What Brendan is suggesting is adding something like this to the k_score
class:
/* Thu, Apr 22, 2010 at 9:26 AM on spctools-discuss, Brendan M said:
I took a quick look at the code, and this function appears to be
related to new handling for phosphorylation. It looked to me like you
could just implement the function in k-score, and return zero without
any ill effects, unless you are trying to use the new phosphorylation
functionality. Then all bets are off, without someone really
understanding the meaning of this function and how the multipliers
applied to the score when ion_check is non-zero apply to k-score, and
then testing a real implementation.
But, I think you can compile and use it with just a zero returning
function.
*/
float k_score::ion_check(long unsigned int foo, size_t bar) {
return 0.0f; // cross your fingers
}
- Brian
On Wed, May 5, 2010 at 7:09 AM, GATTACA <[email protected]> wrote:
> I just downloaded the latest version of X!Tandem (at least I think I
> did).
> I tried to compile the software with the k-score plug-in and it still
> failed to compile:
>
> g++ -O3 -DGCC4 -DPLUGGABLE_SCORING -march=opteron -pipe -c -o
> mscore_k.o mscore_k.cpp
> mscore_k.cpp: In member function ‘virtual mplugin*
> mscorefactory_k::create_plugin()’:
> mscore_k.cpp:34: error: cannot allocate an object of abstract type
> ‘mscore_k’
> mscore_k.h:88: note: because the following virtual functions are
> pure within ‘mscore_k’:
> mscore.h:378: note: virtual float mscore::ion_check(long unsigned
> int, size_t)
>
> Maybe I downloaded the wrong verison?
> This is the link I used from thegpm.org:
> ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-10-01-01-4.tar.gz
>
> Suggestions anyone?
>
>
> On Apr 26, 12:17 pm, "[email protected]" <[email protected]> wrote:
> > Looks like there was an old version of tandem on the FTP site. Ron
> > updated it and now it seems to be working
> >
> > Cheers
> >
> > Brett
> >
> > On Apr 23, 11:16 am, "[email protected]" <[email protected]> wrote:
> >
> >
> >
> > > Thanks Brendan, looks like both new compiled versions (w/ and w/o the
> > > plugin I believe) are doing a core dump
> >
> > > Program terminated with signal 11, Segmentation fault.
> > > [New process 23304]
> > > #0 0x0000000000413b3f in ?? ()
> > > (gdb) backtrace
> > > #0 0x0000000000413b3f in ?? ()
> > > #1 0x000000000000002b in ?? ()
> > > #2 0x0000000000001966 in ?? ()
> > > #3 0x000000000154aad0 in ?? ()
> > > #4 0x000000000154ad68 in ?? ()
> > > #5 0x40e1bcd2926e8319 in ?? ()
> > > #6 0x0101010100000003 in ?? ()
> > > #7 0x000000000000107f in ?? ()
> > > #8 0x0000000000000000 in ?? ()
> >
> > > I'll keep you posted if we figure out what is going on
> >
> > > Cheers
> >
> > > Brett
> >
> > > On Apr 22, 9:26 am, Brendan <[email protected]> wrote:
> >
> > > > Hi Brett,
> > > > We just ran into this issue on the spctools-dev alias this week also.
> > > > I took a quick look at the code, and this function appears to be
> > > > related to new handling for phosphorylation. It looked to me like
> you
> > > > could just implement the function in k-score, and return zero without
> > > > any ill effects, unless you are trying to use the new phosphorylation
> > > > functionality. Then all bets are off, without someone really
> > > > understanding the meaning of this function and how the multipliers
> > > > applied to the score when ion_check is non-zero apply to k-score, and
> > > > then testing a real implementation.
> >
> > > > But, I think you can compile and use it with just a zero returning
> > > > function.
> >
> > > > --Brendan
> >
> > > > On Apr 21, 4:11 pm, "[email protected]" <[email protected]> wrote:
> >
> > > > > Hi everyone, we are trying to compile the most recent version of x!
> > > > > tandem with the k-score plugin, but we ran into a snag
> >
> > > > > Tandem now seems to require that plugins implement an ion_check()
> > > > > method.
> >
> > > > > // finds a specific ion
> > > > > virtual float ion_check(const unsigned long _v,const size_t _d) =
> 0;
> >
> > > > > This method is declared as a pure virtual function (which means
> > > > > plugins MUST implement it) and the k-score files included here
> > > > > (
> https://proteomics.fhcrc.org/CPAS/Project/Published%20Experiments/Tan...
> > > > > ) do not seem to implement one.
> >
> > > > > Can we copy the ion_check() implementation from mscore_tandem.cpp
> or
> > > > > is there a K-score appropriate ion_check() we should use
> >
> > > > > Cheers
> >
> > > > > Brett
> >
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