numSequences

[blakesweeney]

@clzirbel and @jimroll I've been looking at JAR3D again and I see that it uses numSequences to control the number of input sequences processed. It also seems to always be set very high, likely in an attempt to insure that all sequences are process.

I'd like to remove this stuff from the core of jar3d. I notice it is also passed to methods in JAR3DMatlab and I don't know if those are needed. I can retain that behavior in JAR3DMatlab, but remove it from other parts. What do you think?

[clzirbel]

Hi,

I think this is a relic of the past and could be removed as long as it
gets removed in all the relevant places. Maybe Jim has an opinion on it.

Z

On 10/23/2012 4:41 PM, Blake Sweeney wrote:

@clzirbel https://github.com/clzirbel and @jimroll
https://github.com/jimroll I've been looking at JAR3D again and I
see that it uses numSequences to control the number of input sequences
processed. It also seems to always be set very high, likely in an
attempt to insure that all sequences are process.

I'd like to remove this stuff from the core of jar3d. I notice it is
also passed to methods in JAR3DMatlab and I don't know if those are
needed. I can retain that behavior in JAR3DMatlab, but remove it from
other parts. What do you think?

—
Reply to this email directly or view it on GitHub
#6.

[jimroll]

I don't think its needed, for Matlab or core JAR3D

Jim

---

From: Craig L. Zirbel [[email protected]]
Sent: Tuesday, October 23, 2012 5:00 PM
To: BGSU-RNA/JAR3D
Cc: James E Roll
Subject: Re: [JAR3D] numSequences (#6)

Hi,

I think this is a relic of the past and could be removed as long as it
gets removed in all the relevant places. Maybe Jim has an opinion on it.

Z

On 10/23/2012 4:41 PM, Blake Sweeney wrote:

@clzirbel https://github.com/clzirbel and @jimroll
https://github.com/jimroll I've been looking at JAR3D again and I
see that it uses numSequences to control the number of input sequences
processed. It also seems to always be set very high, likely in an
attempt to insure that all sequences are process.

I'd like to remove this stuff from the core of jar3d. I notice it is
also passed to methods in JAR3DMatlab and I don't know if those are
needed. I can retain that behavior in JAR3DMatlab, but remove it from
other parts. What do you think?

—
Reply to this email directly or view it on GitHub
#6.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-9718019.

[blakesweeney]

If I totally remove it from JAR3DMatlab it will break the interface. Is that ok?

[clzirbel]

I think so. We are no longer calling all of the methods in JAR3DMatlab
from Matlab, and the ones we do don't have this parameter.

We are using MotifParseSingle and getQuantilesFromFile.

Z

On 10/24/2012 9:13 AM, Blake Sweeney wrote:

If I totally remove it from JAR3DMatlab it will break the interface.
Is that ok?

—
Reply to this email directly or view it on GitHub
#6 (comment).