diff --git a/js/cells/DMACell.js b/js/cells/DMACell.js
index b6b4185e98b42199dddfcdc1e80db5d66920a8ff..f32e1658a25494d39486811f3a36c92808075eb3 100644
--- a/js/cells/DMACell.js
+++ b/js/cells/DMACell.js
@@ -107,6 +107,11 @@ define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'globals', '
return superCellIndex.add(this.superCell.applyRotation(this.getIndex()).round());
};
+ DMACell.prototype.getLatticeIndex = function(){
+ var parent = lattice.getUItarget();
+ return this.getAbsoluteIndex().sub(parent.get("cellsMin"));
+ };
+
DMACell.prototype.getPosition = function(){
return this.object3D.position.clone();
};
diff --git a/js/cells/DNABrickCell.js b/js/cells/DNABrickCell.js
new file mode 100644
index 0000000000000000000000000000000000000000..273e6c9330bc9467fb9e0ecc491031c0142678c3
--- /dev/null
+++ b/js/cells/DNABrickCell.js
@@ -0,0 +1,30 @@
+/**
+ * Created by aghassaei on 9/14/15.
+ */
+
+
+define(['gikCell'], function(GIKCell){
+
+ function DNABrickCell(json, superCell){
+ GIKCell.call(this, json, superCell);
+ }
+ DNABrickCell.prototype = Object.create(GIKCell.prototype);
+
+ DNABrickCell.prototype.getCompliment = function(nucleotide){
+ if (nucleotide == "a") return "t";
+ if (nucleotide == "t") return "a";
+ if (nucleotide == "c") return "g";
+ if (nucleotide == "g") return "c";
+ if (nucleotide == "unassigned") return null;
+ console.warn("unknown nucleotide " + nucleotide);
+ return null;
+ };
+
+ DNABrickCell.prototype.getNucleotideAtIndex = function(index){
+ if (this.parts && this.parts[index] && this.parts[index].getNucleotide) return this.parts[index].getNucleotide();
+ return "unassigned";
+ };
+
+
+ return DNABrickCell;
+});
\ No newline at end of file
diff --git a/js/cells/GIKCell.js b/js/cells/GIKCell.js
index f01c6aad3c9f2b4e1800cb6277af2e13410b4520..4712e50870fc458fa2b676f4d0608cf426e3d053 100644
--- a/js/cells/GIKCell.js
+++ b/js/cells/GIKCell.js
@@ -42,8 +42,17 @@ define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'cubeCell'],
});
} else if (lattice.get("partType") == "dnaStraight") {
require(['dnaStraightPart'], function(PartSubclass){
+ var parent = lattice.getUItarget();
+ parent._parseSparseCell();//todo this should get checked
+ var index = self.getLatticeIndex();
+ if (parent.cells[index.x][index.y][index.z+1]) var topNeighbor = parent.cells[index.x][index.y][index.z+1];
+ if (parent.cells[index.x][index.y][index.z-1]) var bottomNeighbor = parent.cells[index.x][index.y][index.z-1];
for (var i=0;i<16;i++){
+ var nucleotide = null;
+ if (topNeighbor && i<8) nucleotide = self.getCompliment(topNeighbor.getNucleotideAtIndex(i+8));
+ if (bottomNeighbor && i>7) nucleotide = self.getCompliment(bottomNeighbor.getNucleotideAtIndex(i-8));
parts.push(new PartSubclass(self.index.x, self, {
+ nuclType: nucleotide,
vertIndex: i,
isBridge: false
}));
diff --git a/js/cells/supercells/GIKSuperCell.js b/js/cells/supercells/GIKSuperCell.js
index ea7f1fe997264638e6fdd00670ddf974a48bca5f..e1dbc543bb985453aeec028ae5f3bc0c1eeda3a1 100644
--- a/js/cells/supercells/GIKSuperCell.js
+++ b/js/cells/supercells/GIKSuperCell.js
@@ -4,8 +4,8 @@
-define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'superCell', 'gikCell'],
- function(_, THREE, three, lattice, appState, DMASuperCell, GIKCell){
+define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'superCell', 'gikCell', 'dnaBrickCell'],
+ function(_, THREE, three, lattice, appState, DMASuperCell, GIKCell, DNABrickCell){
var unitGeos = {};
@@ -30,6 +30,10 @@ define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'superCell',
GIKSuperCell.prototype._makeSubCellForIndex = function(json, callback){
json.materialName = this.materialName;
+ if (lattice.get("latticeType") == "dnaBricks"){
+ callback(new DNABrickCell(json, this));
+ return;
+ }
callback(new GIKCell(json, this));
};
diff --git a/js/lattice/Lattice.js b/js/lattice/Lattice.js
index 34283712304a1992a70e60eca4674cda94a9ec80..07d342c5d06609b3894c99da997df7620c2fb150 100644
--- a/js/lattice/Lattice.js
+++ b/js/lattice/Lattice.js
@@ -171,54 +171,6 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
- //cells array
-
- _parseSparseCell: function(){
-
- this.cells = [[[null]]];
-
- console.log("parse cells");
-
- if (this.get("numCells") == 0) {
- console.warn("no cells in assembly");
- this.cells = [[[null]]];
- return;
- }
-
- var bounds = this.calculateBoundingBox();
- this.set("denseCellsMin", bounds.min.clone().add(this.get("cellsMin")));
- var size = bounds.max.sub(bounds.min);
-
- //create array of nulls
- var cells = [];
- for (var x=0;x<size.x;x++){
- cells.push([]);
- for (var y=0;y<size.y;y++){
- cells[x].push([]);
- for (var z=0;z<size.z;z++){
- cells[x][y].push(null);
- }
- }
- }
-
- var min = this.get("cellsMin").sub(bounds.min);
- var overlap = false;
- var forCAM = appState.get("currentNav") == "navAssemble";
- this._loopCells(this.sparseCells, function(cell){
- if (!cell) return;
- overlap |= cell.addToDenseArray(cells, min, forCAM);
- });
- this.set("overlapDetected", overlap);
-
- this.cells = cells;
- },
-
-
-
-
-
-
-
//3d ui
diff --git a/js/lattice/LatticeBase.js b/js/lattice/LatticeBase.js
index 610d65486498461b07e51fd17ad9a63fda82cf37..65db63519f17de6aa971e0ad80567402dfefc11f 100644
--- a/js/lattice/LatticeBase.js
+++ b/js/lattice/LatticeBase.js
@@ -447,6 +447,7 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
if (cell) cell.show();
});
}
+
this._iterCells(this.sparseCells, function(cell){
if (cell) cell.setMode(cellMode, function(){
if (--numCells <= 0) three.render();
@@ -520,6 +521,46 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
return {x:xScale, y:yScale, z:zScale};
},
+ _parseSparseCell: function(){
+
+ this.cells = [[[null]]];
+
+ console.log("parse cells");
+
+ if (this.get("numCells") == 0) {
+ console.warn("no cells in assembly");
+ this.cells = [[[null]]];
+ return;
+ }
+
+ var bounds = this.calculateBoundingBox();
+ this.set("denseCellsMin", bounds.min.clone().add(this.get("cellsMin")));
+ var size = bounds.max.sub(bounds.min);
+
+ //create array of nulls
+ var cells = [];
+ for (var x=0;x<size.x;x++){
+ cells.push([]);
+ for (var y=0;y<size.y;y++){
+ cells[x].push([]);
+ for (var z=0;z<size.z;z++){
+ cells[x][y].push(null);
+ }
+ }
+ }
+
+ var min = this.get("cellsMin").sub(bounds.min);
+ var overlap = false;
+ var forCAM = appState.get("currentNav") == "navAssemble";
+ this._loopCells(this.sparseCells, function(cell){
+ if (!cell) return;
+ overlap |= cell.addToDenseArray(cells, min, forCAM);
+ });
+ this.set("overlapDetected", overlap);
+
+ this.cells = cells;
+ },
+
diff --git a/js/main.js b/js/main.js
index a8fc4fb6366e454188ade1dd2df1f5250cc26e44..3b66cf24ac5e206bd10cdec83cc5fab41315a620 100644
--- a/js/main.js
+++ b/js/main.js
@@ -96,6 +96,7 @@ require.config({
compositeCell: "cells/supercells/CompositeCell",
hexCell: 'cells/HexagonalCell',
hexRotCell: 'cells/HexagonalRotCell',
+ dnaBrickCell: 'cells/DNABrickCell',
//parts
part: 'parts/DMAPart',
diff --git a/js/parts/DNAStraightPart.js b/js/parts/DNAStraightPart.js
index 4fd898efce39f136e94245701eeb95cb604f96eb..9bbd2d3fa1f14686519c6cfd0a965fdb5ba0fa0f 100644
--- a/js/parts/DNAStraightPart.js
+++ b/js/parts/DNAStraightPart.js
@@ -41,6 +41,10 @@ define(['underscore', 'stlLoader', 'gikPart'], function(_, THREE, GIKPart){
return 'g';
};
+ DNAStraightPart.prototype.getNucleotide = function(){
+ return this._nuclType;
+ };
+
DNAStraightPart.prototype._getGeometry = function(){
if (this._isBridge) return bridgeGeo;
return unitGeo;