From 074f9cba8fb5018152468f19e403bff7ea2dfc1f Mon Sep 17 00:00:00 2001
From: BobHanson <hansonr@stolaf.edu>
Date: Sat, 6 Jun 2020 12:36:34 -0500
Subject: [PATCH] JAL-3446 adds Jmol viewer embedding.

---
 .../site-resources/jalview_embedded_example1.html  |   32 ++++++++++++--------
 1 file changed, 20 insertions(+), 12 deletions(-)

diff --git a/utils/jalviewjs/site-resources/jalview_embedded_example1.html b/utils/jalviewjs/site-resources/jalview_embedded_example1.html
index 0dd1052..99ae68e 100644
--- a/utils/jalviewjs/site-resources/jalview_embedded_example1.html
+++ b/utils/jalviewjs/site-resources/jalview_embedded_example1.html
@@ -26,12 +26,13 @@ Info = {
 jvGet = function(what) {
 	switch(what) {
 	case "tree":
-		Jalview.app.openTreePanel$jalview_gui_AlignFrame$S$S(null, "NJ","BLOSUM62")
+		Jalview.app.openTreePanel(null, "NJ","BLOSUM62")
 		break;
 	case "pca":
-		Jalview.app.openPcaPanel$jalview_gui_AlignFrame$S(null, "BLOSUM62")
+		Jalview.app.openPcaPanel(null, "BLOSUM62")
 		break;
 	case "3D":
+		Jalview.app.showStructure(null, "1a70", "mmcif");
 		break;
 	}
 	
@@ -87,11 +88,12 @@ The alignment frame will appear here momentarily. When it does, you can go ahead
 <table style="background-color:lightgray"><tr><td  style="padding:0px 0px 0px 20px">
 <b>Select a few alignments</b> by left-dragging across a few rows of the alignment to make a selection box. 
 Then click one of the buttons below to see more information about your selected subset of the alignment.
-<ul>
-<li><button onclick='jvGet("tree")'>similarity tree</button></li>
-<li><button onclick='jvGet("pca")'>principal component analysis</button></li>
-</ul>
-
+<br><br>
+<button onclick='jvGet("tree")'>similarity tree</button> <button onclick='jvGet("pca")'>principal component analysis</button>
+<br><br>
+One more thing. Let's take a <a href="javascript:jvGet('3D')" style="text-decoration:none;color:red">look at the 3D structure</a> of one these proteins. Ferredoxins are important, because they have 
+iron-sulfur clusters that can accept and deliver electrons in metabolic processes. Let's see if we can find it. 
+<br><br>
 
 
 
@@ -99,12 +101,14 @@ Then click one of the buttons below to see more information about your selected
 <table style="border-spacing:0"><tr><td style="background-color:lightgray;padding:10px 0px 10px 20px">
 <div id="Jalview-tree-div" style="position:relative;top:0px;left:0px;width:500px;height:500px">
 <br><br><br><br>
-Jalview-tree-div
+<a href="javascript:jvGet('tree')">Jalview-tree-div</a>
 </div>
 </td><td style="background-color:lightgray;padding:10px 20px 10px 0px">
 <div id="Jalview-pca-div" style="position:relative;top:0px;left:0px;width:500px;height:500px">
 <br><br><br><br>
-Jalview-pca-div
+<a href="javascript:jvGet('pca')">Jalview-pca-div</a>
+<br><br>
+
 </div>
 </td></tr></table>
 
@@ -113,19 +117,23 @@ Jalview-pca-div
 
 </td></tr>
 
+<!-- let it float
 <tr>
 
 <td valign=top style="padding:20px;height:650px" >
 
 <div id="Jalview-structureviewer-div" style="position:relative;top:0px;left:0px;width:600px;height:600px">
-Jalview-strucddtureviewer-div
-</div>
+<a href="javascript:jvGet('3D')">Jalview-structureviewer-div</a>
+</div> 
 </td>
 <td valign=top style="padding:20px;background-color:white" >
 One more thing. Let's take a look at the 3D structure of one these proteins. Ferredoxins are important, because they have 
 iron-sulfur clusters that can accept and deliver electrons in metabolic processes. Let's see if we can find it. 
 <br><center><button onclick='jvGet("3D")'>add the 3D structure</button>
-</td></tr></table>
+</td></tr>
+ -->
+
+</table>
 
 
 <!-- debugging (hidden) -->
-- 
1.7.10.2