<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi-
<div><br class="webkit-block-placeholder"></div><div>I am just getting started using the latest jalview, and I am confused on a few points:</div><div><br class="webkit-block-placeholder"></div><div>1. I can't seem to find "<span class="Apple-style-span" style="font-family: Courier; font-size: 13px; ">jalview.ButtonAlignApplet" <span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; ">in the <span class="Apple-style-span" style="font-family: Courier; font-size: 13px; ">j</span>alviewApplet.jar file, although this </span></span></div><div>code seems to be used in many of the examples I find on the web. </div><div><br class="webkit-block-placeholder"></div><div>2. I can find and use "jalview/bin/JalviewLite.class". However, I wonder if this will allow me to display</div><div>alignments in the form: </div><div><br class="webkit-block-placeholder"></div><div><div><PARAM name="numseqs" value=3></div><div><PARAM name="seq1" value="ALSDKFHLKRHELKHASLDKHLKHR"></div><div><PARAM name="seq2" value="ALSDKFHLKRHE-----LDKHLKHR"></div><div><PARAM name="seq3" value="ALSDKFHLKRHELKHALKFL-HLKHR"></div><div><br class="webkit-block-placeholder"></div><div>I can not get this to work using the jalviewLite class. I get an error where the button should be</div><div>saying Jalview can't open "NO FILE".</div></div><div><br></div><div>3. Assuming I eventually figure out how to do #2 (above) I am wondering if I can then display a single sequence</div><div>along with some properties (conservation, secondary structure, functional residues, etc.) I am hoping this</div><div>will be a nice way to present such properties at the Protein Data Bank Japan (currently we only show a the </div><div>FASTA sequence in a text window).</div><div><br class="webkit-block-placeholder"></div><div>Thanks in advance, and sorry if my question is not clear. I am not very familiar with java.</div><div><br class="webkit-block-placeholder"></div><div>Best regards,</div><div><br class="webkit-block-placeholder"></div><div>Daron</div></body></html>