Hi Ludovic
I also have your 'Problem 2' with iModelParser.cgi on my TPP 4.6.1 installation
on Mac OS X 10.8.2. The problem seems to come from the 'pos_obs_dens' and
'neg_obs_dens' attribute values that are dealt with in IModelParser.cxx line
317ff.:
//check if the observed values
are present
const char* nObs =
tag->getAttributeValue("neg_obs_dens"); //keep in this order, neg obs first in
xml
const char* pObs =
tag->getAttributeValue("pos_obs_dens");
drawPobs_ = pObs != NULL;
drawNobs_ = nObs != NULL;
next_score->posObs = drawPobs_
? atof(pObs) : 0;
next_score->negObs = drawNobs_
? atof(nObs) : 0;
When removing those values from mixturemodel tags in iproph.pep.xml files plots
are displayed.
Probably, there is a simple fix for this, and it would be great if a TPP
developer could look into it.
Thanks a lot for your help!
Cheers
Ulrich
On Dec 17, 2012, at 7:47 PM, Joseph Slagel wrote:
> Ludovic,
>
> The lorikeet problem is a know issue on Linux. The path to the
> css/javascript files happen to be hard coded in the source to the directory
> "/ISB/..." which works only for Windows. There are two ways to fix it. The
> first is by editing the source file src/Visualization/Comet/plot-
> msms/plot-msms2.cxx and changing/removing the ISB string. But the easier
> solution is to add an alias to your Apache configuration so it can find the
> files. So at the bottom of your http.conf file you'll want to add:
>
> Alias /ISB "/proteomics/sw/tpp"
>
> Replacing the /proteomics/sw/tpp with wherever you have TPP installed.
> You'll then need to restart Apache to have the changes take effect.
>
> Also, the original spectrum viewer is still in TPP. If you want to enable
> it, in the pepxml viewer click on "pick columns" and add the "ions" column to
> the list.
>
> -Joe
>
>
> On Wed, Dec 12, 2012 at 1:16 AM, Ludovic <[email protected]> wrote:
> Dear Group,
>
>
>
> I have recently tried to install the TPP4.6.1 in an Ubuntu server system
> (Ubuntu 10.04.4), following the instructions from the wiki page.
>
> The install seems to have gone fine. All the TPP executable run ok (including
> the InterProphetParser and PTMprophetParser).
>
> However, I have 2 problems related to the Petunia viewer:
>
> Problem 1:
>
> By default, it seems that the “ions2” column is now activated to display the
> MSMS spectra (instead of the “ions” which used to call the plot-msms.cgi).
>
> But this new ions2-Lorikeet spectrum viewer (plot-msms-js.cgi) does not seem
> to work on my install (I get gray screens in my browser; I tried with Chrome
> and Firefox). The problem seems to have been reported on the google group,
> but as far as I know nobody solved it yet:
>
> https://groups.google.com/forum/?hl=en&fromgroups=#!searchin/spctools-discuss/ions2/spctools-discuss/9gx9mxbvews/sat3nZoD1QsJ
>
> Do you know if I need additional libraries to install the Lorikeet? I tried
> to install the libjs-jquery-ui library, but it did not help.
>
> I would not mind using the regular “ions” view, but I don’t know how to
> change the columns displayed in the Petunia viewer by default?
>
>
>
> Problem 2:
>
> I also have a problem for displaying the iProphet plots (iModelParser.cgi). I
> guess this is again a problem with my installation, but I cannot get when it
> went wrong. The most funny thing is that if you try to open the statistical
> distribution of a regular interact.pep.xml file with this iModelParser.cgi
> (by forcing the address/link of the browser instead of the ModelParser.cgi),
> I actually get plots displayed. But the iModelParser.cgi on an
> iProphet-interact.pep.xml just opens a white page (tested on Chrome and
> Firefox).
>
> Any idea?
>
>
>
> Thanks in advance for your help.
>
> Best regards
>
> Ludovic
>
>
>
>
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