs, i);
else non_cpg_tv += mm_get(M, i, j) *
vec_get(model->backgd_freqs, i);
}
}
if (subst_mat != NULL) {
if (mat_get(subst_mat, i, j) == NEGINFTY)
printf("%8s", "-");
else printf("%8.4f", mat_get(subst_mat, i, j));
}
printf("\n");
}
}
if (latex_mode) printf("\\\\\n");
else if (!list_mode) printf("\n");
}
/* equilibrium freqs (table case only) */
if (do_eqfreqs && ! list_mode) {
if (latex_mode)
printf("\\hline\n$\\boldsymbol{\\mathbf{\\pi}}$&");
else
printf("%-5s ", "pi");
for (i = startcol; i < endcol; i++) {
if (latex_mode)
printf("$%8.4f$ ", vec_get(model->backgd_freqs, i));
else
printf("%8.4f ", vec_get(model->backgd_freqs, i));
if (latex_mode && i < endcol-1) printf("& ");
}
if (latex_mode) printf("\\\\\n");
else printf("\n");
}
if (latex_mode) printf("\\hline\n\\end{tabular}\n\n");
}
/* equilibrium freqs (list case only) */
if (do_eqfreqs && list_mode) {
for (i = 0; i < nstates; i++) {
get_state_tuple(model, tuple, i);
printf("%-5s %-5s ", "-", tuple); //!!
printf(rate_format_string, vec_get(model->backgd_freqs, i));
printf("\n");
}
}
if (ti_tv && list_mode) {
printf("\n#Total ti/tv = %.4f\n", total_ti/total_tv);
printf("#CpG ti ratio = %.4f, CpG tv ratio = %.4f\n",
cpg_ti/non_cpg_ti /* * (1 - cpg_eqfreq) */ / cpg_eqfreq,
cpg_tv/non_cpg_tv /* * (1 - cpg_eqfreq) */ / cpg_eqfreq);
}
else if (induced_aa)
printf("\n#Total rho_s/rho_v = %.4f\n", rho_s/(3-rho_s));
if (all_branches == 1) printf("\n\n");
}
tm_free(model);
lst_free(matrix_list);
return 0;
}
/* this function implements the -C option */
void do_context_dependent_ti_tv(TreeModel *mod) {
char *alph = mod->rate_matrix->states;
int alph_size = (int)strlen(alph);
char tuple_i[mod->order+2], tuple_j[mod->order+2];
double context_ti[alph_size][alph_size], context_tv[alph_size][alph_size],
ti_AT_5_pyrim[3][3], tv_AT_5_pyrim[3][3],
all_ti, all_tv, expected_rate;
int mid_src, mid_targ, first, last, at_states[2], gc_states[2], i, j,
num_5_pyrim;
if (mod->order != 2)
die("ERROR do_context_dependent_ti_tv: mod->order (%i) should be 2\n",
mod->order);
if (alph_size != 4)
die("ERROR do_contect_dependent_ti_tv: alph_size (%i) should be 4\n",
alph_size);
tuple_i[mod->order+1] = tuple_j[mod->order+1] = '\0';
/* We only care about substitutions at the middle position */
for (first = 0; first < alph_size; first++) {
for (last = 0; last < alph_size; last++) {
context_ti[first][last] = context_tv[first][last] = 0;
for (mid_src = 0; mid_src < alph_size; mid_src++) {
for (mid_targ = 0; mid_targ < alph_size; mid_targ++) {
if (mid_src == mid_targ) continue;
i = last + mid_src*alph_size + first*alph_size*alph_size;
j = last + mid_targ*alph_size + first*alph_size*alph_size;
expected_rate = mm_get(mod->rate_matrix, i, j) *
vec_get(mod->backgd_freqs, i);
/* get_tuple_str(tuple_i, i, mod->order+1, */
/* mod->rate_matrix->states); */
/* get_tuple_str(tuple_j, j, mod->order+1, */
/* mod->rate_matrix->states); */
/* if ((tuple_i[1] == 'C' && tuple_i[2] == 'G') || tuple_i[0] == 'C' && tuple_i[1] == 'G') continue; */
if (is_transition(alph[mid_src], alph[mid_targ]))
context_ti[first][last] += expected_rate;
else if (i != j)
context_tv[first][last] += expected_rate;
}
}
}
}
/* first print equivalent of table 2 */
/* get "states" associated with A+T bases and G+C bases */
at_states[0] = mod->rate_matrix->inv_states['A'];
at_states[1] = mod->rate_matrix->inv_states['T'];
gc_states[0] = mod->rate_matrix->inv_states['C'];
gc_states[1] = mod->rate_matrix->inv_states['G'];
/* header */
printf("%5s %5s %5s %8s %8s %8s\n", "A+T", "5'", "3'", "Ts", "Tv", "Tv/(Tv+Ts)");
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
ti_AT_5_pyrim[i][j] = tv_AT_5_pyrim[i][j] = 0;
/* AT content 0 (GC either side) */
all_ti = all_tv = 0;
for (first = 0; first < 2; first++) {
for (last = 0; last < 2; last++) {
printf("%5d %5c %5c %8.4f %8.4f %8.4f\n", 0,
alph[(int)gc_states[first]],
alph[(int)gc_states[last]],
context_ti[gc_states[first]][gc_states[last]],
context_tv[gc_states[first]][gc_states[last]],
context_tv[gc_states[first]][gc_states[last]] /
(context_ti[gc_states[first]][gc_states[last]] +
context_tv[gc_states[first]][gc_states[last]]));
all_ti += context_ti[gc_states[first]][gc_states[last]];
all_tv += context_tv[gc_states[first]][gc_states[last]];
num_5_pyrim = IS_PYRIMIDINE(alph[(int)gc_states[first]]);
num_5_pyrim += IS_PYRIMIDINE(msa_compl_char(alph[(int)gc_states[last]]));
ti_AT_5_pyrim[0][num_5_pyrim] +=
context_ti[gc_states[first]][gc_states[last]];
tv_AT_5_pyrim[0][num_5_pyrim] +=
context_tv[gc_states[first]][gc_states[last]];
}
}
printf("%5d %5s %5s %8.4f %8.4f %8.4f\n", 0, "all", "all", all_ti,
all_tv, all_tv / (all_ti + all_tv));
/* AT content 1 (AT one side, GC other side) */
all_ti = all_tv = 0;
for (first = 0; first < 2; first++) {
for (last = 0; last < 2; last++) {
printf("%5d %5c %5c %8.4f %8.4f %8.4f\n", 1,
alph[(int)at_states[first]],
alph[(int)gc_states[last]],
context_ti[at_states[first]][gc_states[last]],
context_tv[at_states[first]][gc_states[last]],
context_tv[at_states[first]][gc_states[last]] /
(context_ti[at_states[first]][gc_states[last]] +
context_tv[at_states[first]][gc_states[last]]));
printf("%5d %5c %5c %8.4f %8.4f %8.4f\n", 1,
alph[(int)gc_states[first]],
alph[(int)at_states[last]],
context_ti[gc_states[first]][at_states[last]],
context_tv[gc_states[first]][at_states[last]],
context_tv[gc_states[first]][at_states[last]] /
(context_ti[gc_states[first]][at_states[last]] +
context_tv[gc_states[first]][at_states[last]]));
all_ti += context_ti[at_states[first]][gc_states[last]] +
context_ti[gc_states[first]][at_states[last]];
all_tv += context_tv[at_states[first]][gc_states[last]] +
context_tv[gc_states[first]][at_states[last]];
num_5_pyrim = IS_PYRIMIDINE(alph[(int)at_states[first]]);
num_5_pyrim += IS_PYRIMIDINE(msa_compl_char(alph[(int)gc_states[last]]));
ti_AT_5_pyrim[1][num_5_pyrim] +=
context_ti[at_states[first]][gc_states[last]];
tv_AT_5_pyrim[1][num_5_pyrim] +=
context_tv[at_states[first]][gc_states[last]];
num_5_pyrim = IS_PYRIMIDINE(alph[(int)gc_states[first]]);
num_5_pyrim += IS_PYRIMIDINE(msa_compl_char(alph[(int)at_states[last]]));
ti_AT_5_pyrim[1][num_5_pyrim] +=
context_ti[gc_states[first]][at_states[last]];
tv_AT_5_pyrim[1][num_5_pyrim] +=
context_tv[gc_states[first]][at_states[last]];
}
}
printf("%5d %5s %5s %8.4f %8.4f %8.4f\n", 1, "all", "all", all_ti,
all_tv, all_tv / (all_ti + all_tv));
/* AT content 2 (AT both sides) */
all_ti = all_tv = 0;
for (first = 0; first < 2; first++) {
for (last = 0; last < 2; last++) {
printf("%5d %5c %5c %8.4f %8.4f %8.4f\n", 2,
alph[(int)at_states[first]],
alph[(int)at_states[last]],
context_ti[at_states[first]][at_states[last]],
context_tv[at_states[first]][at_states[last]],
context_tv[at_states[first]][at_states[last]] /
(context_ti[at_states[first]][at_states[last]] +
context_tv[at_states[first]][at_states[last]]));
all_ti += context_ti[at_states[first]][at_states[last]];
all_tv += context_tv[at_states[first]][at_states[last]];
num_5_pyrim = IS_PYRIMIDINE(alph[(int)at_states[first]]);
num_5_pyrim += IS_PYRIMIDINE(msa_compl_char(alph[(int)at_states[last]]));
ti_AT_5_pyrim[2][num_5_pyrim] +=
context_ti[at_states[first]][at_states[last]];
tv_AT_5_pyrim[2][num_5_pyrim] +=
context_tv[at_states[first]][at_states[last]];
}
}
printf("%5d %5s %5s %8.4f %8.4f %8.4f\n", 2, "all", "all", all_ti,
all_tv, all_tv / (all_ti + all_tv));
/* now print equivalent of table 3 */
printf("\n\n%5s %5s %8s %8s %8s\n", "A+T", "5'Y", "Ts", "Tv", "Tv/(Tv+Ts)");
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
printf("%5d %5d %8.4f %8.4f %8.4f\n", i, j, ti_AT_5_pyrim[i][j], tv_AT_5_pyrim[i][j], tv_AT_5_pyrim[i][j]/(tv_AT_5_pyrim[i][j] + ti_AT_5_pyrim[i][j]));
for (j = 0; j < 3; j++) {
double all_ti = ti_AT_5_pyrim[0][j] + ti_AT_5_pyrim[1][j] +
ti_AT_5_pyrim[2][j];
double all_tv = tv_AT_5_pyrim[0][j] + tv_AT_5_pyrim[1][j] +
tv_AT_5_pyrim[2][j];
printf("%5s %5d %8.4f %8.4f %8.4f\n", "all", j, all_ti, all_tv, all_tv/(all_tv + all_ti));
}
}
