diff --git a/src/mol-base/_spec/collections.spec.ts b/src/mol-base/_spec/collections.spec.ts
index ff3705c608f8da5d1ac19d23bb0cc3317dcc28f6..d8096b9880eee33a233d6a357af88b50750185f0 100644
--- a/src/mol-base/_spec/collections.spec.ts
+++ b/src/mol-base/_spec/collections.spec.ts
@@ -184,6 +184,7 @@ describe('ordered set', () => {
expect(OrderedSet.isSubset(arr136, OrderedSet.ofSortedArray([1, 3, 7]))).toBe(false);
expect(OrderedSet.isSubset(OrderedSet.ofSortedArray([0, 1, 2, 3, 7, 10]), OrderedSet.ofSortedArray([1, 3, 7]))).toBe(true);
expect(OrderedSet.isSubset(arr136, OrderedSet.ofSortedArray([1, 3, 10, 45]))).toBe(false);
+ expect(OrderedSet.isSubset(arr136, OrderedSet.ofSortedArray([12, 13, 16]))).toBe(false);
});
it('access/membership', () => {
@@ -235,6 +236,10 @@ describe('ordered set', () => {
testEq('union AA', OrderedSet.union(arr136, OrderedSet.ofSortedArray([2, 4, 6, 7])), [1, 2, 3, 4, 6, 7]);
testEq('union AA1', OrderedSet.union(arr136, OrderedSet.ofSortedArray([2, 3, 4, 6, 7])), [1, 2, 3, 4, 6, 7]);
testEq('union AA2', OrderedSet.union(arr136, OrderedSet.ofSortedArray([2, 4, 5, 6, 7])), [1, 2, 3, 4, 5, 6, 7]);
+ testEq('union AA3', OrderedSet.union(OrderedSet.ofSortedArray([1, 3]), OrderedSet.ofSortedArray([2, 4])), [1, 2, 3, 4]);
+ testEq('union AA4', OrderedSet.union(OrderedSet.ofSortedArray([1, 3]), OrderedSet.ofSortedArray([1, 3, 4])), [1, 3, 4]);
+ testEq('union AA5', OrderedSet.union(OrderedSet.ofSortedArray([1, 3, 4]), OrderedSet.ofSortedArray([1, 3])), [1, 3, 4]);
+ it('union AA6', () => expect(OrderedSet.union(arr136, OrderedSet.ofSortedArray([1, 3, 6]))).toBe(arr136));
testEq('intersect ES', OrderedSet.intersect(empty, singleton10), []);
testEq('intersect ER', OrderedSet.intersect(empty, range1_4), []);
@@ -246,6 +251,7 @@ describe('ordered set', () => {
testEq('intersect RR2', OrderedSet.intersect(range1_4, OrderedSet.ofRange(3, 5)), [3, 4]);
testEq('intersect RA', OrderedSet.intersect(range1_4, arr136), [1, 3]);
testEq('intersect AA', OrderedSet.intersect(arr136, OrderedSet.ofSortedArray([2, 3, 4, 6, 7])), [3, 6]);
+ it('intersect AA1', () => expect(OrderedSet.union(arr136, OrderedSet.ofSortedArray([1, 3, 6]))).toBe(arr136));
testEq('subtract ES', OrderedSet.subtract(empty, singleton10), []);
testEq('subtract ER', OrderedSet.subtract(empty, range1_4), []);
diff --git a/src/mol-base/collections/ordered-set.ts b/src/mol-base/collections/ordered-set.ts
index c8ca6ac6fbdae4954662c0c4a49f98ea805347e9..c51ba055ac4ddb17c1acb54803872c2891d5e992 100644
--- a/src/mol-base/collections/ordered-set.ts
+++ b/src/mol-base/collections/ordered-set.ts
@@ -152,7 +152,11 @@ function hasA(set: SortedArray, x: number) { return x >= set[0] && x <= set[set.
function indexOfA(set: SortedArray, x: number) { return x >= set[0] && x <= set[set.length - 1] ? binarySearch(set, x) : -1; }
function binarySearch(xs: SortedArray, value: number) {
- let min = 0, max = xs.length - 1;
+ return binarySearchRange(xs, value, 0, xs.length);
+}
+
+function binarySearchRange(xs: SortedArray, value: number, start: number, end: number) {
+ let min = start, max = end - 1;
while (min <= max) {
if (min + 11 > max) {
for (let i = min; i <= max; i++) {
@@ -234,17 +238,17 @@ function areIntersectingAA(xs: SortedArray, ys: SortedArray) {
return false;
}
-function isSubsetAA(xs: SortedArray, ys: SortedArray) {
- if (xs === ys) return true;
+function isSubsetAA(a: SortedArray, b: SortedArray) {
+ if (a === b) return true;
- const lenB = ys.length;
- let { i, j, endA, endB } = getMaxIntersectionRange(xs, ys);
- // the 2nd array must be able to advance by at least lenB elements
- if (endB - j + 1 < lenB || endA - j + 1 < lenB) return false;
+ const lenB = b.length;
+ let { i, j, endA, endB } = getMaxIntersectionRange(a, b);
+ // must be able to advance by lenB elements
+ if (endB - j + 1 < lenB || endA - i + 1 < lenB) return false;
let equal = 0;
while (i <= endA && j <= endB) {
- const x = xs[i], y = ys[j];
+ const x = a[i], y = b[j];
if (x < y) { i++; }
else if (x > y) { j++; }
else { i++; j++; equal++; }
@@ -302,8 +306,6 @@ function unionAR(a: SortedArray, b: Range) {
function unionAA(a: SortedArray, b: SortedArray) {
if (a === b) return a;
- const lenA = a.length, lenB = b.length;
-
let { i: sI, j: sJ, endA, endB } = getMaxIntersectionRange(a, b);
let i = sI, j = sJ;
let commonCount = 0;
@@ -314,8 +316,11 @@ function unionAA(a: SortedArray, b: SortedArray) {
else { i++; j++; commonCount++; }
}
- if (!commonCount) return a;
- if (commonCount >= lenA) return OrderedSet.Empty
+ const lenA = a.length, lenB = b.length;
+ // A === B || B is subset of A ==> A
+ if ((commonCount === lenA && commonCount === lenB) || commonCount === lenB) return a;
+ // A is subset of B ===> B
+ if (commonCount === lenA) return b;
const resultSize = lenA + lenB - commonCount;
const l = Math.min(a[0], b[0]), r = Math.max(a[lenA - 1], b[lenB - 1]);
@@ -375,27 +380,33 @@ function intersectAR(a: SortedArray, r: Range) {
return OrderedSet.ofSortedArray(indices);
}
-function intersectAA(xs: SortedArray, ys: SortedArray) {
- if (xs === ys) return xs;
+function intersectAA(a: SortedArray, b: SortedArray) {
+ if (a === b) return a;
- let { i: sI, j: sJ, endA, endB } = getMaxIntersectionRange(xs, ys);
+ let { i: sI, j: sJ, endA, endB } = getMaxIntersectionRange(a, b);
let i = sI, j = sJ;
- let resultSize = 0;
+ let commonCount = 0;
while (i <= endA && j <= endB) {
- const x = xs[i], y = ys[j];
+ const x = a[i], y = b[j];
if (x < y) { i++; }
else if (x > y) { j++; }
- else { i++; j++; resultSize++; }
+ else { i++; j++; commonCount++; }
}
- if (!resultSize) return OrderedSet.Empty;
-
- const indices = new Int32Array(resultSize);
+ const lenA = a.length, lenB = b.length;
+ // no common elements
+ if (!commonCount) return OrderedSet.Empty;
+ // A === B || B is subset of A ==> B
+ if ((commonCount === lenA && commonCount === lenB) || commonCount === lenB) return b;
+ // A is subset of B ==> A
+ if (commonCount === lenA) return a;
+
+ const indices = new Int32Array(commonCount);
let offset = 0;
i = sI;
j = sJ;
while (i <= endA && j <= endB) {
- const x = xs[i], y = ys[j];
+ const x = a[i], y = b[j];
if (x < y) { i++; }
else if (x > y) { j++; }
else { indices[offset++] = x; i++; j++; }
@@ -417,6 +428,7 @@ function substractRR(a: Range, b: Range) {
if (isRangeSubset(a, b)) {
// this splits the interval into two, gotta represent it as a set.
const l = _sRB.fst - _sRA.fst, r = _sRA.snd - _sRB.snd;
+ // TODO: check if l === 0 || r === 0 ==> result would be a range
const ret = new Int32Array(l + r);
let offset = 0;
for (let i = 0; i < l; i++) ret[offset++] = _sRA.fst + i;
@@ -439,7 +451,11 @@ function subtractAR(a: SortedArray, b: Range) {
const min = _sAR.fst, max = _sAR.snd;
const { start, end } = getStartEnd(a, min, max);
const size = a.length - (end - start);
+ // A is subset of B
if (size <= 0) return OrderedSet.Empty;
+ // No common elements
+ if (size === a.length) return a;
+
const ret = new Int32Array(size);
let offset = 0;
for (let i = 0; i < start; i++) ret[offset++] = a[i];
@@ -458,15 +474,21 @@ function subtractRA(a: Range, b: SortedArray) {
const rSize = max - min + 1;
const { start, end } = getStartEnd(b, min, max);
const commonCount = end - start;
+
+ // No common elements.
+ if (commonCount === 0) return a;
+
const resultSize = rSize - commonCount;
+ // A is subset of B
if (resultSize <= 0) return OrderedSet.Empty;
+
const ret = new Int32Array(resultSize);
const li = b.length - 1;
const fst = b[Math.min(start, li)], last = b[Math.min(end, li)];
let offset = 0;
for (let i = min; i < fst; i++) ret[offset++] = i;
for (let i = fst; i <= last; i++) {
- if (binarySearch(b, i) < 0) ret[offset++] = i;
+ if (binarySearchRange(b, i, start, end) < 0) ret[offset++] = i;
}
for (let i = last + 1; i <= max; i++) ret[offset++] = i;
return OrderedSet.ofSortedArray(ret);
@@ -487,7 +509,9 @@ function subtractAA(a: SortedArray, b: SortedArray) {
else { i++; j++; commonCount++; }
}
+ // A isnt intersecting B ===> A
if (!commonCount) return a;
+ // A === B || A is subset of B ===> Empty
if (commonCount >= lenA) return OrderedSet.Empty;
const indices = new Int32Array(lenA - commonCount);
diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index 0711c4f44de2dfcf15e02d407fbd32f263abb665..b941373a3038cc3e935514d1dd69c42daeb354d0 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -8,6 +8,11 @@
interface Model {
+ // Incremented when data changes
+ dataVersion: number,
+
+ // Incremented when the underlying conformation changes
+ conformationVersion: number,
}
export default Model
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
index 16b0d72f04b3d049343b06c2b1b1d66c64605627..37727d2497c437e5c38584d8dc5b0bb4b21981fe 100644
--- a/src/mol-data/structure.ts
+++ b/src/mol-data/structure.ts
@@ -21,7 +21,7 @@ export interface Unit extends Readonly<{
id: number,
// Each unit can only contain atoms from a single "chain"
- // the reason for this is to make symmetry and assembly transforms fast
+ // the reason for this is to make certain basic data transforms fast
// without having to look at the actual contents of the unit
// multiple units can point to the same chain
chainIndex: number,
@@ -30,7 +30,7 @@ export interface Unit extends Readonly<{
model: Model,
// Determines the operation applied to this unit.
- // The transform and and inverse a baked into the "getPosition" function
+ // The transform and and inverse are baked into the "getPosition" function
operator: Operator
}> {
// returns the untransformed position. Used for spatial queries.