Source: Unknown via funpics.nextmail.ru

A 2006 survey on java.net posed a simple question to developers: What's wrong with applets? By a significant margin, the number one complaint was that they are "too hard to deploy." This article, the first in a series, takes a look at the issue of Java applet deployment and in particular how using the <object> tag can radically simplify and enhance both the developer and end user experience.

Applets? You Must Be Joking!

Applets got a well-deserved bad reputation in the early days of Java. They were slow, difficult to deploy across browsers, and over-hyped. The situation has signficantly changed for the better, but the bad reputation lingers.

There are many situations in which applets are inappropriate. The most important of these is when simple interactivity can be achieved through HTML or JavaScript (Ajax).

But in many situations, HTML and JavaScript make a poor platform choice. As a specific example, consider Web-based chemical structure editors. The high level of graphical manipulation, sophistication of data processing, and responsiveness required by these components, coupled by their ubiquity, means that it will be a long time indeed before Ajax (or Flash for that matter) is up to the challenge - and they may never be, given their design constraints.

For a large number of specialized Web components, applets are the only platform.

Regarding the "uncool factor", it's worth pointing out that not more than four years ago JavaScript was one of the most loathed, ridiculed, and ignored technologies around. Now it finally works - meaning it's reliable enough to be used on all modern browsers. The result is Ajax and a host of interactive Web technologies that played a major role in redefining what the Web was all about.

Whether a similar renaissance happens for applets is anybody's guess, but most of the prerequisites have already been met.

Deployment with the <applet> Tag

If you decide to develop Web applications with applets, a major consideration will eventually become how to deploy them. Unfortunately, a bewildering array of often contradictory advice is available on the subject - most of it outdated.

Many sources recommend using the <applet> tag. It's the oldest method, and will generally work on most browsers. For example, to deploy my company's structure editor applet ChemWriter, the following code could be used:

<applet code="com/metamolecular/chemwriter/applet/EditorApplet.class"
        archive="/path/to/applets/chemwriter.jar"
        width="600" height="300">
  <param name="persistState" value="false" />
</applet>

Unfortunately, the <applet> tag has some very important strikes against it. The first is that its use is now deprecated in HTML. In other words, whatever support browsers now have for it is living on borrowed time.

The second problem with the <applet> tag is an insidious bug in Internet Explorer (as if there were any other kind). Most hardware suppliers pre-install Java onto their Microsoft-based machines, which is a good thing. The bad thing is that at least one major manufacturer disables the Java console in IE 7 at the same time. Under IE 7, disabling the Java console renders all <applet> tags invisible. Counterintuitive as it may seem, this is what happens. The insidious part is that perplexed users know they have Java installed because they can see the plug-in, are being told by IE that it's active, can find some applets that *do* work and - well, you get the idea.

The third problem with the <applet> tag is that, by itself, it has no mechanism to indicate which version of Java is required. This can be a very important consideration for applets that take advantage of the major advances in functionality and performance of the Java platform in recent years.

A Better Way: Deployment with the <object> Tag

All major browsers support the <object> tag, and this is the preferred method for deploying applets. Provided that Internet Explorer's peculiarities are accounted for, a single piece of valid HTML can render applets on all major browsers including:

• IE 6/7
• Firefox 1.5/2
• Safari

As a specific example using ChemWriter, the <applet> tag above can be re-written with the <object> tag:

<!--[if !IE]> -->
<object classid="java:com/metamolecular/chemwriter/applet/EditorApplet.class" 
              type="application/x-java-applet"
              archive="/path/to/applets/chemwriter.jar" 
              height="350" width="550" >
  <param name="code" value="com/metamolecular/chemwriter/applet/EditorApplet.class" />
  <!-- For Konqueror -->
  <param name="archive" value="/path/to/applets/chemwriter.jar" />
  <param name="persistState" value="false" />
  <center>
    <img src="/path/to/images/chemwriter_logo.png" />
    <p><strong>ChemWriter content requires Java 1.4.2 or higher, which your browser does not appear to have.</strong></p>

    <p><a href="http://www.java.com/en/download/index.jsp">Get the latest Java Plug-in.</a></p>
  </center>
</object>
<!--<![endif]-->
<!--[if IE]>
<object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" 
                codebase="http://java.sun.com/products/plugin/autodl/jinstall-1_4-windows-i586.cab#Version=1,4,0,0"
                height="350" width="550" > 
  <param name="code" value="com/metamolecular/chemwriter/applet/EditorApplet.class" />
  <param name="archive" value="/path/to/applets/chemwriter.jar" />
  <param name="persistState" value="false" />
  <center>
    <img src="/path/to/images/chemwriter_logo.png" />
    <p><strong>ChemWriter content requires Java 1.4.2 or higher, which your browser does not appear to have.</strong></p>
    <p><a href="http://www.java.com/en/download/index.jsp">Get the latest Java Plug-in.</a></p>
  </center>
</object>
<![endif]-->

Before explaining the code, here's what the verbosity buys:

• It works with both IE 6/7 and standards-compliant browsers such as Firefox.

• It avoids the use of JavaScript JVM detection methods.

• It prompts the user to download the correct JVM, without immediately directing them away from the current page.

• Firefox and IE users can opt to install the Java plugin without ever leaving their current page.

• It works in IE 7 with the Java console disabled.

You've Got Some 'Splainin' to Do

The code above is based on documentation found on this site, which also details the meaning of the codebase and classid attributes.

The main idea is that Internet Explorer handles the <object> tag in its own idiosyncratic, lovable way. Most of this difference is in the <object> element itself and the classid attribute in particular. By taking advantage of Internet Explorer's support for conditional comments, we can handle both IE and the rest with one chunk of HTML.

A Live Demonstration

For a live demonstration of the above technique, see the ChemWriter Home Page. If you have Java 1.4.2 or higher installed and activated in your browser, you'll see the most recent version of the ChemWriter editor applet. If not, you'll see the ChemWriter logo and a link to install Java. Firefox and IE will also display an "Install Plugin" bar at the top of the browser for in-place installation of the JVM.

Click to Activate: Working Around Eolas

A recent Depth-First article discussed the problem that IE 6 and 7 have involving a "click to activate" (or "Eolas") message that appears with applets and all other browser plugins. To eliminate this issue, the ChemWriter Home Page uses the excellent jActivating library. This JavaScript library, which is included in the HTML <head> tag, obviates the need to write the <object> tag using JavaScript. All that's left is pure, standards-compliant HTML to debug, deploy, and maintain.

Conclusions

Applet deployment, like Java itself, has come a long way in the last ten years. This article has shown one method to deploy applets into highly heterogeneous computing environments with relatively little effort.

But deployment is only one aspect of interactive Web development using applets. Future articles will discuss some of the others.

Image Credit: oskay

Source: Lunazzi, Mancinelli, and Mazzanti J. Org. Chem.

Source: Astronomy Picture of the Day

Of the many problems to be solved when building software to view and manipulate 2D chemical structures, one of the trickiest is getting all features to scale proportionally. This problem is widespread because it can seldom be predicted at which resolution a chemical structure will be viewed.

This article describes some ways in which this problem was addressed in the Web-based chemical structure editor ChemWriter.

Chemically-Aware Vector Graphics

ChemWriter is at its a core chemically-aware vector graphics system. It was designed with the belief that chemical structures should remain readable regardless of size.

The ability to scale 2D chemical structures to any resolution and retain readability is essential when creating cheminformatics systems because magnification factors are so varied. For example, in many cases, structures are user-resizable. In others, the size of the structure is statically set by the developer. In others, the bond length needs to remain fixed and the overall image size needs to adapt accordingly. Even when a chemical structure display context may seem static, future design constraints may force a change.

A robust chemical structure graphics system needs to gracefully enable the resizing of its output.

A Demonstration

The live applet shown above lets you scale a chemical structure using the ">" and "<" keys, or the View->Zoom In and View->Zoom Out menu items.

Note: if you haven't installed and activated Java in your browser, you'll need to do so before viewing the above demonstration.

Scaling Chemical Structure Features

Properly scaling 2D chemical structure diagrams may not seem that difficult, but consider some of the properties involved:

• Atom Label Size. Hardcoding font sizes is simply not an option.

• Atom Label Padding. The empty space around a heteroatom bond label prevents bonds from making direct contact with the atoms they connect.

• Line Thickness. Lines have variable absolute thickness that ensure they're visible at lower magnification and not too thin at higher magnification.

• Multiple Bond Offset Distance. Double and triple bonds contain lines that are offset from the center bond line.

• Stereo Bond Maximum Width Wedge and hash bonds have a maximum thickness.

To retain readability, each of these properties must proportionally scale when a chemical structure is reduced or enlarged.

The ChemWriter System

What does it mean to resize a chemical structure?

The dimensions of a structure are determined by its underlying atom coordinates. Resizing a chemical structure scales these coordinates. It's convenient to think of this process as a proportional change in the absolute length of the bonds between atoms; relative bond lengths, and relative atom positions remain fixed.

Given that only bond lengths change during scaling, it's useful to adopt bond length as a yardstick. Although not all bonds in a molecule will have the same length, for the most part these values will be tightly clustered around a median.

For this reason, a molecule's median bond length is the standard unit of measurement in ChemWriter.

As an example, setting atom label height can be done by calling ChemWriter's setAtomLabelHeight method (or using the atomLabelHeight parameter). The double-precision value represents a fraction of the median bond length. To make atom labels appear half as high as the median bond length, use a value of 0.5. To make them appear smaller by half, use a value of 0.25.

The demonstration above shows the effect of each of these settings.

Conclusions

ChemWriter uses a vector graphics system that can create consistent, readable output for a wide range of image sizes. This flexibility is essential in creating cheminformatics systems that work well across a broad range of platforms and output formats.

Image Credit: cattypumkinhead