complementary strands

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();
     };

js/cells/DNABrickCell.js

+/**
+ * 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

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
                     }));

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));
     };
 

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
 

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;
+        },
+
 
 
 

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',

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;