The Friend Applet file can be downloaded here. To embed the Friend Applet into the web page you have to include the following text into your html page
<OBJECT classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93"
WIDTH = "85" HEIGHT = "40" NAME = "friend"
codebase="http://www.java.com/en/download">
<PARAM NAME = CODE VALUE = "friendMain/FriendApplet" >
<PARAM NAME = ARCHIVE VALUE = "friend_app.jar" >
<PARAM NAME = NAME VALUE = "friend" >
<PARAM NAME = "type" VALUE="application/x-java-applet;version=1.4">
<PARAM NAME = "scriptable" VALUE="false">
<PARAM NAME = "file_to_load" VALUE ="pdb1d2r.ent">
<PARAM NAME = "script_to_execute" VALUE ="center">
<COMMENT>
<EMBED type="application/x-java-applet;version=1.4"
CODE="friendMain/FriendApplet" WIDTH="85" HEIGHT="40"
ARCHIVE="friend_app.jar"
NAME="friend"
file_to_load="pdb1d2r.ent"
script_to_execute="center"
scriptable=false
pluginspage="http://www.java.com/en/download/">
<NOEMBED>
</NOEMBED>
</EMBED>
</COMMENT>
</OBJECT>
This code will produce such a button ==>
Pressing the button (might have to press twice) will open a main applet window with structure and sequence views.
This is a universal
syntax which will work with both Mozilla based browsers (FireFox, Safari,
Netscape, Mozilla, etc.) and Internet Explorer.
The parameter CODE describes the applet class in Friend.
The parameter should be left unchanged.
The parameter ARCHIVE describes filename with applet.
Change it only if you rename the applet file.
The parameter NAME names the object. You can name object as you like but
be sure to reference to it by its name (see examples below).
The parameters file_to_load is Friend specific and describes semi-colon delimited
set of files to be loaded after main applet window is opened. The type of file
is determined by its extension. In cases when file is not located in the
directory of the web page, its filename must include the full path to it.
The parameter script_to_execute is Friend specific and describes semi-colon delimited
set of friend commands to be executed after main applet window is opened and
structures are loaded.
Note, all parameters appear
in two places, and in both places you have to provide them with exactly the
same values to allow different browsers to display the web page in the same
way.
Since access to embedded objects
is also browser specific we recommend the use of a JavaScript function, implementing
browser dependent access to the applet. While this can be done in a number of
ways, a very simple example is shown below.
First, the function tries to
locate the applet object, named friend,
in the list of embedded objects. This is Mozilla specific way of object access.
Then, the function tries to locate the applet object directly in the document,
i.e., in the current web page. This is Internet Explorer specific way.
Statement try{...}catch(){...}
ensures that the function does not
abort and proceeds to the next line if the applet object is null, i.e., the
object is not found. Function runScript
is implemented in Friend Applet and executes the commands provided as an argument.
This peace of the code has to be inserted into the header of web page, between tags <head> and </head>.
Manipulation buttons can be created using standard html tags <form> and <input>
The mechanism of structure view
manipulation in Friend Applet from html page is summarized in the following picture
Abyzov A, Errami M, Leslin CM, Ilyin VA. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15(18):3677-8. PubMed
