<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">I don't have any objection against tool classes, but I have a lot of problems with the way things got out of hand in BioJava, there you can't do ANYTHING without tools. So names aside, I don't get what pI and digest do in 1 protein tool object. I plea to do very simplethings like MW and pI inside BCSequence where ever possible, and use specialized tools like a BCTranslatorTool and BCDigesterTool instead of one Proteintool and one DNAtool that bundle a lot of non-related stuff...<DIV>Alex<DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On 6-jul-2005, at 10:34, Koen van der Drift wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Jul 6, 2005, at 3:53 AM, Alexander Griekspoor wrote:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I agree that in some cases tools are the way to go, but one of the things I dislike most of the biojava project (and I remember from previous discussions that I was not alone) is in fact that you can't do a thing without needing a bunch of helper, factory, and/or tool objects. Please, let us stay far from that. It's really un-cocoa like, imagine NSString and you would need a "exporter tool" to save it to file, a "converter tool" to return it in a different encoding etc etc. Help!!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BCSequenceTool -> MW, ...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BCProteinTool -> pI, digest, ...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BCDNATool -> translate, ...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BCRNATool -> transcribe, ...</DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please not, the names of these tools alone are terrible!!!! I agree that for some relatively difficult things like a translation, digests or alignments, we need a tool, but even then I would like to have convenience methods that do the job of creating and handling the tool object in the background. For the rest, a simple MW should be one call and not need a tool! And IF we need a tool, make it specialized: BCDigester or what else instead of BCSequenceTool.</DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">These names were only put in as an example, not a proposal :)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Anyway, using tools classes makes the framework very modular and maintainable, in fact we are already using them. So I am not sure what your objection is against tools classes? Do you want to put all code in the subclasses?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">cheers,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- Koen.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR class="Apple-interchange-newline"></BLOCKQUOTE></DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>** Alexander Griekspoor **</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>The Netherlands Cancer Institute</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Department of Tumorbiology (H4)</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Plesmanlaan 121, 1066 CX, Amsterdam</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Tel:<SPAN class="Apple-converted-space"> </SPAN>+ 31 20 - 512 2023</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Fax:<SPAN class="Apple-converted-space"> </SPAN>+ 31 20 - 512 2029</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>AIM: <A href="mailto:mekentosj@mac.com">mekentosj@mac.com</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>E-mail: <A href="mailto:a.griekspoor@nki.nl">a.griekspoor@nki.nl</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Web: <A href="http://www.mekentosj.com">http://www.mekentosj.com</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Windows is a 32-bit patch to a 16-bit shell for an 8-bit<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">operating system, written for a 4-bit processor by a 2-</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">bit company without 1 bit of sense.<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************</FONT></P> <BR class="Apple-interchange-newline"> </DIV><BR></DIV></DIV></BODY></HTML>