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 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.
