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Re: [sbml-arrays] Zero size arrays
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From: Lucian S. <luc...@gm...> - 2014-08-13 18:36:27
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Right, I am claiming that even if SBML arrays are officially static, they can be used in non-static contexts (such as parameter scan-like functions in tools, and in hierarchical models), and therefore should behave more like lists than arrays. When they are zero-length, they would, like empty lists, be equivalent to not including it in the model at all, except that references to it would be allowed. -Lucian On Wed, Aug 13, 2014 at 11:18 AM, Bruce Shapiro <bru...@gm...> wrote: > I still don't understand how there would be an array parameter of zero > length in a model. Are you saying that something might or might not exist > in the model, and that zero length means it does not exist? > > > On Wed, Aug 13, 2014 at 11:09 AM, Lucian Smith <luc...@gm...> > wrote: > >> There might be the case where the SBML model is under control of some >> other force, such as SED-ML or another simulation tool. A parameter scan, >> for example, does not require the parameter being scanned to be >> non-constant, but various different values are used for it over the course >> of several experiments, in each of which the parameter in question is >> constant. I can imagine a similar situation here, where someone is testing >> the behavior of a model under different circumstances, the simplest of >> which has a zero-sized array. >> >> Even within-SBML, one might have a hierarchical model where a submodel >> has a zero-sized array that becomes longer when imported and changed, or >> visa versa. >> >> I would say that since it doesn't seem terribly difficult to support, has >> a clear meaning, and is potentially useful, that we allow it. >> >> -Lucian >> >> >> On Wed, Aug 13, 2014 at 11:00 AM, Chris J. Myers <my...@ec...> >> wrote: >> >>> I think in programming languages, there is often a difference between a >>> zero-size array and a null pointer. You can use zero-size arrays as an >>> initialization value, so you don't need to check for null all the time. >>> However, this is with the assumption that you can later change the size of >>> the array and add things to it. >>> >>> For arrays package with SBML, we made the decision that these would be >>> static-size arrays. Therefore, a zero-size array will always be a >>> zero-size array, and when this gets flattened to SBML core, the object is >>> simply removed entirely. So, is such a behavior useful or simply create an >>> unnecessary complication? >>> >>> Chris >>> >>> On Aug 13, 2014, at 11:06 AM, Bruce Shapiro <bru...@gm...> >>> wrote: >>> >>> Do any computer languages allow this? Isn't there already a symbol for >>> the empty set for this this that one would normally use instead? Nil null >>> bupkis >>> >>> Sent by an Android from another Galaxy. >>> On Aug 13, 2014 9:41 AM, "Chris J. Myers" <my...@ec...> wrote: >>> >>>> Hi, >>>> >>>> We were wondering if anyone sees a use for zero size arrays. When you >>>> declare something as zero-szie, you are essentially declaring that it does >>>> not exist. A zero-size species, parameter, rule, etc. would flatten to it >>>> not being present. I suppose it is a bizarre way to delete something. You >>>> can change its size variable to zero-size which effectively removes it. >>>> This though likely creates validation rules as index computations may go >>>> out-of-bounds, but this may not always be the case. >>>> >>>> So, my question is should we limit parameters used for size as >>>> "non-negative" as we do now, or change it to "positive"? >>>> >>>> Chris >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> _______________________________________________ >>>> sbml-arrays mailing list >>>> sbm...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>>> >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> sbml-arrays mailing list >>> sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> sbml-arrays mailing list >>> sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>> >>> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> sbml-arrays mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >> >> > > > -- > Bruce E. Shapiro, Ph.D. > Department of Mathematics > California State University, Northridge > 18111 Nordhoff Street > Northridge, CA 91330-8313 > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sbml-arrays mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-arrays > > |