libXpertMassCore and libXpertMassGui Developer Documentation
  • libXpertMassCore
  • CrossLinkedRegion

    • Contents

    CrossLinkedRegion Class

    class MsXpS::libXpertMassCore::CrossLinkedRegion

    The CrossLinkedRegion class provides abstractions to work with cross-links and detect the region of oligomers that are linked together. More...

    Header: #include <CrossLinkedRegion.hpp>

    Public Functions

    CrossLinkedRegion()
    CrossLinkedRegion(std::size_t index_start, std::size_t index_stop)
    CrossLinkedRegion(const MsXpS::libXpertMassCore::CrossLinkedRegion &other)
    ~CrossLinkedRegion()
    std::size_t appendCrossLink(const MsXpS::libXpertMassCore::CrossLinkSPtr &cross_link_sp)
    std::size_t appendCrossLinks(const std::vector<MsXpS::libXpertMassCore::CrossLinkSPtr> &cross_links)
    const std::vector<MsXpS::libXpertMassCore::CrossLinkSPtr> &getCrossLinksCstRef() const
    std::vector<MsXpS::libXpertMassCore::CrossLinkSPtr> &getCrossLinksRef()
    std::size_t getStartIndex()
    std::size_t getStopIndex()
    std::size_t removeCrossLink(MsXpS::libXpertMassCore::CrossLinkSPtr &cross_link_sp)
    std::size_t removeCrossLinkAt(std::size_t index)
    void setStartIndex(std::size_t index)
    void setStopIndex(std::size_t index)
    MsXpS::libXpertMassCore::CrossLinkedRegion &operator=(const MsXpS::libXpertMassCore::CrossLinkedRegion &other)

    Protected Variables

    std::vector<MsXpS::libXpertMassCore::CrossLinkSPtr> m_crossLinks
    std::size_t m_startIndex
    std::size_t m_stopIndex

    Detailed Description

    In the following representation, a polymer sequence has a number of CrossLink instances that are intertwined:

               [3] [4] [5] [6]        [9]    [11]     [13]
o---o---o---o---o--o---o---o---o---o---o---o---o---o---o
            |   |__|   |       |   |       |       |
            |          +-----------+       +-------+
            |                  |
            +------------------+

    In this example, there are two cross-linked regions: [3–9] and [11–13].

    The first cross-linked region has a start index of 3 and a stop index of 9 and involves three cross-links.

    The second cross-linked region only involves a single cross-link involving two monomers at indices 11 and 13.

    This class is most useful when performing fragmentations of Oligomer instances.

    Member Function Documentation

    CrossLinkedRegion::CrossLinkedRegion()

    CrossLinkedRegion::CrossLinkedRegion(std::size_t index_start, std::size_t index_stop)

    Constructs a CrossLinkedRegion instance with indices index_start and index_stop.

    CrossLinkedRegion::CrossLinkedRegion(const MsXpS::libXpertMassCore::CrossLinkedRegion &other)

    Constructs a CrossLinkedRegion instance as a copy of other.

    The copy of the CrossLink instances is shallow (the shared pointers are copied).

    [noexcept] CrossLinkedRegion::~CrossLinkedRegion()

    Destructs a CrossLinkedRegion instance.

    Adds a the cross_link_sp CrossLink to the back of the CrossLink container.

    Returns the size of the container of CrossLink instances.

    Adds the CrossLink item in the cross_links container to the back of the member CrossLink container.

    Returns the size of the container of CrossLink instances.

    const std::vector<MsXpS::libXpertMassCore::CrossLinkSPtr> &CrossLinkedRegion::getCrossLinksCstRef() const

    Returns a const reference to the container of CrossLink instances.

    std::vector<MsXpS::libXpertMassCore::CrossLinkSPtr> &CrossLinkedRegion::getCrossLinksRef()

    Returns a reference to the container of CrossLink instances.

    std::size_t CrossLinkedRegion::getStartIndex()

    Returns the start index of this instance.

    std::size_t CrossLinkedRegion::getStopIndex()

    Returns the stop index of this instance.

    Removes the cross_link_sp CrossLink item from the member CrossLink container.

    Returns the size of the container of CrossLink instances.

    std::size_t CrossLinkedRegion::removeCrossLinkAt(std::size_t index)

    Removes the CrossLink at index from the member CrossLink container.

    Returns the size of the container of CrossLink instances.

    void CrossLinkedRegion::setStartIndex(std::size_t index)

    Sets the start index of this instance to index.

    void CrossLinkedRegion::setStopIndex(std::size_t index)

    Sets the stop index of this instance to index.

    MsXpS::libXpertMassCore::CrossLinkedRegion &CrossLinkedRegion::operator=(const MsXpS::libXpertMassCore::CrossLinkedRegion &other)

    Assigns other to this instance.

    The copy of the CrossLink instances is shallow (the shared pointers are copied).

    Member Variable Documentation

    This variable holds the CrossLink instances that are contained in this CrossLinkedRegion instance.

    std::size_t CrossLinkedRegion::m_startIndex

    This variable holds the start index of this cross-linked region.

    std::size_t CrossLinkedRegion::m_stopIndex

    This variable holds the stop index of this cross-linked region.

    Filippo Rusconi