Hello Daron.
Daron Standley wrote:
1. I can't seem to find "jalview.ButtonAlignApplet" in the jalviewApplet.jar file, although this code seems to be used in many of the examples I find on the web.
You can be almost 100% certain that all these examples are using the old version of Jalview, which had a package structure like jalview.<classname> for many of the classes. Jalview 2 has a class structure like jalview.<mainpackage>.<class> for nearly all of its source code.
2. I can find and use "jalview/bin/JalviewLite.class".
That is most definitely the one to use. You'll find examples of the applet being launched here:
http://www.jalview.org/examples/applet.html
http://www.jalview.org/examples/appletParameters.html
However, I wonder if this will allow me to display
alignments in the form:
<PARAM name="numseqs" value=3>
<PARAM name="seq1" value="ALSDKFHLKRHELKHASLDKHLKHR">
<PARAM name="seq2" value="ALSDKFHLKRHE-----LDKHLKHR">
<PARAM name="seq3" value="ALSDKFHLKRHELKHALKFL-HLKHR">
These parameters are wrong. The format for passing an alignment as applet parameters is given on the appletParameters link above. Firstly - you don't need numseqs at all, and secondly, jalview searches for parameters called 'sequence<i>' - where <i> is 1,2,3,.... The value of each sequence<i> parameter is the i'th line of the alignment file. For example:
<param name="sequence1" value="s1 a-cde">
<param name="sequence2" value="s2 apcde">
<param name="sequence3" value="s3 a--de">
Each line specifies a sequence name and alignment row in PFAM format.
I can not get this to work using the jalviewLite class. I get an error where the button should be
saying Jalview can't open "NO FILE".
this is the generic error that the applet gives when the formats or parameters are incorrect. Always check on the browser's Java console for more information about what has caused the error.
3. Assuming I eventually figure out how to do #2 (above) I am wondering if I can then display a single sequence
along with some properties (conservation, secondary structure, functional residues, etc.) I am hoping this
will be a nice way to present such properties at the Protein Data Bank Japan (currently we only show a the FASTA sequence in a text window).
all possible. Have a look at the current development version of the applet's parameters and (rudimentary) API. Secondary structure annotation is passed into Jalview via it's own alignment annotations file format, and sequence features (ie DAS style sequence annotation) can be read from GFF or via a Jalview Features file. You don't need to create these files statically - the location of a servlet that generates the appropriate annotation file is all that's necessary.
Thanks in advance, and sorry if my question is not clear. I am not very familiar with java.
no problem. Now if only it were possible to eliminate all incorrect documentation 
hope it helps..
Jim
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J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
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