Thank you.Will do it. Regards, Rishika
On Fri, Jul 26, 2013 at 2:03 PM, Joseph Slagel < [email protected]> wrote: > Rishika, > > The TPP version of X!Tandem has some dependencies (such as mzParser) that > are outside of the src_tpp directory. > > I hate to say it but the easiest thing to do is download and build all of > TPP. > > -Joe > > > > On Fri, Jul 26, 2013 at 9:44 AM, Rishika Bisaria > <[email protected]>wrote: > >> Hi, >> Thank you for the reply. >> I copied all teh files to src folder , changed the permission0 and ran >> the make command. >> But still I am getting this error: >> >> >> In file included from loadmzparser.cpp:7:0: >> loadmzparser.h:47:2: error: ‘BasicSpectrum’ does not name a type >> loadmzparser.h:48:2: error: ‘MzParser’ does not name a type >> loadmzparser.cpp: In constructor >> ‘loadmzparser::loadmzparser(std::vector<mspectrum>&, mspectrumcondition&, >> mscore&)’: >> loadmzparser.cpp:13:2: error: ‘mzp’ was not declared in this scope >> loadmzparser.cpp:13:12: error: expected type-specifier before ‘MzParser’ >> loadmzparser.cpp:13:12: error: expected ‘;’ before ‘MzParser’ >> loadmzparser.cpp: In destructor ‘virtual loadmzparser::~loadmzparser()’: >> loadmzparser.cpp:20:9: error: ‘mzp’ was not declared in this scope >> loadmzparser.cpp: In member function ‘virtual bool loadmzparser::get()’: >> loadmzparser.cpp:25:8: error: ‘mzp’ was not declared in this scope >> loadmzparser.cpp:26:6: error: ‘s’ was not declared in this scope >> loadmzparser.cpp:28:6: error: ‘s’ was not declared in this scope >> loadmzparser.cpp: In member function ‘int loadmzparser::guessCharge()’: >> loadmzparser.cpp:54:17: error: ‘s’ was not declared in this scope >> loadmzparser.cpp: In member function ‘virtual bool >> loadmzparser::open(std::string&)’: >> loadmzparser.cpp:66:9: error: ‘mzp’ was not declared in this scope >> loadmzparser.cpp: In member function ‘void >> loadmzparser::processSpectrum(int)’: >> loadmzparser.cpp:74:12: error: ‘s’ was not declared in this scope >> loadmzparser.cpp:79:24: error: ‘CID’ was not declared in this scope >> loadmzparser.cpp:80:29: error: ‘ETD’ was not declared in this scope >> loadmzparser.cpp:80:55: error: ‘ETDSA’ was not declared in this scope >> make: *** [loadmzparser.o] Error 1 >> >> Thank you. >> >> Regards , >> Rishika >> >> >> On Thu, Jul 25, 2013 at 8:09 PM, Jimmy Eng <[email protected]> wrote: >> >>> That's an old page you're referencing. Try these files: >>> >>> >>> http://sourceforge.net/p/sashimi/code/6253/tree/tags/release_4-6-3/trans_proteomic_pipeline/extern/xtandem/src_tpp/ >>> >>> >>> >>> On Thu, Jul 25, 2013 at 4:46 PM, Rishika Bisaria < >>> [email protected]> wrote: >>> >>>> Hi , >>>> Thank you for the reply. >>>> I downloaded the two files in src folder of XTandem from >>>> https://proteomics.fhcrc.org/CPAS/Project/Published%20Experiments/Tandem%20Pluggable%20Scoring/begin.view >>>> ?. >>>> But I am getting error on running the make command. >>>> >>>> g++ -M -O2 -DGCC4_3 mscore_k.cpp > mscore_k.d >>>> g++ -M -O2 -DGCC4_3 mscore_k.cpp | sed s/\\.o/.d/ > mscore_k.d >>>> g++ -O2 -DGCC4_3 -c -o mscore_k.o mscore_k.cpp >>>> mscore_k.cpp: In member function ‘virtual mplugin* >>>> mscorefactory_k::create_plugin()’: >>>> mscore_k.cpp:34:25: error: cannot allocate an object of abstract type >>>> ‘mscore_k’ >>>> mscore_k.h:84:7: note: because the following virtual functions are >>>> pure within ‘mscore_k’: >>>> mscore.h:382:21: note: virtual float mscore::ion_check(long >>>> unsigned int, size_t) >>>> mscore_k.cpp: At global scope: >>>> mscore_k.cpp:365:7: error: ‘mscore_tandem’ has not been declared >>>> mscore_k.cpp: In function ‘float ion_check(long unsigned int, size_t)’: >>>> mscore_k.cpp:371:36: error: ‘m_vmiType’ was not declared in this scope >>>> make: *** [mscore_k.o] Error 1 >>>> >>>> Thanks, >>>> Rishika >>>> >>>> >>>> >>>> On Thu, Jul 25, 2013 at 4:44 PM, Jimmy Eng <[email protected]> wrote: >>>> >>>>> You would need a version of X!Tandem that has k-score in it so use the >>>>> one distributed with the TPP. Beyond that, the minimum parameter to set >>>>> would be: >>>>> >>>>> <note type="input" label="scoring, algorithm">k-score</note> >>>>> >>>>> >>>>> On Thu, Jul 25, 2013 at 1:15 PM, Rishika Bisaria < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi, >>>>>> I am a newbie to proteomics analysis. >>>>>> I wanted to know how can we use k-score in XTandem. Just modifying >>>>>> the parameter in the file is sufficient or we have to make other changes >>>>>> also. >>>>>> Thank You. >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to [email protected]. >>>>>> >>>>>> To post to this group, send email to >>>>>> [email protected]. >>>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "spctools-discuss" group. >>>>> To unsubscribe from this topic, visit >>>>> https://groups.google.com/d/topic/spctools-discuss/lpKfFoMiQS0/unsubscribe >>>>> . >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> [email protected]. >>>>> >>>>> To post to this group, send email to [email protected] >>>>> . >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>>> >>>>> >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>>> >>>> >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "spctools-discuss" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/spctools-discuss/lpKfFoMiQS0/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, send an email to >>> [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/lpKfFoMiQS0/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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