#include <TextWriter.hpp>

Public Member Functions
	TextWriter (std::ostream &os, int depth=0)
TextWriter	child ()
TextWriter &	operator() (const std::string &text)
TextWriter &	operator() (const CVParam &cvParam)
TextWriter &	operator() (const UserParam &userParam)
template<typename object_type >
TextWriter &	operator() (const std::string &label, const std::vector< object_type > &v)
template<typename object_type >
TextWriter &	operator() (const std::string &label, const object_type &v)
TextWriter &	operator() (const TraData &msd)
TextWriter &	operator() (const CV &cv)
TextWriter &	operator() (const ParamContainer &paramContainer)
TextWriter &	operator() (const Publication &publication)
TextWriter &	operator() (const Software &software)
TextWriter &	operator() (const Contact &contact)
TextWriter &	operator() (const RetentionTime &retentionTime)
TextWriter &	operator() (const Prediction &prediction)
TextWriter &	operator() (const Evidence &evidence)
TextWriter &	operator() (const Validation &validation)
TextWriter &	operator() (const Protein &protein)
TextWriter &	operator() (const Modification &modification)
TextWriter &	operator() (const Peptide &peptide)
TextWriter &	operator() (const Compound &compound)
TextWriter &	operator() (const Precursor &precursor)
TextWriter &	operator() (const Product &product)
TextWriter &	operator() (const Transition &transition)
TextWriter &	operator() (const Target &target)
TextWriter &	operator() (const TargetList &targetList)
template<typename object_type >
TextWriter &	operator() (const boost::shared_ptr< object_type > &p)

Private Attributes
std::ostream &	os_
int	depth_
std::string	indent_

Detailed Description

Definition at line 43 of file TextWriter.hpp.

Constructor & Destructor Documentation

pwiz::tradata::TextWriter::TextWriter	(	std::ostream &	os,
		int	depth = `0`
	)

inline

Definition at line 47 of file TextWriter.hpp.

: os_(os), depth_(depth), indent_(depth*2, ' ')

{}

Member Function Documentation

TextWriter pwiz::tradata::TextWriter::child ( )

inline

Definition at line 51 of file TextWriter.hpp.

References os_.

{return TextWriter(os_, depth_+1);}

TextWriter& pwiz::tradata::TextWriter::operator() ( const std::string & text )

inline

Definition at line 53 of file TextWriter.hpp.

References os_.

    {
        os_ << indent_ << text << std::endl;
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const CVParam & cvParam )

inline

Definition at line 59 of file TextWriter.hpp.

References pwiz::data::CVParam::cvid, CVID_Unknown, pwiz::cv::cvTermInfo(), pwiz::cv::CVTermInfo::name, os_, pwiz::data::CVParam::units, pwiz::data::CVParam::unitsName(), and pwiz::data::CVParam::value.

    {
        os_ << indent_ << "cvParam: " << cvTermInfo(cvParam.cvid).name;
        if (!cvParam.value.empty())
            os_ << ", " << cvParam.value;
        if (cvParam.units != CVID_Unknown)
            os_ << ", " << cvParam.unitsName();
        os_ << std::endl; 
        return *this;    
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const UserParam & userParam )

inline

Definition at line 70 of file TextWriter.hpp.

References CVID_Unknown, pwiz::cv::cvTermInfo(), pwiz::data::UserParam::name, pwiz::cv::CVTermInfo::name, os_, pwiz::data::UserParam::type, pwiz::data::UserParam::units, and pwiz::data::UserParam::value.

    {
        os_ << indent_ << "userParam: " << userParam.name;
        if (!userParam.value.empty()) os_ << ", " << userParam.value; 
        if (!userParam.type.empty()) os_ << ", " << userParam.type; 
        if (userParam.units != CVID_Unknown) os_ << ", " << cvTermInfo(userParam.units).name;
        os_ << std::endl; 
        return *this;    
    }

template<typename object_type >

TextWriter& pwiz::tradata::TextWriter::operator()	(	const std::string &	label,
		const std::vector< object_type > &	v
	)

inline

Definition at line 81 of file TextWriter.hpp.

    {
        (*this)(label);
        for_each(v.begin(), v.end(), child());
        return *this;
    }

template<typename object_type >

TextWriter& pwiz::tradata::TextWriter::operator()	(	const std::string &	label,
		const object_type &	v
	)

inline

Definition at line 89 of file TextWriter.hpp.

    {
        (*this)(label)(boost::lexical_cast<std::string>(v));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const TraData & msd )

inline

Definition at line 96 of file TextWriter.hpp.

References pwiz::tradata::TraData::compoundPtrs, pwiz::tradata::TraData::contactPtrs, pwiz::tradata::TraData::cvs, pwiz::tradata::TargetList::empty(), pwiz::tradata::TraData::instrumentPtrs, pwiz::tradata::TraData::peptidePtrs, pwiz::tradata::TraData::proteinPtrs, pwiz::tradata::TraData::publications, pwiz::tradata::TraData::softwarePtrs, pwiz::tradata::TraData::targets, pwiz::tradata::TraData::transitions, and pwiz::tradata::TraData::version().

    {
        (*this)("tradata:");
        child()("version: " + msd.version());
        if (!msd.cvs.empty())
            child()("cvList: ", msd.cvs);
        if (!msd.contactPtrs.empty())
            child()("contactList: ", msd.contactPtrs);
        if (!msd.publications.empty())
            child()("publicationList: ", msd.publications);
        if (!msd.instrumentPtrs.empty())
            child()("instrumentList: ", msd.instrumentPtrs);
        if (!msd.softwarePtrs.empty())
            child()("softwareList: ", msd.softwarePtrs);
        if (!msd.proteinPtrs.empty())
            child()("proteinList: ", msd.proteinPtrs);
        if (!msd.peptidePtrs.empty())
            child()("peptideList: ", msd.peptidePtrs);
        if (!msd.compoundPtrs.empty())
            child()("compoundList: ", msd.compoundPtrs);
        if (!msd.transitions.empty())
            child()("transitionList: ", msd.transitions);
        if (!msd.targets.empty())
            child()(msd.targets);
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const CV & cv )

inline

Definition at line 124 of file TextWriter.hpp.

References pwiz::cv::CV::fullName, pwiz::cv::CV::id, pwiz::cv::CV::URI, and pwiz::cv::CV::version.

    {
        (*this)("cv:");
        child()
            ("id: " + cv.id)
            ("fullName: " + cv.fullName)
            ("version: " + cv.version)
            ("URI: " + cv.URI);
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const ParamContainer & paramContainer )

inline

Definition at line 135 of file TextWriter.hpp.

References pwiz::data::ParamContainer::cvParams, and pwiz::data::ParamContainer::userParams.

    {
        for_each(paramContainer.cvParams.begin(), paramContainer.cvParams.end(), *this);
        for_each(paramContainer.userParams.begin(), paramContainer.userParams.end(), *this);
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Publication & publication )

inline

Definition at line 142 of file TextWriter.hpp.

References pwiz::tradata::Publication::id.

    {
        (*this)("publication:");
        child()
            ("id: " + publication.id)
            (static_cast<const ParamContainer&>(publication));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Software & software )

inline

Definition at line 151 of file TextWriter.hpp.

References pwiz::tradata::Software::id, and pwiz::tradata::Software::version.

    {
        (*this)("software:");
        child()
            ("id: " + software.id)
            ("version: " + software.version)
            (static_cast<const ParamContainer&>(software));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Contact & contact )

inline

Definition at line 161 of file TextWriter.hpp.

    {
        (*this)("contact:");
        child()(static_cast<const ParamContainer&>(contact));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const RetentionTime & retentionTime )

inline

Definition at line 168 of file TextWriter.hpp.

References pwiz::tradata::RetentionTime::softwarePtr.

    {
        (*this)("retentionTime:");
        child()(static_cast<const ParamContainer&>(retentionTime));
        if (retentionTime.softwarePtr.get() &&
            !retentionTime.softwarePtr->empty())
            child()("softwareRef: " + retentionTime.softwarePtr->id);
        return *this;    
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Prediction & prediction )

inline

Definition at line 178 of file TextWriter.hpp.

    {
        (*this)("prediction:");
        child()(static_cast<const ParamContainer&>(prediction));
        return *this;   
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Evidence & evidence )

inline

Definition at line 185 of file TextWriter.hpp.

    {
        (*this)("evidence:");
        child()(static_cast<const ParamContainer&>(evidence));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Validation & validation )

inline

Definition at line 192 of file TextWriter.hpp.

    {
        (*this)("validation:");
        child()(static_cast<const ParamContainer&>(validation));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Protein & protein )

inline

Definition at line 199 of file TextWriter.hpp.

References pwiz::proteome::Protein::id, and pwiz::proteome::Peptide::sequence().

    {
        (*this)("protein:");
        child()("id: " + protein.id)
               ("sequence: " + protein.sequence);
        child()(static_cast<const ParamContainer&>(protein));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Modification & modification )

inline

Definition at line 208 of file TextWriter.hpp.

References boost::lexical_cast(), and pwiz::data::unimod::modification().

    {
        (*this)("modification:");
        child()("location: ", lexical_cast<string>(modification.location))
               ("monoisotopicMassDelta: " + lexical_cast<string>(modification.monoisotopicMassDelta))
               ("averageMassDelta: " + lexical_cast<string>(modification.averageMassDelta));
        child()(static_cast<const ParamContainer&>(modification));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Peptide & peptide )

inline

Definition at line 218 of file TextWriter.hpp.

References pwiz::util::virtual_map< keyT, valueT, _Pr, _Alloc >::empty(), pwiz::proteome::Peptide::modifications(), pwiz::identdata::peptide(), and pwiz::proteome::Peptide::sequence().

    {
        (*this)("peptide:");
        child()("id: " + peptide.id)
               ("sequence: " + peptide.sequence)
               (peptide.evidence);
        if (!peptide.proteinPtrs.empty())
            child()("proteinRefs:", peptide.proteinPtrs);
        if (!peptide.modifications.empty())
            child()("modifications:", peptide.modifications);
        if (!peptide.retentionTimes.empty())
            child()("retentionTimes:", peptide.retentionTimes);
        child()(static_cast<const ParamContainer&>(peptide));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Compound & compound )

inline

Definition at line 236 of file TextWriter.hpp.

References pwiz::tradata::Compound::id, and pwiz::tradata::Compound::retentionTimes.

    {
        (*this)("compound:");
        child()("id: " + compound.id)
               ("retentionTimes:", compound.retentionTimes);
        child()(static_cast<const ParamContainer&>(compound));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Precursor & precursor )

inline

Definition at line 245 of file TextWriter.hpp.

    {
        (*this)("precursor:");
        child()(static_cast<const ParamContainer&>(precursor));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Product & product )

inline

Definition at line 252 of file TextWriter.hpp.

    {
        (*this)("product:");
        child()(static_cast<const ParamContainer&>(product));
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Transition & transition )

inline

Definition at line 259 of file TextWriter.hpp.

References pwiz::tradata::Transition::compoundPtr, pwiz::tradata::Transition::configurationList, pwiz::tradata::Prediction::empty(), pwiz::tradata::Precursor::empty(), pwiz::tradata::Product::empty(), pwiz::tradata::Transition::id, pwiz::tradata::Transition::interpretationList, pwiz::tradata::Transition::peptidePtr, pwiz::tradata::Transition::precursor, pwiz::tradata::Transition::prediction, and pwiz::tradata::Transition::product.

    {
        (*this)("transition:");
        child()("id: ", transition.id);
            if (!transition.precursor.empty())
                child()(transition.precursor);
            if (!transition.product.empty())
                child()(transition.product);
            if (!transition.prediction.empty())
                child()(transition.prediction);
            if (!transition.interpretationList.empty())
                child()("interpretationList: ", transition.interpretationList);
            if (!transition.configurationList.empty())
                child()("configurationList: ", transition.configurationList);
            if (transition.peptidePtr.get() && !transition.peptidePtr->empty())
                child()("peptideRef: " + transition.peptidePtr->id);
            if (transition.compoundPtr.get() && !transition.compoundPtr->empty())
                child()("compoundRef: " + transition.compoundPtr->id);
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const Target & target )

inline

Definition at line 280 of file TextWriter.hpp.

References pwiz::tradata::Target::compoundPtr, pwiz::tradata::Target::configurationList, pwiz::tradata::Precursor::empty(), pwiz::tradata::Target::id, pwiz::tradata::Target::peptidePtr, and pwiz::tradata::Target::precursor.

    {
        (*this)("target:");
        child()("id: ", target.id);
            if (!target.precursor.empty())
                child()(target.precursor);
            if (!target.configurationList.empty())
                child()("configurationList: ", target.configurationList);
            if (target.peptidePtr.get() && !target.peptidePtr->empty())
                child()("peptideRef: " + target.peptidePtr->id);
            if (target.compoundPtr.get() && !target.compoundPtr->empty())
                child()("compoundRef: " + target.compoundPtr->id);
        return *this;
    }

TextWriter& pwiz::tradata::TextWriter::operator() ( const TargetList & targetList )

inline

Definition at line 295 of file TextWriter.hpp.

References pwiz::tradata::TargetList::targetExcludeList, and pwiz::tradata::TargetList::targetIncludeList.

    {
        (*this)("targetList:");
        child()(static_cast<const ParamContainer&>(targetList));
            if (!targetList.targetExcludeList.empty())
                child()("targetExcludeList: ", targetList.targetExcludeList);
            if (!targetList.targetIncludeList.empty())
                child()("targetIncludeList: ", targetList.targetIncludeList);
        return *this;
    }

template<typename object_type >

TextWriter& pwiz::tradata::TextWriter::operator() ( const boost::shared_ptr< object_type > & p )

inline

Definition at line 308 of file TextWriter.hpp.

    {
        return p.get() ? (*this)(*p) : *this;
    }

Member Data Documentation

std::ostream& pwiz::tradata::TextWriter::os_

private

Definition at line 314 of file TextWriter.hpp.

int pwiz::tradata::TextWriter::depth_

private

Definition at line 315 of file TextWriter.hpp.

std::string pwiz::tradata::TextWriter::indent_

private

Definition at line 316 of file TextWriter.hpp.

The documentation for this class was generated from the following file:

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/tradata/TextWriter.hpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation