4 <title>Embedded JalviewJS Example 1</title><meta charset="utf-8" />
5 <script src="swingjs/swingjs2.js"></script>
7 if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
10 main: "jalview.bin.JalviewJS2",
14 serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
15 j2sPath: 'swingjs/j2s',
17 allowjavascript: true,
20 // note that desktop-frame-div has been set to display:none
21 jalview_SCREEN_WIDTH: 0, // desktop width -- 0 to hide
22 jalview_SCREEN_HEIGHT: 0, // desktop height -- 0 to hide
25 jalview_EMBEDDED: true
29 jvGet = function(what) {
40 <body style="background-image: url(images/coolVeryLightBG.png);">
41 <table style="width:1400px;border:2px solid lightblue;border-spacing:0;font-size:16pt;" padding="10" valign="top">
42 <tr><td style="font-size:24;font-weight:bold;background-color:lightblue" colspan=2><center>Demonstration of embedded JalviewJS components</center>
44 <tr><td valign=top style="padding:20px" rowspan=2>
45 This simple page illustrates how one can embed the JalviewJS desktop into a web page.
46 The basic idea is that we have something interesting to say — some sort of scientific context — something we want to get
47 across to our visitors with more than just text and images. The idea is to have a <b>dynamic</b> page that will involve <b>user interaction</b>.
49 We start with a Jalview desktop. You can't see it, because I have placed it in a <code>div</code> tag with style <i>width:0px;height:0px</i> just after the period that ends this sentence.
50 <div id="jalview-desktop-div" style="width:0px;height:0px;"></div>
52 The idea is NOT to teach visitors how to use Jalview. The idea is to seamlessly integrate components of Jalview that can be used to enrich a discussion.
53 Like JSmol in <a target="_blank" href="http://proteopedia.org/wiki/index.php/Main_Page"><img src=https://pbs.twimg.com/profile_images/818051034/proteopedia_135x200_small_logo_for_Twitter_400x400.png width=16 height=16/>Proteopedia</a>.
54 For example, in the space to the right, after a few seconds, you will see an alignment frame. This alignment is for 15 genes that code for one of the domains in the ferredoxin family (<a href=https://pfam.xfam.org/family/NIR_SIR_ferr target=_blank>NIR_SIR_ferr (PF03460)</a>).
56 What you first see is just the first few bases. Doesn't look like much of an alignment, does it? But <b>scroll to the right</b>.
57 See the big block of red color? That's the <i>Ferredoxin fold</i>domain.
59 <b>Select a few alignments</b> by left-dragging across a few rows of the alignment to make a selection box.
60 Then click one of the buttons below to see more information about your selected subset of the alignment.
62 <li><button onclick='jvGet("tree")'>similarity tree</button></li>
63 <li><button onclick='jvGet("pca")'>principal component analysis</button></li>
66 </td><td style="background-color:lightgray;padding:20px">
68 <div id="jalview-alignment-div" style="position:relative;top:0px;left:0px;width:600px;height:400px">
70 The alignment frame will appear here momentarily. When it does, you can go ahead and manipulate the alignment with your mouse.
74 <!-- first column continued from above -->
75 <td><table style="border-spacing:0"><tr><td style="background-color:lightgray;padding:10px 0px 10px 20px">
76 <div id="jalview-tree-div" style="position:relative;top:0px;left:0px;width:300px;height:300px">
80 </td><td style="background-color:lightgray;padding:10px 20px 10px 0px">
81 <div id="jalview-pca-div" style="position:relative;top:0px;left:0px;width:300px;height:300px">
85 </td></tr></table></td></tr>
95 <div id="jalview-structureviewer-div" style="position:relative;top:0px;left:0px;width:400px;height:400px">
96 jalview-structureviewer-div
108 SwingJS.getApplet('testApplet', Info)
109 getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\n'))}
113 <div style="display:none;position:absolute;left:900px;top:30px;width:600px;height:300px;">
114 <div id="sysoutdiv" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
115 This is System.out. <a href="javascript:testApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>