diff --git a/js/cells/DNABrickCell.js b/js/cells/DNABrickCell.js
index 273e6c9330bc9467fb9e0ecc491031c0142678c3..fda51dd6defb2369f1bba9e8837518ea6e70429e 100644
--- a/js/cells/DNABrickCell.js
+++ b/js/cells/DNABrickCell.js
@@ -25,6 +25,22 @@ define(['gikCell'], function(GIKCell){
return "unassigned";
};
+ DNABrickCell.prototype.getSequence = function(){
+ if (this._sequence) return this._sequence;
+ var sequence = "";
+ if (!this.parts || this.parts.length < 16) {
+ console.warn("need to calc nucleotides for this cell");
+ return sequence;
+ }
+ for (var i=0;i<16;i++){
+ var nucleotide = this.parts[i].getNucleotide();
+ if (nucleotide) sequence += nucleotide;
+ else console.warn("no nucleotide found for this part");
+ }
+ this._sequence = sequence;
+ return sequence;
+ };
+
return DNABrickCell;
});
\ No newline at end of file
diff --git a/js/cells/GIKCell.js b/js/cells/GIKCell.js
index b81dab5da187e7822777f6901434f04c08cecb01..f4ef144423612d26fe608eb431237861a3e1fdec 100644
--- a/js/cells/GIKCell.js
+++ b/js/cells/GIKCell.js
@@ -51,10 +51,13 @@ define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'cubeCell'],
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];
+ var seq = this._sequence;
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));
+ if (seq === undefined){
+ if (topNeighbor && i<8) nucleotide = self.getCompliment(topNeighbor.getNucleotideAtIndex(i+8));
+ if (bottomNeighbor && i>7) nucleotide = self.getCompliment(bottomNeighbor.getNucleotideAtIndex(i-8));
+ } else nucleotide = seq[i];
parts.push(new PartSubclass(self.index.x, self, {
nuclType: nucleotide,
vertIndex: i,
diff --git a/js/cells/supercells/GIKSuperCell.js b/js/cells/supercells/GIKSuperCell.js
index e1dbc543bb985453aeec028ae5f3bc0c1eeda3a1..14988e2e28d900209a3f1f548fd629ebbc350dbc 100644
--- a/js/cells/supercells/GIKSuperCell.js
+++ b/js/cells/supercells/GIKSuperCell.js
@@ -90,5 +90,15 @@ define(['underscore', 'three', 'threeModel', 'lattice', 'appState', 'superCell',
this.length = null;
};
+
+ GIKSuperCell.prototype.getSequence = function(){//todo this goes somewhere else
+ var sequence = "";
+ for (var i=0;i<this.length;i++){
+ if (i>0) sequence += "-";//linker
+ sequence += this.cells[i][0][0].getSequence();
+ }
+ return sequence;
+ };
+
return GIKSuperCell;
});
\ No newline at end of file
diff --git a/js/dnaExport/dnaExport.js b/js/dnaExport/dnaExport.js
new file mode 100644
index 0000000000000000000000000000000000000000..fd5dbfd1a815726e0c58c8638f75de1a314c2dd7
--- /dev/null
+++ b/js/dnaExport/dnaExport.js
@@ -0,0 +1,51 @@
+/**
+ * Created by aghassaei on 9/15/15.
+ */
+
+
+define(['underscore', 'backbone', 'lattice', 'appState', 'fileSaver'],
+ function(_, Backbone, lattice, appState, fileSaver){
+
+ var DNAExport = Backbone.Model.extend({
+
+ defaults: {
+ sequence32: [],
+ sequence16: []
+ },
+
+
+ initialize: function(){
+
+ this.listenTo(appState, "change:currentNav", this._navChanged);
+
+ this.generateSequences();
+ },
+
+ _navChanged: function(){
+ if (appState.get("currentNav") == "navDNAAssemble") this.generateSequences();
+ },
+
+ generateSequences: function(){
+ var sequences32 = [];
+ var sequences16 = [];
+ lattice.loopCells(function(cell, x, y, z){
+ if (!cell) return;
+ if (cell.getLength() == 2) sequences32.push(cell.getSequence());
+ else if (cell.getLength() == 1) sequences16.push(cell.getSequence());
+ else console.warn("unexpected cell of length " + cell.getLength());
+ });
+ this.set("sequence32", sequences32);
+ this.set("sequence16", sequences16);
+ },
+
+ save: function(){
+ var data = this.toJSON();
+ fileSaver.saveSequences(data);
+ }
+
+ });
+
+
+ return new DNAExport();
+
+});
\ No newline at end of file
diff --git a/js/lattice/LatticeBase.js b/js/lattice/LatticeBase.js
index 65db63519f17de6aa971e0ad80567402dfefc11f..378cdcbaba6cfefb423511a2896c5949a1245a14 100644
--- a/js/lattice/LatticeBase.js
+++ b/js/lattice/LatticeBase.js
@@ -504,6 +504,10 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
});
},
+ loopCells: function(callback){
+ this._loopCells(this.sparseCells, callback);
+ },
+
_loopCells: function(cells, callback){
for (var x=0;x<cells.length;x++){
for (var y=0;y<cells[0].length;y++){
diff --git a/js/main.js b/js/main.js
index c73073d12872c0b8510679e21f6be78f2ba68b36..183b62a71c3607db82a176df2e2341d2dbe12b2c 100644
--- a/js/main.js
+++ b/js/main.js
@@ -35,6 +35,7 @@ require.config({
globals: 'models/Globals',
appState: 'models/AppState',
fileSaver: 'models/FileSaver',
+ dnaExport: 'dnaExport/dnaExport',
//communication
socketio: '../dependencies/socket.io-1.3.5',
diff --git a/js/menus/DNAExportMenuView.js b/js/menus/DNAExportMenuView.js
index be46f0b904453903a61937fb0a746bce0f0d83b1..2581d0dd49c13e895f14b9f88b5691cdad49ee00 100644
--- a/js/menus/DNAExportMenuView.js
+++ b/js/menus/DNAExportMenuView.js
@@ -3,21 +3,27 @@
*/
-define(['jquery', 'underscore', 'menuParent', 'plist', 'lattice', 'text!menus/templates/DNAExportMenuView.html'],
- function($, _, MenuParentView, plist, lattice, template){
+define(['jquery', 'underscore', 'menuParent', 'dnaExport', 'text!menus/templates/DNAExportMenuView.html'],
+ function($, _, MenuParentView, dnaExport, template){
return MenuParentView.extend({
events: {
+ "click #saveSequences": "_saveToFile"
},
_initialize: function(){
},
+ _saveToFile: function(e){
+ e.preventDefault();
+ dnaExport.save();
+ },
+
_makeTemplateJSON: function(){
- return {};
+ return dnaExport.toJSON();
},
template: _.template(template)
diff --git a/js/menus/templates/DNAExportMenuView.html b/js/menus/templates/DNAExportMenuView.html
index 206addaa25c733eda9ea53dd417d8130dc91abef..fc06e73547875546725829f777d096d9287032b3 100644
--- a/js/menus/templates/DNAExportMenuView.html
+++ b/js/menus/templates/DNAExportMenuView.html
@@ -1 +1,9 @@
-export sequences
\ No newline at end of file
+32bp sequences:<br/>
+<% _.each(sequence32, function(seq){ %>
+ <%= seq %><br/>
+<% }); %><br/>
+16bp sequences:<br/>
+<% _.each(sequence16, function(seq){ %>
+ <%= seq %><br/>
+<% }); %><br/>
+<a href="#" id="saveSequences" class="btn btn-block btn-lg btn-success">Save to File</a><br/>
diff --git a/js/models/FileSaver.js b/js/models/FileSaver.js
index 2902c199c4a5bf895e82564384cba205c0391c79..8283b87abec01f11c2ca175bde7f2bcbd27f1c08 100644
--- a/js/models/FileSaver.js
+++ b/js/models/FileSaver.js
@@ -5,11 +5,15 @@
define(['underscore', 'fileSaverLib', 'lattice', 'materials', 'ribbon', 'menuWrapper'], function(_, saveAs, lattice, materials, ribbon, menuWrapper){
- function _saveFile(data, name, extension){
+ function _saveFile(data, name, extension, noQuotes){
// require(['jsonFn'], function(JSONfn){
// console.log(data.toString());
var jsonString = JSON.stringify(data, null, '\t');
+ if (noQuotes){
+ jsonString = jsonString.replace(/"/g, '');
+ }
+
var blob = new Blob([jsonString], {type: "text/plain;charset=utf-8"});
saveAs(blob, name + extension);
if (data.assembler){
@@ -54,6 +58,10 @@ define(['underscore', 'fileSaverLib', 'lattice', 'materials', 'ribbon', 'menuWra
_saveFile(data, name, ".user");
}
+ function saveSequences(seqArray, name){
+ _saveFile(seqArray, name || "seqs", ".txt", true);
+ }
+
function saveMaterial(id, material){
var data = {materials:{}};
data.materials[id] = material || _getMaterialDataToSave(id);
@@ -139,7 +147,8 @@ define(['underscore', 'fileSaverLib', 'lattice', 'materials', 'ribbon', 'menuWra
saveMachineConfig: saveMachineConfig,
// saveAssembler: saveAssembler,
// saveUser: saveUser,
- loadFile: loadFile
+ loadFile: loadFile,
// loadUser: loadUser
+ saveSequences: saveSequences
}
});
\ No newline at end of file