Merge pull request biocore#305 from antgonza/issue_300

Issue 300

ChangeLog.md

@@ -8,6 +8,7 @@ Emperor 0.9.4-dev (changes since Emperor 0.9.4 go here)
 * Add numpydoc generated documentation setup.
 * Emperor's documentation requires `sphinx-boostrap-theme` and `sphinx`.
 * Add documentation about file formats.
+* Updated to three.js revision 68.
 
 
 Emperor 0.9.4 (10 Sept 2014)

LICENSE.md

@@ -5,7 +5,7 @@ Emperor makes usage of all of the following copyrighted packages; their licenses
 
 --------------------------------------------------------------------------------
 
-### THREE.js ([r58](https://github.com/mrdoob/three.js/tree/r58)) is released under the MIT License
+### THREE.js ([r68](https://github.com/mrdoob/three.js/tree/r68)) is released under the MIT License
 
 The MIT License
 
@@ -171,7 +171,7 @@ EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 --------------------------------------------------------------------------------
 
-### THREEx.screenshot [v1](http://learningthreejs.com/data/THREEx/docs/THREEx.screenshot.html) 
+### THREEx.screenshot [v1](http://learningthreejs.com/data/THREEx/docs/THREEx.screenshot.html)
 [repository](https://github.com/jeromeetienne/threex)
 
 Copyright (c) 2011 Jerome Etienne, http://jetienne.com
@@ -197,7 +197,7 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 --------------------------------------------------------------------------------
 
-### FileSaver.js [283e78fd3c](https://github.com/eligrey/FileSaver.js/) 
+### FileSaver.js [283e78fd3c](https://github.com/eligrey/FileSaver.js/)
 
 Copyright (c) 2011 [Eli Grey](http://eligrey.com).
 

emperor/format.py

@@ -37,7 +37,7 @@ class EmperorLogicError(ValueError):
     pass
 
 def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
-                    coords_low=None, coords_high=None, number_of_axes=10, 
+                    coords_low=None, coords_high=None, number_of_axes=10,
                     number_of_segments=8):
     """Write the javascript necessary to represent a pcoa file in emperor
 
@@ -50,7 +50,7 @@ def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
     coords_low: coordinates representing the lower edges of an ellipse
     coords_high: coordinates representing the highere edges of an ellipse
     number_of_axes: number of axes to be returned
-    number_of_segments: number of segments and rings for each sphere 
+    number_of_segments: number of segments and rings for each sphere
 
     Output:
     string: javascript representation of the PCoA data inputed, contains a list
@@ -61,7 +61,7 @@ def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
     declarations.
     """
     js_pcoa_string = ''
-    
+
     # validating that the number of coords in coords
     if number_of_axes>len(coords[0]):
         number_of_axes = len(coords[0])
@@ -88,7 +88,7 @@ def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
     min_z = min(coords[:,2:3])
     maximum = max(abs(coords[:,:number_of_axes]))
     pcoalabels = pct_var[:number_of_axes]
-    
+
     radius = (max_x-min_x)*.012
 
     # write the values for all the spheres
@@ -110,8 +110,8 @@ def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
                 "'color': 0, 'width': %f, 'height': %f, 'length': %f , 'x': %f,"
                 " 'y': %f, 'z': %f, %s }\n" % (s_header, s_header,delta[0], delta[1],
                 delta[2], s_coord[0], s_coord[1], s_coord[2], all_coords))
-    
-    js_pcoa_string += 'var g_segments = %d, g_rings = %d, g_radius = %f;\n' % (number_of_segments, 
+
+    js_pcoa_string += 'var g_segments = %d, g_rings = %d, g_radius = %f;\n' % (number_of_segments,
         number_of_segments, radius)
     js_pcoa_string += 'var g_xAxisLength = %f;\n' % (abs(max_x)+abs(min_x))
     js_pcoa_string += 'var g_yAxisLength = %f;\n' % (abs(max_y)+abs(min_y))
@@ -139,7 +139,7 @@ def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
             js_pcoa_string += 'var g_pc%dLabel = \"PC%d (%.2f %%)\";\n' %\
                 (i+1, i+1-offset, pcoalabels[i-offset])
     js_pcoa_string += 'var g_number_of_custom_axes = %d;\n' % offset
-    
+
     js_pcts = []
     js_pcts_round = []
     if custom_axes == None: custom_axes = []
@@ -153,7 +153,7 @@ def format_pcoa_to_js(header, coords, eigvals, pct_var, custom_axes=[],
             js_pcts_round.append('%.2f' % (pct_var[0]))
     js_pcoa_string += 'var g_fractionExplained = [%s];\n' % ', '.join(js_pcts)
     js_pcoa_string += 'var g_fractionExplainedRounded = [%s];\n' % ', '.join(js_pcts_round)
-    
+
     return js_pcoa_string
 
 def format_mapping_file_to_js(mapping_file_data, mapping_file_headers, columns):
@@ -203,7 +203,7 @@ def format_mapping_file_to_js(mapping_file_data, mapping_file_headers, columns):
 def format_taxa_to_js(otu_coords, lineages, prevalence, min_taxon_radius=0.5,
                     max_taxon_radius=5, radius=1.0):
     """Write a string representing the taxa in a PCoA plot as javascript
-    
+
     Inputs:
     otu_coords: numpy array where the taxa is positioned
     lineages: label for each of these lineages
@@ -503,9 +503,11 @@ def format_emperor_autograph(metadata_fp, coords_fp, language='HTML'):
     <script type="text/javascript" src="emperor_required_resources/js/d3.parcoords.js"></script>
 
     <!-- THREE.js and plugins for screenshots -->
-    <script type="text/javascript" src="emperor_required_resources/js/Three.js"></script>
+    <script type="text/javascript" src="emperor_required_resources/js/three.min.js"></script>
     <script type="text/javascript" src="emperor_required_resources/js/js/Detector.js"></script>
-    <script type="text/javascript" src="emperor_required_resources/js/js/RequestAnimationFrame.js"></script>
+    <script type="text/javascript" src="emperor_required_resources/js/js/OrbitControls.js"></script>
+    <script type="text/javascript" src="emperor_required_resources/js/js/ColorConverter.js"></script>
+    <script type="text/javascript" src="emperor_required_resources/js/js/SVGRenderer.js"></script>
     <script type="text/javascript" src="emperor_required_resources/js/THREEx.screenshot.js"></script>
 
     <!-- General utilities (underscore.js and FileSaver.js) -->
@@ -521,7 +523,7 @@ def format_emperor_autograph(metadata_fp, coords_fp, language='HTML'):
     <script type="text/javascript" src="emperor_required_resources/emperor/js/util.js"></script>
 
     <script type="text/javascript">
-    
+
 """
 
 _ELLIPSE_OPACITY_SLIDER = """
@@ -808,7 +810,7 @@ def format_emperor_autograph(metadata_fp, coords_fp, language='HTML'):
                 </td></tr>
             </table>
         </div>
-    </div>  
+    </div>
 </div>
 </body>
 

emperor/support_files/emperor/js/emperor.js

@@ -568,18 +568,13 @@ function showByMenuChanged() {
 		// get all of the values for the selected category
 		vals.push(g_mappingFileData[sid][showByMenuIndex]);
 		// set everything to visible
-		try {
-			g_elementsGroup.add(g_plotEllipses[sid])
-		}
-		catch(TypeError){}
-		try {
-			g_elementsGroup.add(g_plotSpheres[sid])
-		}
-		catch(TypeError){}
-		try {
-			g_elementsGroup.add(g_plotVectors[sid])
-		}
-		catch(TypeError){}
+    if (typeof g_plotEllipses[sid] != 'undefined')
+      g_elementsGroup.add(g_plotEllipses[sid])
+    if (typeof g_plotSpheres[sid] != 'undefined')
+      g_elementsGroup.add(g_plotSpheres[sid])
+    if (typeof g_plotVectors[sid] != 'undefined')
+      g_elementsGroup.add(g_plotVectors[sid])
+
 		$('#'+divid+"_label").css('display','block');
 	}