pappso::MsRunDataSetTreeNode Class Reference

#include <msrundatasettreenode.h>

Public Member Functions
	MsRunDataSetTreeNode ()
	MsRunDataSetTreeNode (const MsRunDataSetTreeNode &other)
	MsRunDataSetTreeNode (QualifiedMassSpectrumCstSPtr mass_spectrum_csp, MsRunDataSetTreeNode *parent_p=nullptr)
virtual	~MsRunDataSetTreeNode ()
MsRunDataSetTreeNode &	operator= (const MsRunDataSetTreeNode &other)
void	setQualifiedMassSpectrum (QualifiedMassSpectrumCstSPtr qualified_mass_spectrum_csp)
QualifiedMassSpectrumCstSPtr	getQualifiedMassSpectrum () const
void	setParent (MsRunDataSetTreeNode *parent)
MsRunDataSetTreeNode *	getParent () const
bool	hasParent () const
void	size (std::size_t &cumulative_node_count) const
MsRunDataSetTreeNode *	findNode (std::size_t spectrum_index)
MsRunDataSetTreeNode *	findNode (QualifiedMassSpectrumCstSPtr mass_spectrum_csp)
void	flattenedView (std::vector< MsRunDataSetTreeNode * > &nodes, bool with_descendants=false)
void	flattenedViewChildrenOnly (std::vector< MsRunDataSetTreeNode * > &nodes, bool with_descendants=false)
void	flattenedViewMsLevelNodes (std::size_t ms_level, std::size_t depth, std::vector< MsRunDataSetTreeNode * > &nodes, bool with_descendants=false)
std::vector< MsRunDataSetTreeNode * >	productNodesByPrecursorMz (pappso_double precursor_mz, PrecisionPtr precision_ptr, std::vector< MsRunDataSetTreeNode * > &nodes)
std::vector< MsRunDataSetTreeNode * >	precursorIonNodesByPrecursorMz (pappso_double precursor_mz, PrecisionPtr precision_ptr, std::vector< MsRunDataSetTreeNode * > &nodes)
void	accept (MsRunDataSetTreeNodeVisitorInterface &visitor)
std::size_t	depth (std::size_t depth) const
QString	toString (bool with_data=false) const

Private Attributes
QualifiedMassSpectrumCstSPtr	mcsp_massSpectrum = nullptr
MsRunDataSetTreeNode *	mp_parent = nullptr
std::vector< MsRunDataSetTreeNode * >	m_children

Friends
class	MsRunDataSetTree

Detailed Description

Definition at line 32 of file msrundatasettreenode.h.

Constructor & Destructor Documentation

MsRunDataSetTreeNode() [1/3]

pappso::MsRunDataSetTreeNode::MsRunDataSetTreeNode

(

)

Definition at line 28 of file msrundatasettreenode.cpp.

{
}

Referenced by MsRunDataSetTreeNode(), MsRunDataSetTreeNode(), findNode(), findNode(), MsRunDataSetTree, operator=(), precursorIonNodesByPrecursorMz(), and setParent().

MsRunDataSetTreeNode() [2/3]

pappso::MsRunDataSetTreeNode::MsRunDataSetTreeNode

(

const MsRunDataSetTreeNode &

other

)

Definition at line 40 of file msrundatasettreenode.cpp.

  : mcsp_massSpectrum(other.mcsp_massSpectrum), mp_parent(other.mp_parent)
{
  for(auto &&node : other.m_children)
    m_children.push_back(new MsRunDataSetTreeNode(*node));
}

References MsRunDataSetTreeNode(), m_children, mcsp_massSpectrum, and mp_parent.

MsRunDataSetTreeNode() [3/3]

pappso::MsRunDataSetTreeNode::MsRunDataSetTreeNode	(	QualifiedMassSpectrumCstSPtr	mass_spectrum_csp,
		MsRunDataSetTreeNode *	parent_p = nullptr )

Definition at line 33 of file msrundatasettreenode.cpp.

  : mcsp_massSpectrum(mass_spectrum_csp), mp_parent(parent_p)
{
}

References MsRunDataSetTreeNode(), mcsp_massSpectrum, and mp_parent.

~MsRunDataSetTreeNode()

pappso::MsRunDataSetTreeNode::~MsRunDataSetTreeNode ( )

virtual

Definition at line 48 of file msrundatasettreenode.cpp.

{
  for(auto &&node : m_children)
    delete node;
 
  m_children.clear();
}

References m_children.

Member Function Documentation

accept()

void pappso::MsRunDataSetTreeNode::accept

(

MsRunDataSetTreeNodeVisitorInterface &

visitor

)

Definition at line 363 of file msrundatasettreenode.cpp.

{
  // qDebug() << "now calling visitor.visit(*this);";
 
  visitor.visit(*this);
 
  // qDebug() << "and now calling node->accept(visitor) for each child node.";
 
  visitor.setNodesToProcessCount(m_children.size());
 
  for(auto &&node : m_children)
    node->accept(visitor);
}

References m_children, pappso::MsRunDataSetTreeNodeVisitorInterface::setNodesToProcessCount(), and pappso::MsRunDataSetTreeNodeVisitorInterface::visit().

Referenced by MsRunDataSetTree.

depth()

std::size_t pappso::MsRunDataSetTreeNode::depth

(

std::size_t

depth

)

const

Definition at line 379 of file msrundatasettreenode.cpp.

{
 
  // qDebug() << "Got depth:" << depth;
 
  // If there are no children in this node, that is the end of the tree.
  // Do not change anything an return.
 
  if(!m_children.size())
    {
      // qDebug() << "No children, returning" << depth;
 
      return depth;
    }
 
  // qDebug() << "There are" << m_children.size() << "children nodes";
 
 
  // At this point we know we can already increment depth by one because
  // we go down one level by iterating in the m_children vector of nodes.
 
  // qDebug() << "Children found, incrementing depth to" << depth + 1;
 
  std::size_t local_depth = depth + 1;
 
  std::size_t tmp_depth      = 0;
  std::size_t greatest_depth = 0;
 
  for(auto &node : m_children)
    {
      // qDebug() << "In the children for loop";
 
      tmp_depth = node->depth(local_depth);
 
      // qDebug() << "Got depth from iterated node:" << tmp_depth;
 
      if(tmp_depth > greatest_depth)
        greatest_depth = tmp_depth;
    }
 
  // qDebug() << "Returning:" << greatest_depth;
 
  return greatest_depth;
}

References depth(), and m_children.

Referenced by depth(), flattenedViewMsLevelNodes(), and MsRunDataSetTree.

findNode() [1/2]

MsRunDataSetTreeNode * pappso::MsRunDataSetTreeNode::findNode

(

QualifiedMassSpectrumCstSPtr

mass_spectrum_csp

)

Definition at line 168 of file msrundatasettreenode.cpp.

{
  // qDebug();
 
  // Finding a node that contains a qualified mass spectrum requires checking if
  // that node is not *this and if not if it is not one of the children. By
  // essence, this work is recursive.
 
  if(mass_spectrum_csp == mcsp_massSpectrum)
    {
      // qDebug() << "The mass spectrum's node is this node.";
 
      return this;
    }
 
  // qDebug() << "Need to go searching in the children.";
 
  for(auto &node : m_children)
    {
      MsRunDataSetTreeNode *iterNode = node->findNode(mass_spectrum_csp);
 
      if(iterNode != nullptr)
        {
          // qDebug() << "Found the mass spectrum's node.";
 
          return iterNode;
        }
    }
 
  return nullptr;
}

References MsRunDataSetTreeNode(), m_children, and mcsp_massSpectrum.

findNode() [2/2]

MsRunDataSetTreeNode * pappso::MsRunDataSetTreeNode::findNode

(

std::size_t

spectrum_index

)

Definition at line 133 of file msrundatasettreenode.cpp.

{
  // qDebug();
 
  // Finding a node that contains a qualified mass spectrum that has been
  // acquired at spectrum_index, requires checking if that node is not *this and
  // if not if it is not one of the children. By essence, this work is
  // recursive.
 
  if(mcsp_massSpectrum->getMassSpectrumId().getSpectrumIndex() == spectrum_index)
    {
      // qDebug() << "The mass spectrum's node is this node.";
 
      return this;
    }
 
  // qDebug() << "Need to go searching in the children.";
 
  for(auto &node : m_children)
    {
      MsRunDataSetTreeNode *iterNode = node->findNode(spectrum_index);
 
      if(iterNode != nullptr)
        {
          // qDebug() << "Found the mass spectrum's node.";
 
          return iterNode;
        }
    }
 
  return nullptr;
}

References MsRunDataSetTreeNode(), m_children, and mcsp_massSpectrum.

Referenced by pappso::MsRunDataSetTree::findNode(), pappso::MsRunDataSetTree::findNode(), MsRunDataSetTree, and precursorIonNodesByPrecursorMz().

flattenedView()

void pappso::MsRunDataSetTreeNode::flattenedView	(	std::vector< MsRunDataSetTreeNode * > &	nodes,
		bool	with_descendants = false )

Definition at line 202 of file msrundatasettreenode.cpp.

{
 
  // Do store this.
 
  nodes.push_back(this);
 
  // And now the descendants.
 
  if(with_descendants)
    {
      for(auto &&node : m_children)
        {
          node->flattenedView(nodes, with_descendants);
        }
    }
  else
    {
    }
}

References m_children.

Referenced by flattenedViewMsLevelNodes(), and MsRunDataSetTree.

flattenedViewChildrenOnly()

void pappso::MsRunDataSetTreeNode::flattenedViewChildrenOnly	(	std::vector< MsRunDataSetTreeNode * > &	nodes,
		bool	with_descendants = false )

Definition at line 226 of file msrundatasettreenode.cpp.

{
 
  // Do not store this, only this->m_children !
 
  for(auto &&node : m_children)
    node->flattenedView(nodes, with_descendants);
}

References m_children.

Referenced by MsRunDataSetTree.

flattenedViewMsLevelNodes()

void pappso::MsRunDataSetTreeNode::flattenedViewMsLevelNodes	(	std::size_t	ms_level,
		std::size_t	depth,
		std::vector< MsRunDataSetTreeNode * > &	nodes,
		bool	with_descendants = false )

Definition at line 238 of file msrundatasettreenode.cpp.

{
 
  if(ms_level == (depth + 1))
    {
 
      // There we are. The ms_level that is asked matches the current depth of
      // the node we are in.
 
      flattenedView(nodes, with_descendants);
    }
  else if(ms_level > (depth + 1))
    {
      // We still do not have to store the nodes, because what we are
      // searching is down the tree...
 
      for(auto &&node : m_children)
        {
          node->flattenedViewMsLevelNodes(ms_level, depth + 1, nodes, with_descendants);
        }
    }
}

References depth(), flattenedView(), and m_children.

Referenced by MsRunDataSetTree.

getParent()

MsRunDataSetTreeNode * pappso::MsRunDataSetTreeNode::getParent

(

)

const

Definition at line 95 of file msrundatasettreenode.cpp.

{
  // qDebug();
 
  return mp_parent;
}

References mp_parent.

Referenced by MsRunDataSetTree.

getQualifiedMassSpectrum()

QualifiedMassSpectrumCstSPtr pappso::MsRunDataSetTreeNode::getQualifiedMassSpectrum

(

)

const

Definition at line 81 of file msrundatasettreenode.cpp.

{
  return mcsp_massSpectrum;
}

References mcsp_massSpectrum.

Referenced by MsRunDataSetTree.

hasParent()

bool pappso::MsRunDataSetTreeNode::hasParent

(

)

const

Definition at line 104 of file msrundatasettreenode.cpp.

{
  // qDebug();
 
  if(mp_parent != nullptr)
    return true;
  else
    return false;
}

References mp_parent.

Referenced by MsRunDataSetTree.

operator=()

MsRunDataSetTreeNode & pappso::MsRunDataSetTreeNode::operator=

(

const MsRunDataSetTreeNode &

other

)

Definition at line 58 of file msrundatasettreenode.cpp.

{
  if(this == &other)
    return *this;
 
  mcsp_massSpectrum = other.mcsp_massSpectrum;
  mp_parent         = other.mp_parent;
 
  for(auto &&node : other.m_children)
    m_children.push_back(new MsRunDataSetTreeNode(*node));
 
  return *this;
}

References MsRunDataSetTreeNode(), m_children, mcsp_massSpectrum, and mp_parent.

Referenced by MsRunDataSetTree.

precursorIonNodesByPrecursorMz()

std::vector< MsRunDataSetTreeNode * > pappso::MsRunDataSetTreeNode::precursorIonNodesByPrecursorMz	(	pappso_double	precursor_mz,
		PrecisionPtr	precision_ptr,
		std::vector< MsRunDataSetTreeNode * > &	nodes )

Definition at line 309 of file msrundatasettreenode.cpp.

{
  if(precision_ptr == nullptr)
    throw ExceptionNotPossible(
      QObject::tr("Fatal error at msrundatasettreenode.cpp "
                  "-- ERROR precision_ptr cannot be nullptr. "
                  "Program aborted."));
 
  // Calculate the mz range using the tolerance.
  pappso_double lower_mz = precursor_mz - (precision_ptr->delta(precursor_mz) / 2);
  pappso_double upper_mz = precursor_mz + (precision_ptr->delta(precursor_mz) / 2);
 
  // Check if this node matches the requirements.
 
  pappso_double mz = mcsp_massSpectrum->getPrecursorMz();
 
  if(mz != std::numeric_limits<double>::max())
    {
      if(mz >= lower_mz && mz <= upper_mz)
        {
          // We are iterating in a node that hold a mass spectrum that was
          // acquired by fragmenting an ion matching the searched mz value. We
          // can extract the spectrum index of that precursor mass spectrum and
          // then get its corresponding node, that we'll store.
 
          std::size_t precursor_spectrum_index = mcsp_massSpectrum->getPrecursorSpectrumIndex();
 
          MsRunDataSetTreeNode *found_node = findNode(precursor_spectrum_index);
 
          if(precursor_spectrum_index !=
             found_node->mcsp_massSpectrum->getMassSpectrumId().getSpectrumIndex())
            throw ExceptionNotPossible(
              QObject::tr("Fatal error at msrundatasettreenode.cpp "
                          "-- ERROR precursor_spectrum_index bad value. "
                          "Program aborted."));
 
          nodes.push_back(found_node);
        }
    }
 
  // Now handle in the same way, but recursively, all the children of this node.
 
  for(auto &&node : m_children)
    {
      node->precursorIonNodesByPrecursorMz(precursor_mz, precision_ptr, nodes);
    }
 
  return nodes;
}

References MsRunDataSetTreeNode(), pappso::PrecisionBase::delta(), findNode(), m_children, and mcsp_massSpectrum.

Referenced by MsRunDataSetTree.

productNodesByPrecursorMz()

std::vector< MsRunDataSetTreeNode * > pappso::MsRunDataSetTreeNode::productNodesByPrecursorMz	(	pappso_double	precursor_mz,
		PrecisionPtr	precision_ptr,
		std::vector< MsRunDataSetTreeNode * > &	nodes )

Definition at line 266 of file msrundatasettreenode.cpp.

{
  if(precision_ptr == nullptr)
    throw ExceptionNotPossible(
      QObject::tr("Fatal error at msrundatasettreenode.cpp "
                  "-- ERROR precision_ptr cannot be nullptr. "
                  "Program aborted."));
 
  // Check if this node matches the requirements.
 
  pappso_double mz = mcsp_massSpectrum->getPrecursorMz();
 
  if(mz != std::numeric_limits<double>::max())
    {
 
      // Calculate the mz range using the tolerance.
 
      pappso_double lower_mz = precursor_mz - (precision_ptr->delta(precursor_mz) / 2);
      pappso_double upper_mz = precursor_mz + (precision_ptr->delta(precursor_mz) / 2);
 
      if(mz >= lower_mz && mz <= upper_mz)
        {
          // We are iterating in a node that holds a mass spectrum that was
          // acquired by fragmenting an ion that matches the searched mz value.
 
          nodes.push_back(this);
        }
    }
 
  // Now handle in the same way, but recursively, all the children of this node.
 
  for(auto &&node : m_children)
    {
      node->productNodesByPrecursorMz(precursor_mz, precision_ptr, nodes);
    }
 
  return nodes;
}

References pappso::PrecisionBase::delta(), m_children, and mcsp_massSpectrum.

Referenced by MsRunDataSetTree.

setParent()

void pappso::MsRunDataSetTreeNode::setParent

(

MsRunDataSetTreeNode *

parent

)

Definition at line 88 of file msrundatasettreenode.cpp.

{
  mp_parent = parent;
}

References MsRunDataSetTreeNode(), and mp_parent.

Referenced by MsRunDataSetTree.

setQualifiedMassSpectrum()

void pappso::MsRunDataSetTreeNode::setQualifiedMassSpectrum

(

QualifiedMassSpectrumCstSPtr

qualified_mass_spectrum_csp

)

Definition at line 73 of file msrundatasettreenode.cpp.

{
  mcsp_massSpectrum = qualified_mass_spectrum_csp;
}

References mcsp_massSpectrum.

Referenced by MsRunDataSetTree.

size()

void pappso::MsRunDataSetTreeNode::size

(

std::size_t &

cumulative_node_count

)

const

Definition at line 116 of file msrundatasettreenode.cpp.

{
 
  // First account for this node.
  ++cumulative_node_count;
 
  // Then ask for each child to recursively account for themselves and their
  // children.
 
  for(auto &&node : m_children)
    {
      node->size(cumulative_node_count);
    }
}

References m_children.

Referenced by MsRunDataSetTree.

toString()

QString pappso::MsRunDataSetTreeNode::toString

(

bool

with_data = false

)

const

Definition at line 426 of file msrundatasettreenode.cpp.

{
  QString text =
    QString("mcsp_massSpectrum: %1 ; to string: %2 ; children: %3\n")
      .arg(Utils::pointerToString(const_cast<QualifiedMassSpectrum *>(mcsp_massSpectrum.get())))
      .arg(mcsp_massSpectrum->toString())
      .arg(m_children.size());
 
  if(with_data)
    text += mcsp_massSpectrum->getMassSpectrumCstSPtr()->toString();
 
  return text;
}

References m_children, mcsp_massSpectrum, and pappso::Utils::pointerToString().

Referenced by MsRunDataSetTree.

Friends And Related Symbol Documentation

MsRunDataSetTree

friend class MsRunDataSetTree

friend

Definition at line 34 of file msrundatasettreenode.h.

References MsRunDataSetTreeNode(), accept(), depth(), findNode(), flattenedView(), flattenedViewChildrenOnly(), flattenedViewMsLevelNodes(), getParent(), getQualifiedMassSpectrum(), hasParent(), MsRunDataSetTree, operator=(), precursorIonNodesByPrecursorMz(), productNodesByPrecursorMz(), setParent(), setQualifiedMassSpectrum(), size(), and toString().

Referenced by MsRunDataSetTree.

Member Data Documentation

m_children

std::vector<MsRunDataSetTreeNode *> pappso::MsRunDataSetTreeNode::m_children

private

Definition at line 95 of file msrundatasettreenode.h.

Referenced by MsRunDataSetTreeNode(), ~MsRunDataSetTreeNode(), accept(), pappso::MsRunDataSetTree::addMassSpectrum(), pappso::MsRunDataSetTree::addMassSpectrum(), depth(), findNode(), findNode(), flattenedView(), flattenedViewChildrenOnly(), flattenedViewMsLevelNodes(), operator=(), precursorIonNodesByPrecursorMz(), productNodesByPrecursorMz(), pappso::MsRunDataSetTree::productNodesByPrecursorSpectrumIndex(), size(), and toString().

mcsp_massSpectrum

QualifiedMassSpectrumCstSPtr pappso::MsRunDataSetTreeNode::mcsp_massSpectrum = nullptr

private

Definition at line 91 of file msrundatasettreenode.h.

Referenced by MsRunDataSetTreeNode(), MsRunDataSetTreeNode(), findNode(), findNode(), getQualifiedMassSpectrum(), operator=(), precursorIonNodesByPrecursorMz(), pappso::MsRunDataSetTree::precursorNodeByProductSpectrumIndex(), productNodesByPrecursorMz(), setQualifiedMassSpectrum(), and toString().

mp_parent

MsRunDataSetTreeNode* pappso::MsRunDataSetTreeNode::mp_parent = nullptr

private

Definition at line 93 of file msrundatasettreenode.h.

Referenced by MsRunDataSetTreeNode(), MsRunDataSetTreeNode(), getParent(), hasParent(), operator=(), and setParent().

---

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

• pappsomspp/core/msrun/msrundatasettreenode.h
• pappsomspp/core/msrun/msrundatasettreenode.cpp