Skip to content

Commit

Permalink
fix rendering of 1J5E in some browsers
Browse files Browse the repository at this point in the history 
This was caused by running out of indices while generating the geometry
for chain A, a very long RNA molecule. Now proper splits are introduced
when that happens.
  • Loading branch information
@biasmv
biasmv committed Feb 28, 2015
1 parent 7c656ee commit f9e3c5f
Show file tree
Hide file tree
Showing 4 changed files with 59 additions and 12 deletions.
4 changes: 4 additions & 0 deletions src/gfx/indexed-vertex-array.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,10 @@ utils.derive(IndexedVertexArray, VertexArrayBase, {
numIndices : function() { return this._numTriangles * 3; },

addVertex : function(pos, normal, color, objId) {
if (this._numVerts === this._maxVerts) {
console.error('maximum number of vertices reached');
return;
}
var i = this._numVerts * this._FLOATS_PER_VERT;
this._vertData[i++] = pos[0];
this._vertData[i++] = pos[1];
Expand Down
15 changes: 13 additions & 2 deletions src/gfx/mesh-geom.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -93,14 +93,25 @@ utils.derive(MeshGeom, BaseGeom, {
return newVa;
},

// makes sure the current vertex array has at least space for numVerts more
// vertices. If so, the current vertex array is returned. If not, a new
// vertex array is created with as much space as possible:
// - if there are still more than 2^16 vertices required for this mesh geom,
// a new vertex array with 2^16 vertices is returned
// - if there are less than 2^16 vertices are required, a new vertex array
// with the number of remaining vertices is returned.
//
// Note: this depends on the total number of vertices provided to
// addVertArray/addChainVertArray. In case there are too few vertices passed
// to addVertArray/addChainVertArray, bad stuff will happen!
vertArrayWithSpaceFor : function(numVerts) {
var currentVa = this._indexedVAs[this._indexedVAs.length - 1];
var remaining = currentVa.maxVerts() - currentVa.numVerts();
if (remaining >= numVerts) {
return currentVa;
}
this._remainingVerts = this._remainingVerts - currentVa.numVerts();
this._remainingIndices = this._remainingIndices - currentVa.numIndices();
this._remainingVerts -= currentVa.numVerts();
this._remainingIndices -= currentVa.numIndices();
numVerts = this._boundedVertArraySize(this._remainingVerts);
var newVa = null;
if (currentVa instanceof MeshChainData) {
Expand Down
43 changes: 33 additions & 10 deletions src/gfx/render.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -523,7 +523,13 @@ exports.trace = function(structure, gl, opts) {
var _cartoonNumVerts = function(traces, vertsPerSlice, splineDetail) {
var numVerts = 0;
for (var i = 0; i < traces.length; ++i) {
numVerts += ((traces[i].length() - 1) * splineDetail + 1) * vertsPerSlice;
var traceVerts =
((traces[i].length() - 1) * splineDetail + 1) * vertsPerSlice;
// in case there are more than 2^16 vertices for a single trace, we
// need to manually split the trace in two and duplicate one of the
// trace slices. Let's make room for some additional space...
var splits = Math.ceil((traceVerts + 2)/65536);
numVerts += traceVerts + (splits - 1) * vertsPerSlice;
// triangles for capping the tube
numVerts += 2;
}
Expand All @@ -549,13 +555,14 @@ var _addNucleotideSticks = (function() {
var color = vec4.create();
return function(meshGeom, vertAssoc, traces, opts) {
var radius = opts.radius * 1.8;
var vertsPerNucleotideStick = opts.protoCyl.numVerts() +
2 * opts.protoSphere.numVerts();
for (var i = 0; i < traces.length; ++i) {
var trace = traces[i];
var idRange = opts.idPool.getContinuousRange(trace.length());
meshGeom.addIdRange(idRange);
for (var j = 0; j < trace.length(); ++j) {
var atomVerts = opts.protoCyl.numVerts();
var va = meshGeom.vertArrayWithSpaceFor(atomVerts);
var va = meshGeom.vertArrayWithSpaceFor(vertsPerNucleotideStick);
var vertStart = va.numVerts();
var residue = trace.residueAt(j);
var resName = residue.name();
Expand All @@ -581,12 +588,13 @@ var _addNucleotideSticks = (function() {
geom.buildRotation(rotation, dir, left, up, false);

opts.protoCyl.addTransformed(va, center, length, radius,
rotation, color, color, objId, objId);
rotation, color, color, objId, objId);
opts.protoSphere.addTransformed(va, endAtom.pos(), radius,
color, objId);
color, objId);
opts.protoSphere.addTransformed(va, startAtom.pos(), radius,
color, objId);
color, objId);
var vertEnd = va.numVerts();
console.assert(vertEnd <= 65536, 'too many vertices');
vertAssoc.addAssoc(endAtom, va, vertStart, vertEnd);
}
}
Expand Down Expand Up @@ -620,9 +628,8 @@ var cartoonForChain = function(meshGeom, vertAssoc, nucleotideAssoc, opts,
}
meshGeom.addChainVertArray(chain, numVerts, numIndices);
for (var ti = 0; ti < traces.length; ++ti) {
_cartoonForSingleTrace(meshGeom, vertAssoc, traces[ti], traceIndex,
opts);
traceIndex++;
traceIndex = _cartoonForSingleTrace(meshGeom, vertAssoc, traces[ti],
traceIndex, opts);
}
_addNucleotideSticks(meshGeom, nucleotideAssoc, nucleicAcidTraces, opts);
return traceIndex;
Expand Down Expand Up @@ -795,6 +802,7 @@ function capTubeEnd(va, baseIndex, numTubeVerts) {
va.addTriangle(center, baseIndex, baseIndex + numTubeVerts - 1);
}


// constructs a cartoon representation for a single consecutive backbone
// trace.
var _cartoonForSingleTrace = (function() {
Expand All @@ -805,7 +813,6 @@ var _cartoonForSingleTrace = (function() {
return function(meshGeom, vertAssoc, trace, traceIndex, opts) {
var numVerts =
_cartoonNumVerts([trace], opts.arcDetail * 4, opts.splineDetail);

var positions = opts.float32Allocator.request(trace.length() * 3);
var colors = opts.float32Allocator.request(trace.length() * 4);
var normals = opts.float32Allocator.request(trace.length() * 3);
Expand Down Expand Up @@ -845,6 +852,7 @@ var _cartoonForSingleTrace = (function() {
var vertStart = vertArray.numVerts();
vertArray.addVertex(pos, [-tangent[0], -tangent[1], -tangent[2]],
color, objIds[0]);

_cartoonAddTube(vertArray, pos, normal, trace.residueAt(0).ss(), tangent,
color, radius, true, opts, 0, objIds[0]);
capTubeStart(vertArray, vertStart, opts.arcDetail * 4);
Expand All @@ -858,6 +866,7 @@ var _cartoonForSingleTrace = (function() {
var steps = geom.catmullRomSplineNumPoints(trace.length(),
opts.splineDetail, false);

var vertsPerSlice = opts.arcDetail * 4;
for (var i = 1, e = steps; i < e; ++i) {
// compute 3*i, 3*(i-1), 3*(i+1) once and reuse
var ix3 = 3 * i, ix4 = 4 * i, ipox3 = 3 * (i + 1), imox3 = 3 * (i - 1);
Expand Down Expand Up @@ -939,6 +948,19 @@ var _cartoonForSingleTrace = (function() {
var objId = objIds[Math.min(objIds.length - 1, objIndex)];
_cartoonAddTube(vertArray, pos, normal, thisSS,
tangent, color, radius, false, opts, offset, objId);
// in case we are running out of indices, start new vertex array and
// duplicate last slice. If we are on the last slice, we only need one
// additional vertex for the capping, otherwise we need a full slice
// worth of vertices.
var additionalVerts = (i === e - 1) ? 1 : vertsPerSlice;
if (vertArray.numVerts() + additionalVerts > vertArray.maxVerts()) {
vertEnd = vertArray.numVerts();
vertAssoc.addAssoc(traceIndex, vertArray, slice, vertStart, vertEnd);
vertArray = meshGeom.vertArrayWithSpaceFor(additionalVerts);
vertStart = 0;
_cartoonAddTube(vertArray, pos, normal, thisSS,
tangent, color, radius, true, opts, 0, objId);
}
if (drawArrow) {
vertAssoc.addAssoc(traceIndex, vertArray, slice, vertStart, vertEnd);
// FIXME: arrow has completely wrong normals. Profile normals are
Expand All @@ -963,6 +985,7 @@ var _cartoonForSingleTrace = (function() {
capTubeEnd(vertArray, vertStart, opts.arcDetail * 4);
opts.float32Allocator.release(normals);
opts.float32Allocator.release(positions);
return traceIndex + 1;
};
})();

Expand Down
9 changes: 9 additions & 0 deletions src/gfx/vertex-array-base.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,15 @@ VertexArrayBase.prototype = {
center[0] += this._vertData[index + 0];
center[1] += this._vertData[index + 1];
center[2] += this._vertData[index + 2];
if (isNaN(center[0])) {
console.log(this, i, numVerts, 'x NaN');
}
if (isNaN(center[2])) {
console.log(this, i, numVerts, 'y NaN');
}
if (isNaN(center[2])) {
console.log(this, i, numVerts, 'z NaN');
}
}
vec3.scale(center, center, 1.0/numVerts);
var radiusSquare = 0.0;
Expand Down

0 comments on commit f9e3c5f

Please sign in to comment.