Using JUMBO for viewing CML files

Even if you are impatient to see the demos, it's worth reading this to avoid a number of simple errors and misconceptions

This distribution contains all the Java classes for the molecular viewer JUMBO. The demos are constructed so that you can use your browser automatically without installation or configuration. This is therefore one of the first projects to produce portable interactive installation-free molecular science, and represents a milestone in chemical publishing. However it is using very new technology (the first main release of Java) and there are some rough edges which we hope you will forgive. (The next release out soon, JDK 1.1, makes a lot of difference).

It relies on your having a Java-enabled browser, such as Netscape V3 or greater. (If your browser does not support Java, it will simply fail to do anything, without giving a message.) One useful way to check is to locate the Java console (under Options in Netscape) and to open it. This is a useful check to see if anything is happening or what errors occur.

Differences in portability

JUMBO has been tested on several platforms running Netscape (SUN-Sparc, SGI, Windows95 and Mac) and works on all. However there are slight differences between these and your local configuration could also have an effect. (Remember that we cannot test all combinations of machine and browser.) Here are some areas (primarily Netscape) where we have found variations over which we don't have control and which might disconcert you:

• Scrolling (particularly on W95) can be jerky and slow
• When a window first comes up it is resized, and I can't change this from the program. Every window will need manual resizing (sorry!).
• Some windows are not packed properly until they are resized
.
• Every applet starts with a request box (asking if you want help). On SUN/Netscape it suddenly disappears. That doesn't matter. Also on the SUN the screen flashes dramatically at that stage.
• Machines vary very much in speed and sometimes you need to be patient for a refresh.
• Colours can vary - Color.pink looks brown on some machines!
• JUMBO downloads all the class files from your local disk. Your browser may not give you very clear information when this finishes. It's always useful to have the Java console open.
• Netscape and other browsers cache Java classes as well as data files. If you have a problem repeatedly, it may be useful to clear the disk and memory caches.

Advice on using JUMBO

The main purpose of these demos is to show the breadth and power of CML. JUMBO is at alpha level and there are features in the GUI which I expect to change in later releases. Bugs in JUMBO do not reflect on CML, and I hope that other CML browsers will become available. (The XML project has already produced two robust parsers which will be bolted into JUMBO shortly). JUMBO is being developed as an editor as well as a browser and a number of features (e.g. the File, Trash, Clipboard, Object selection) are not required for browsing. JUMBO also has search facilities which you should ignore.

Here are some points to be aware of:

• JUMBO is based on a TableOfContents (TOC) as the main metaphor. The level is shown by the indentation. The two square pink boxes to the left of each line are the 'Hide Object' box, and the 'Hide Children Box' (and they may have a '-' or '+'). Clicking the 'Hide Object' will hide it, and you can only get it back by 'Hide Children' on the parent and then unhiding. Get used to hiding and unhiding children (it's similar to some file browsers) (e.g. W95).
• Clicking on the text of an Object will SELECT it (goes green). This is used for editing and is not useful at this stage.
• Clicking on the pink '?' will give you help for that Object.
• The thing to the right of the '?' is the Object's icon. This is what you need to click to display the Object.
• Do not attempt to drag anything on the TOC at this stage.
• There is a special generic Object container, XLIST (square book-like icon). Clicking on this icon will not normally be useful (except unless it containd BIB entries). This is an active area of development.

Problems and Errors

It is extremely difficult to debug interactive applications by e-mail or on the phone! I know how frustrating it is when you can't get something to work. I am afraid I can't guarantee any help for this distribution, because there are two many variables (machines, browsers, local settings that I don't have access to). I have had errors that I don't understand (particularly ClassLoader errors, VerifyErrors and other fundamental Java problems). In some cases these may result from your local settings (e.g. CLASSPATH, memory, etc.).

• Blame me :-) (too much)
• Let it affect your opinion of CML as a language.
• Write Java off as a useful language.
• Write to tell me it doesn't work
• Send me the error messages!!

Good luck, and Smile!