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Fix helix position set on crossover for #488
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@UnHumbleBen
UnHumbleBen committed Nov 8, 2020
1 parent c5625b2 commit bc5bc99
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Showing 4 changed files with 41 additions and 41 deletions.
26 changes: 13 additions & 13 deletions lib/src/middleware/helices_positions_set_based_on_crossovers.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ List<actions.UndoableAction> helix_positions_set_based_on_crossovers(AppState st
continue;
}
double first_roll = helices[0].roll;
List<RollZY> rolls_and_positions =
List<RollXY> rolls_and_positions =
_calculate_rolls_and_positions(state.design, helices, addresses, first_roll);
var all_actions_this_group = set_rolls_and_positions(helices, rolls_and_positions);
all_actions.addAll(all_actions_this_group);
Expand Down Expand Up @@ -262,41 +262,41 @@ Map<Tuple2<int, int>, List<Tuple2<Address, Address>>> _get_addresses_of_selected

/// Represents a roll and 2D (x,y) position. The roll and position are both assigned to helices
/// after gather what these should be by examining crossovers.
class RollZY {
class RollXY {
double roll;
double z;
double x;
double y;

RollZY({this.roll, this.z, this.y});
RollXY({this.roll, this.x, this.y});

String toString() => 'RollZY(roll=$roll, z=$z, y=$y)';
String toString() => 'RollZY(roll=$roll, x=$x, y=$y)';
}

//XXX: be careful editing this function; this logic was very tricky to get correct
/// Return list of rolls, same length as [helices], giving the roll that each should be to point
/// each pair of helix backbones at each other through the given [addresses].
/// The first roll is [first_roll].
List<RollZY> _calculate_rolls_and_positions(
List<RollXY> _calculate_rolls_and_positions(
Design design, List<Helix> helices, List<Tuple2<Address, Address>> addresses, double first_roll) {
assert(helices.length == addresses.length + 1);

Geometry geometry = design.geometry;

double x = helices[0].position3d().x;
double z = helices[0].position3d().z;
double y = helices[0].position3d().y;
List<RollZY> rollxys = [RollZY(roll: first_roll, z: x, y: y)];
List<RollXY> rollxys = [RollXY(roll: first_roll, x: z, y: y)];

for (int i = 0; i < addresses.length; i++) {
var address_top = addresses[i].item1;
var address_bot = addresses[i].item2;
var roll = rollxys[i].roll;
var z = rollxys[i].z;
var x = rollxys[i].x;
var y = rollxys[i].y;

var degrees_top = design.helix_rotation_at(address_top, roll);
// 0 is straight up, not right as in Cartesian rotation, so we have to convert
var radians_top_cartesian = util.to_radians(degrees_top - 90);
var next_z = z + cos(radians_top_cartesian) * geometry.distance_between_helices_nm;
var next_x = x + cos(radians_top_cartesian) * geometry.distance_between_helices_nm;
var next_y = y + sin(radians_top_cartesian) * geometry.distance_between_helices_nm;

// now back to using our "0 is straight up" rotation coordinate system
Expand All @@ -316,19 +316,19 @@ List<RollZY> _calculate_rolls_and_positions(
Helix helix_bot = helices[i + 1];
// add this difference to the roll (which is defined at offset min_offset)
var new_roll = (helix_bot.roll + delta_roll) % 360;
rollxys.add(RollZY(roll: new_roll, z: next_z, y: next_y));
rollxys.add(RollXY(roll: new_roll, x: next_x, y: next_y));
}

return rollxys;
}

List<actions.UndoableAction> set_rolls_and_positions(List<Helix> helices, List<RollZY> rolls_and_positions) {
List<actions.UndoableAction> set_rolls_and_positions(List<Helix> helices, List<RollXY> rolls_and_positions) {
List<actions.UndoableAction> all_actions = [];
for (int i = 0; i < helices.length; i++) {
var helix = helices[i];
var rollxy = rolls_and_positions[i];
var roll_action = actions.HelixRollSet(helix_idx: helix.idx, roll: rollxy.roll);
var position = Position3D(z: rollxy.z, y: rollxy.y, x: helix.position3d().x);
var position = Position3D(x: rollxy.x, y: rollxy.y, z: helix.position3d().z);
var pos_action = actions.HelixPositionSet(helix_idx: helix.idx, position: position);
all_actions.add(roll_action);
all_actions.add(pos_action);
Expand Down
10 changes: 5 additions & 5 deletions lib/src/state/helix.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ abstract class Helix with BuiltJsonSerializable, UnusedFields implements Built<H

@memoized
Position3D get default_position {
num x = min_offset * geometry.rise_per_base_pair;
num z = min_offset * geometry.rise_per_base_pair;

// normalized so helices are diameter 1
Point<num> point_zy;
Expand All @@ -184,7 +184,7 @@ abstract class Helix with BuiltJsonSerializable, UnusedFields implements Built<H
}

num y = point_zy.y * geometry.distance_between_helices_nm;
num z = point_zy.x * geometry.distance_between_helices_nm;
num x = point_zy.x * geometry.distance_between_helices_nm;
Position3D pos = Position3D(x: x, y: y, z: z);
return pos;
}
Expand All @@ -202,13 +202,13 @@ abstract class Helix with BuiltJsonSerializable, UnusedFields implements Built<H
return default_position;
}

/// Calculates z-y angle in degrees, according to position3d(), from this [Helix] to [other].
/// Calculates x-y angle in degrees, according to position3d(), from this [Helix] to [other].
num angle_to(Helix other) {
var pos1 = position3d();
var pos2 = other.position3d();
num z = pos2.z - pos1.z;
num x = pos2.x - pos1.x;
num y = pos2.y - pos1.y;
num angle_radians = (atan2(z, -y)) % (2 * pi); // using SVG "reverse y" coordinates
num angle_radians = (atan2(x, -y)) % (2 * pi); // using SVG "reverse y" coordinates
return util.to_degrees(angle_radians);
}

Expand Down
24 changes: 12 additions & 12 deletions test/helix_rotation_set_test.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -231,13 +231,13 @@ main() {
idx: 1,
grid: Grid.none,
geometry: geometry,
position: Position3D(x: 0, z: helix_dist, y: helix_dist),
position: Position3D(x: helix_dist, z: 0, y: helix_dist),
roll: 0),
Helix(
idx: 2,
grid: Grid.none,
geometry: geometry,
position: Position3D(x: 0, z: 2 * helix_dist, y: 2 * helix_dist),
position: Position3D(x: 2 * helix_dist, z: 0, y: 2 * helix_dist),
roll: 0),
];
design = Design(grid: Grid.none, helices: helices, geometry: geometry);
Expand All @@ -257,8 +257,8 @@ main() {

num helix_dist = design.geometry.distance_between_helices_nm;
expect(helix0.position, Position3D(x: 0, z: 0, y: 0));
expect(helix1.position, Position3D(x: 0, z: helix_dist, y: helix_dist));
expect(helix2.position, Position3D(x: 0, z: 2 * helix_dist, y: 2 * helix_dist));
expect(helix1.position, Position3D(x: helix_dist, z: 0, y: helix_dist));
expect(helix2.position, Position3D(x: 2 * helix_dist, z: 0, y: 2 * helix_dist));

expect(util.rotation_between_helices(helix0, helix1, true, design.geometry), 90 + 45);
expect(util.rotation_between_helices(helix1, helix2, true, design.geometry), 90 + 45);
Expand All @@ -272,11 +272,11 @@ main() {

test('h0_h1_crossover_0_h1_h2_crossover_10', () {
// with helix0.roll = 0, the forward backbone points up, so helix1 should be directly above
// y = -2.5, z = 0
// x = 0, y = -2.5
// On helix1, the reverse backbone will point down, so the forward backbone will point 30 degrees
// clockwise from straight up, which is 60 degrees counterclockwise from the x-axis in Cartesian.
// So helix2 will be at
// y = -sin(60), z = cos(60)
// x = cos(60), y = -sin(60)
List<actions.UndoableAction> all_actions = helix_positions_set_based_on_crossovers(state);

expect(all_actions.length, 6);
Expand All @@ -293,18 +293,18 @@ main() {
expect(helix0.position.y, closeTo(0, eps));
expect(helix0.position.z, closeTo(0, eps));

num z1 = 0;
num x1 = 0;
num y1 = -design.geometry.distance_between_helices_nm;
expect(helix1.position.x, closeTo(0, eps));
expect(helix1.position.x, closeTo(x1, eps));
expect(helix1.position.y, closeTo(y1, eps));
expect(helix1.position.z, closeTo(z1, eps));
expect(helix1.position.z, closeTo(0, eps));

num radians_60_deg = util.to_radians(60);
num z2 = cos(radians_60_deg) * design.geometry.distance_between_helices_nm;
num x2 = cos(radians_60_deg) * design.geometry.distance_between_helices_nm;
num y2 = -sin(radians_60_deg) * design.geometry.distance_between_helices_nm;
expect(helix2.position.x, closeTo(0, eps));
expect(helix2.position.x, closeTo(x1 + x2, eps));
expect(helix2.position.y, closeTo(y1 + y2, eps));
expect(helix2.position.z, closeTo(z1 + z2, eps));
expect(helix2.position.z, closeTo(0, eps));
});
});
}
22 changes: 11 additions & 11 deletions test/middleware_test.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -213,67 +213,67 @@ main() {
},
{
"roll": 330,
"position": {"x": 0, "y": 1.0847093477938932, "z": 2.2524221697560485},
"position": {"z": 0, "y": 1.0847093477938932, "x": 2.2524221697560485},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 300,
"position": {"x": 0, "y": 0.17135678687790956, "z": 4.5796065413665605},
"position": {"z": 0, "y": 0.17135678687790956, "x": 4.5796065413665605},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 270,
"position": {"x": 0, "y": -1.2369433582811473, "z": 6.645203477156547},
"position": {"z": 0, "y": -1.2369433582811473, "x": 6.645203477156547},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 240,
"position": {"x": 0, "y": -3.7090204238439677, "z": 7.017809142596987},
"position": {"z": 0, "y": -3.7090204238439677, "x": 7.017809142596987},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 210,
"position": {"x": 0, "y": -6.202029916796918, "z": 6.830983908630923},
"position": {"z": 0, "y": -6.202029916796918, "x": 6.830983908630923},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 180,
"position": {"x": 0, "y": -7.760754421443755, "z": 4.876405202460852},
"position": {"z": 0, "y": -7.760754421443755, "x": 4.876405202460852},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 150,
"position": {"x": 0, "y": -8.845463769237648, "z": 2.6239830327048033},
"position": {"z": 0, "y": -8.845463769237648, "x": 2.6239830327048033},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 120,
"position": {"x": 0, "y": -7.932111208321665, "z": 0.2967986610942912},
"position": {"z": 0, "y": -7.932111208321665, "x": 0.2967986610942912},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 90,
"position": {"x": 0, "y": -6.523811063162608, "z": -1.7687982746956945},
"position": {"z": 0, "y": -6.523811063162608, "x": -1.7687982746956945},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 60,
"position": {"x": 0, "y": -4.051733997599787, "z": -2.1414039401361347},
"position": {"z": 0, "y": -4.051733997599787, "x": -2.1414039401361347},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
},
{
"roll": 30,
"position": {"x": 0, "y": -1.558724504646837, "z": -1.9545787061700721},
"position": {"z": 0, "y": -1.558724504646837, "x": -1.9545787061700721},
"major_ticks": [0, 10, 21, 31, 42, 52, 63],
"max_offset": 64
}
Expand Down

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