Re: [Jmol-users] what are the different applet files?
I'm interested in any observations on this. So far the idea is to wait and see if there really is any issue. My guess is that a 50-60K download generally won't be noticed, as it is about the size of a small image. But it's possible that the delay would be noticeable and that we need to allow for preloading. One thing I can tell you is that just downloading the files in some other way does not do anything for you -- they must be downloaded as jar files within an object tag. I guess that's because they go into a special cache, not the main browser page cache. Actually, now that I think of it, I was wrong about cartoons. Loading of a PDB file itself initiates the ShapeBio.jar download, because as the PDB model is built helixes are identified, and that requires the ShapeBio package. Cartoons have nothing to do with it. Issuing an isosurface, lcaoCartoon, MO, or polyhedra command, on the other hand, IS what initiates the download of the ShapeSpecial package, but it is only 36K. Really, I think it won't be noticeable. But let's see Bob Angel Herraez wrote: >>But you use cartoons, so >>JmolApplet0_ShapesBio.jar (52K) is downloaded when the first script that >>involves a cartoon is invoked. >> >> > >Yes, I've understood that, and it's a great advantage to have reduced >downloads adjusted to needs. It can, however, be disconcerting that >the first "cartoon" (or other, similarly) command will have a delay. > >Just a reflection: > I won't request a way to force loading of certain modules (I know >that calling JmolApplet.jar will load everything, but I prefer the >modular variety), but we have to think of ways for the webpage author >for pre-loading the module which will be needed later, e.g. while >the user is reading the entry page. The user may be prepared for an >initial delay, for hardly for one when he clicks on a button. >I did something similar yesterday by including, in a homepage that >doesn't need to show models, a "Wait until Jmol is ready" message >above a small applet that only does an echo "Jmol is ready". >Meanwhile, the user can go on reading the presentation, and when the >"reay" is shown, move to the first page with real content. > > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what are the different applet files?
> But you use cartoons, so > JmolApplet0_ShapesBio.jar (52K) is downloaded when the first script that > involves a cartoon is invoked. Yes, I've understood that, and it's a great advantage to have reduced downloads adjusted to needs. It can, however, be disconcerting that the first "cartoon" (or other, similarly) command will have a delay. Just a reflection: I won't request a way to force loading of certain modules (I know that calling JmolApplet.jar will load everything, but I prefer the modular variety), but we have to think of ways for the webpage author for pre-loading the module which will be needed later, e.g. while the user is reading the entry page. The user may be prepared for an initial delay, for hardly for one when he clicks on a button. I did something similar yesterday by including, in a homepage that doesn't need to show models, a "Wait until Jmol is ready" message above a small applet that only does an echo "Jmol is ready". Meanwhile, the user can go on reading the presentation, and when the "reay" is shown, move to the first page with real content. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what are the different applet files?
Frieda Reichsman wrote: > > On May 11, 2007, at May 11, 7:34 AM, Bob Hanson wrote: > >> JmolApplet.jar >> >> --- >> >> A single jar file containing all Jmol applet components. Use this if >> >> you want to keep your website simple or you just want to upload a single >> >> JAR file whenever new versions are released. Loads Jmol somewhat slower >> >> than the previous option, as JmolApplet.jar is all of Jmol, and all of >> >> it must get loaded onto a user's machine before any structure is >> displayed. >> > > The last sentence seems to imply that the JmolApplet0*.jar series > files do *not* all load before the user starts using the applet, and > that some of the jar files load only when the user accesses certain > features. But I do not see it stated explicitly in the paragraph about > the JmolApplet0*.jar series that appeared above this one, though I > seem to remember it being said in earlier posts about this new file > system. So, just confirming - the 0* series load as needed? correct. This is a new feature introduced in 11.1.30. About 650K load initially, and then there are about 350K of options that only load as needed, piece-by-piece. For example, Frieda, since you pretty much stick to PDB and CIF files, your users would never download the JmolApplet0_ReadersMore.jar file (61K). But you use cartoons, so JmolApplet0_ShapesBio.jar (52K) is downloaded when the first script that involves a cartoon is invoked. This is all automatic. For reference, JmolApplet.jar for Jmol 10.2 was 820K. Bob > > Frieda > > > /// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /// > > > > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what are the different applet files?
Bob Hanson wrote: > What a timely question! I was just drafting a message to users > > Jmol users: > > We were all a bit confused with the new file naming, so we've decided to > rename the applet files again -- just to thoroughly confuse you. > Actually, this is much better. What follows refers to Jmol 11.1.36. > > There are four distinct options that you can use when using the Jmol > applet. The typical user would only use one of these; we recommend the > first. > > JmolApplet0*.jar > JmolApplet.jar > JmolAppletSigned.jar > JmolAppletSigned0*.jar > > (Note: * here is a wildcard character meaning "all files starting with".) > I would suggest renaming the "README.txt" file to "READ_ME_RIGHT_NOW_OR_ELSE_ALL_YOUR_MOLECULES_WILL_BE_CURSED.TXT" >:o (just remember to update the text before the cursing :-) ) Seriously now: why not organizing the zip (tar, etc) file in directories: / COPYRIGHT.txt LICENSE.txt README.txt | +--Jmol | +--jmol | +--jmol.bat | +--Jmol.jar | +--jmol.mac | +--jmol.sh | +--Jmol_applet +--Jmol.js +--Signed | +--Multiple_files | | +--JmolAppletSigned0*.jar | | +-- ... | | +-- ... | | | +--Single_file | +--JmolAppletSigned.jar | +--Unsigned +--Multiple_files | +--JmolApplet0*.jar | +-- ... | | +-- ... | +--Single_file +--JmolApplet.jar - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what are the different applet files?
On May 11, 2007, at May 11, 7:34 AM, Bob Hanson wrote: JmolApplet.jar --- A single jar file containing all Jmol applet components. Use this if you want to keep your website simple or you just want to upload a single JAR file whenever new versions are released. Loads Jmol somewhat slower than the previous option, as JmolApplet.jar is all of Jmol, and all of it must get loaded onto a user's machine before any structure is displayed. The last sentence seems to imply that the JmolApplet0*.jar series files do *not* all load before the user starts using the applet, and that some of the jar files load only when the user accesses certain features. But I do not see it stated explicitly in the paragraph about the JmolApplet0*.jar series that appeared above this one, though I seem to remember it being said in earlier posts about this new file system. So, just confirming - the 0* series load as needed? Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what are the different applet files?
Stephen Hillier wrote:
>Hi,
>
>could someone tell me what the all the different applet files are?
>
>And why a signed and an unsigned set?
>
>
>
What a timely question! I was just drafting a message to users
Jmol users:
We were all a bit confused with the new file naming, so we've decided to
rename the applet files again -- just to thoroughly confuse you.
Actually, this is much better. What follows refers to Jmol 11.1.36.
There are four distinct options that you can use when using the Jmol
applet. The typical user would only use one of these; we recommend the
first.
JmolApplet0*.jar
JmolApplet.jar
JmolAppletSigned.jar
JmolAppletSigned0*.jar
(Note: * here is a wildcard character meaning "all files starting with".)
While we release all files associated with all of these options, you
only need the files associated with one of them. Most people will use
the first of these options.
Executive Summary
If you are a typical Jmol user, just transfer the JmolApplet0*.jar files
to your server along with Jmol.js and include the simple form of
jmolInitialize on your page:
jmolInitialize("directory-containing-jar-files")
JmolApplet0*.jar
--
A set of 16 files (currently) that together comprise all of Jmol but
arranged so that if your page does not require a component, that
component is not downloaded from the server. If you never use molecular
orbitals, that part won't be downloaded; if you only use PDB or CIF
files, only the PDB and CIF file readers will be downloaded. (They are
together in one of the files.) We still recommend putting all 16
JmolApplet0*.jar files on your server even if your page does not use the
capabilities provided by some of the files, because the pop-up menu and
Jmol console both allow users to access parts of Jmol you might not have
considered.
To use JmolApplet0*.jar use the simplest form of jmolInitialize(), just
indicating the directory containing the set of jar files:
jmolInitialize("directory-containing-jar-files")
for example,
jmolInitialize(".") // jar files are in the same directory as the web page
jmolInitialize("../jmol") // jar files are in a parallel subdirectory
JmolApplet.jar
---
A single jar file containing all Jmol applet components. Use this if
you want to keep your website simple or you just want to upload a single
JAR file whenever new versions are released. Loads Jmol somewhat slower
than the previous option, as JmolApplet.jar is all of Jmol, and all of
it must get loaded onto a user's machine before any structure is displayed.
To use JmolApplet.jar either:
a) just put it in the directory containing the HTML page requiring it
and do not use jmolInitialize(), or
b) identify it explicitly in jmolInitialize(), for example:
jmolInitialize("directory-containing-jar-files", "JmolApplet.jar")
JmolAppletSigned.jar
--
The signed version of JmolApplet.jar. This version allows the user to
access files anywhere on a hard drive and from any location on the web.
Typically the user gets a message asking if they want to accept the
"certificate", but this is security feature is not always enabled.
JmolAppletSigned.jar should be used with this in mind. Other than
reading files, Jmol does not currently utilize other capabilities of
signed applets, such as accessing the System clipboard or writing files.
Use only if you know what you are doing and have considered the security
issues.
To use JmolAppletSigned.jar use:
jmolInitialize("directory-containing-jar-files", "JmolAppletSigned.jar")
JmolAppletSigned0*.jar
The signed version of JmolApplet0*.jar. This version allows the user to
access files anywhere on a hard drive and from any location on the web.
Typically the user gets a message asking if they want to accept the
certificate for EACH of the 16 loadable files. For this reason,
JmolAppletSigned0*.jar may not be of general use.
To use JmolAppletSigned0*.jar, use the form:
jmolInitialize("directory-containing-jar-files", true)
or
jmolInitialize("directory-containing-jar-files", "JmolAppletSigned0.jar")
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[Jmol-users] what are the different applet files?
Hi, could someone tell me what the all the different applet files are? And why a signed and an unsigned set? I'm guessing maybe they are if you only need some limited functionallity? thanks for the patience and time to answer, much appreciated, steve -- Please note that the views expressed in this e-mail are those of the sender and do not necessarily represent the views of the Macaulay Institute. This email and any attachments are confidential and are intended solely for the use of the recipient(s) to whom they are addressed. If you are not the intended recipient, you should not read, copy, disclose or rely on any information contained in this e-mail, and we would ask you to contact the sender immediately and delete the email from your system. Thank you. Macaulay Institute and Associated Companies, Macaulay Drive, Craigiebuckler, Aberdeen, AB15 8QH. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
