#22 Rename header files

[William S Noble]

To add to this point, one error I dealt with when I started integrating Tide was because Crux's Peptide.h and Tide's peptide.h both had the same include guard ("#ifndef PEPTIDE_H \ #define PEPTIDE_H").
I don't think renaming conflicting header files would be a bad idea, but probably doesn't need to be done right away.

I'd say the patch is good to check in but Charles mentioned that he was going to take a look at it as well, so you may or may not want to wait on that.

Thanks,
Kaipo

On 9/11/2013 8:31 AM, William S Noble wrote:
To me, renaming the header files makes a lot of sense. It seems like having two files with exactly the same name and different content is bound to lead to confusion.

Bill

On Wed, Sep 11, 2013 at 8:19 AM, Sean McIlwain sjoemac@gmail.com wrote:
Kaipo,

This issue arises in our Spectrum.h because there is also a Spectrum.h in the MSToolkit library. So to include the Spectrum.h header from Comet into the Spectrum.h file in Crux, we have to specify a exact path. Other than renaming our header files to something like CruxSpectrum.h I don't see another way around this.

Thanks,
Sean

[Kaipo]

I had an idea when removing the search-for-matches code.
Most of the code is in the root of the src directory. I think there would be several benefits if we could reorganize the source code into separate folders, maybe something like:

src/
|-- app/
|-- io/
|-- model/
|-- util/

One side benefit would be that we could include only the root src directory, and if we wanted to include the Crux Spectrum header file for example, we would do #include "model/Spectrum.h".

Also this is probably more of a preference thing but I like the idea of moving the src/c, src/c/test, and src/external directories into the root directory, i.e.:

/src/c --> /src
/src/c/test --> /test
/src/external --> /ext

[William S Noble]

All of these sounds like good ideas to me. Anyone else care to comment?
Otherwise, Kaipo, you can do this. But you might want to coordinate with
anyone (e.g., Alice) who currently is working in a branch, so that they can
propagate the changes from the trunk to their branch.

Bill

On Thu, Jan 15, 2015 at 3:17 PM, Kaipo kaipot@users.sf.net wrote:

I had an idea when removing the search-for-matches code.
Most of the code is in the root of the src directory. I think there would
be several benefits if we could reorganize the source code into separate
folders, maybe something like:

src/
|-- app/
|-- io/
|-- model/
|-- util/

One side benefit would be that we could include only the root src
directory, and if we wanted to include the Crux Spectrum header file for
example, we would do #include "model/Spectrum.h".

Also this is probably more of a preference thing but I like the idea of
moving the src/c, src/c/test, and src/external directories into the root
directory, i.e.:

/src/c --> /src
/src/c/test --> /test
/src/external --> /ext

---

• [issues:#22] http://sourceforge.net/p/cruxtoolkit/issues/22 Rename
  header files*

Status: open
Milestone: post v2.0
Labels: High priority
Created: Thu Sep 12, 2013 06:35 PM UTC by William S Noble
Last Updated: Thu Jun 05, 2014 10:27 PM UTC
Owner: Kaipo

To add to this point, one error I dealt with when I started integrating
Tide was because Crux's Peptide.h and Tide's peptide.h both had the same
include guard ("#ifndef PEPTIDE_H \ #define PEPTIDE_H").
I don't think renaming conflicting header files would be a bad idea, but
probably doesn't need to be done right away.

I'd say the patch is good to check in but Charles mentioned that he was
going to take a look at it as well, so you may or may not want to wait on
that.

Thanks,
Kaipo

On 9/11/2013 8:31 AM, William S Noble wrote:
To me, renaming the header files makes a lot of sense. It seems like
having two files with exactly the same name and different content is bound
to lead to confusion.

Bill

On Wed, Sep 11, 2013 at 8:19 AM, Sean McIlwain sjoemac@gmail.com wrote:
Kaipo,

This issue arises in our Spectrum.h because there is also a Spectrum.h in
the MSToolkit library. So to include the Spectrum.h header from Comet into
the Spectrum.h file in Crux, we have to specify a exact path. Other than
renaming our header files to something like CruxSpectrum.h I don't see
another way around this.

Thanks,
Sean

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[Charles E. Grant]

Hi Kaipo.

On Thu, Jan 15, 2015 at 3:17 PM, Kaipo kaipot@users.sf.net wrote:

I had an idea when removing the search-for-matches code.
Most of the code is in the root of the src directory. I think there would
be several benefits if we could reorganize the source code into separate
folders, maybe something like:

src/
|-- app/
|-- io/
|-- model/
|-- util/

One side benefit would be that we could include only the root src
directory, and if we wanted to include the Crux Spectrum header file for
example, we would do #include "model/Spectrum.h".

Also this is probably more of a preference thing but I like the idea of
moving the src/c, src/c/test, and src/external directories into the root
directory, i.e.:

/src/c --> /src
/src/c/test --> /test
/src/external --> /ext

This sounds like a reasonable restructuring to me. What about directories like rankprop-qranker and bullseye? Would they be directly under src or go under src/app?

Once 'gotcha' to keep in mind is that Windows has a hard limit of 260 characters for file path lengths. Under certain circumstances we have hit that limit for some of the dependencies in external. Your suggested changes would actually relieve that problem a bit, but as we rearrange and rename directories we should definitely favor shorter over longer.

Charles

[Kaipo]

I was thinking that each application would have its own directory under app (except maybe the applications that have only 1 file).

I am not sure how well svn handles merging changes when renaming/moving things around, so maybe I will wait until any branches have been reintegrated into the trunk?

[William S Noble]

Ok, sounds good.
On Jan 16, 2015 12:34 PM, "Kaipo" kaipot@users.sf.net wrote:

I was thinking that each application would have its own directory under
app (except maybe the applications that have only 1 file).

I am not sure how well svn handles merging changes when renaming/moving
things around, so maybe I will wait until any branches have been
reintegrated into the trunk?

---

• [issues:#22] http://sourceforge.net/p/cruxtoolkit/issues/22 Rename
  header files*

Status: open
Milestone: post v2.0
Labels: High priority
Created: Thu Sep 12, 2013 06:35 PM UTC by William S Noble
Last Updated: Thu Jan 15, 2015 11:17 PM UTC
Owner: Kaipo

To add to this point, one error I dealt with when I started integrating
Tide was because Crux's Peptide.h and Tide's peptide.h both had the same
include guard ("#ifndef PEPTIDE_H \ #define PEPTIDE_H").
I don't think renaming conflicting header files would be a bad idea, but
probably doesn't need to be done right away.

I'd say the patch is good to check in but Charles mentioned that he was
going to take a look at it as well, so you may or may not want to wait on
that.

Thanks,
Kaipo

On 9/11/2013 8:31 AM, William S Noble wrote:
To me, renaming the header files makes a lot of sense. It seems like
having two files with exactly the same name and different content is bound
to lead to confusion.

Bill

On Wed, Sep 11, 2013 at 8:19 AM, Sean McIlwain sjoemac@gmail.com wrote:
Kaipo,

This issue arises in our Spectrum.h because there is also a Spectrum.h in
the MSToolkit library. So to include the Spectrum.h header from Comet into
the Spectrum.h file in Crux, we have to specify a exact path. Other than
renaming our header files to something like CruxSpectrum.h I don't see
another way around this.

Thanks,
Sean

---

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https://sourceforge.net/p/cruxtoolkit/issues/22/

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[Kaipo]

I was playing with this and I put a patch at http://proteome.gs.washington.edu/~kaipot/share/restructure.diff

The patch is 168mb, so it might be difficult to review, but if anyone wants to try it they can see if it works for them.

[Kaipo]

Also, this patch does not include a fix for duplicate names in include guards (#ifndef PEPTIDE_H).

I suggest that we use "#pragma once", instead of #ifndefs.