"too many" is less informative than previously outputting a single entry

[zrolfs]

Have output be "XXXXXXXXX or too many"

[stefanks]

what's XXXXXXXXX ?

[zrolfs]

a sequence, a number, anything that uses resolve to potentially return "too many".

[stefanks]

Could you give a specific example?

[zrolfs]

LIAQKVRGVDVVVGGHSNTFLYT or (too many)

[stefanks]

The whole reason "too many" is returned is because of ambiguity! There is no single base sequence that matches

[zrolfs]

"too many" is returned because the ambiguity results in a length over 32000, not because there is "too much" ambiguity. We know nothing about the putative sequence if "too many" is returned.

[stefanks]

Sure. But I don't like outputting a specific match. I feel that it's misleading

[zrolfs]

I'm outputting 31990 chars and then (too many)

[stefanks]

not a fan of this. It still arbitrarily gives preference to some sequences that made it over some that didn't

[zrolfs]

If there are 31990 characters worth of sequences, nobody is going to look at every single one of them. I want as many as possible, though, to allow the viewer to find the pattern. If multiple sequences scored the same, they have to have something in common that hits those peaks.

[stefanks]

Let's make a new column instead! That contains the "common pattern"

[zrolfs]

If there are really over 31990 characters, it's probably a crummy spectra and nobody will care about it. I care because of fusion peptide searches yielding low scoring initial identifications. I need something for Neo to grab.

[zrolfs]

I don't think the feature would be worth the time put into it.

[stefanks]

It might be useful to people! I don't think it's not worth the time.

And I have two problems with displaying partial info: 1. Misleading 2. Makes files bigger

[zrolfs]

The "Matched Ion Masses" column should be enough info to obtain a common pattern. I need an example sequence! It is not misleading if we put "(too many)" at the end, as that is the disclaimer that not all possible sequences are being shown. I understand that including many entries will make files bigger, but we already do that with sequences that contain 31999 characters!

[zrolfs]

Going off of that thought, I notice that "Matched Ion Masses" is left blank in the case of ambiguity. Shouldn't those peaks be identical?

[stefanks]

I believe its currently blank if the compact peptide is ambiguous. But I see your point, even in case of ambiguity the peaks matched should be identical... Hm. The only way to get identical scores is to match identical peaks. Good point. You are welcome to change this!

[zrolfs]

Begrudgingly agree to disagree.