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 () 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 27 of file msrundatasettreenode.cpp.

{
}

Referenced by MsRunDataSetTreeNode(), and operator=().

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 m_children, and MsRunDataSetTreeNode().

MsRunDataSetTreeNode() [3/3]

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

Definition at line 32 of file msrundatasettreenode.cpp.

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

~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 385 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().

depth()

std::size_t pappso::MsRunDataSetTreeNode::depth

(

std::size_t

depth

)

const

Definition at line 401 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 m_children.

Referenced by flattenedViewMsLevelNodes().

findNode() [1/2]

MsRunDataSetTreeNode * pappso::MsRunDataSetTreeNode::findNode

(

QualifiedMassSpectrumCstSPtr

mass_spectrum_csp

)

Definition at line 169 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 findNode(), 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 findNode(), m_children, and mcsp_massSpectrum.

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

flattenedView()

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

Definition at line 203 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().

flattenedViewChildrenOnly()

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

Definition at line 227 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.

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 239 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.

getParent()

MsRunDataSetTreeNode * pappso::MsRunDataSetTreeNode::getParent

(

)

const

Definition at line 95 of file msrundatasettreenode.cpp.

{
  // qDebug();
 
  return mp_parent;
}

References mp_parent.

getQualifiedMassSpectrum()

QualifiedMassSpectrumCstSPtr pappso::MsRunDataSetTreeNode::getQualifiedMassSpectrum

(

)

const

Definition at line 81 of file msrundatasettreenode.cpp.

{
  return mcsp_massSpectrum;
}

References mcsp_massSpectrum.

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.

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 m_children, mcsp_massSpectrum, mp_parent, and MsRunDataSetTreeNode().

precursorIonNodesByPrecursorMz()

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

Definition at line 319 of file msrundatasettreenode.cpp.

{
  if(precision_ptr == nullptr)
    qFatal(
      "Fatal error at %s@%d -- %s(). "
      "precision_ptr cannot be nullptr."
      "Program aborted.",
      __FILE__,
      __LINE__,
      __FUNCTION__);
 
 
  // 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())
            qFatal(
              "Fatal error at %s@%d -- %s(). "
              "."
              "Program aborted.",
              __FILE__,
              __LINE__,
              __FUNCTION__);
 
          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 findNode(), m_children, mcsp_massSpectrum, and pappso::mz.

productNodesByPrecursorMz()

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

Definition at line 269 of file msrundatasettreenode.cpp.

{
  if(precision_ptr == nullptr)
    qFatal(
      "Fatal error at %s@%d -- %s(). "
      "precision_ptr cannot be nullptr."
      "Program aborted.",
      __FILE__,
      __LINE__,
      __FUNCTION__);
 
 
  // 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 m_children, mcsp_massSpectrum, and pappso::mz.

setParent()

void pappso::MsRunDataSetTreeNode::setParent

(

MsRunDataSetTreeNode *

parent

)

Definition at line 88 of file msrundatasettreenode.cpp.

{
  mp_parent = parent;
}

References mp_parent.

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.

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.

toString()

QString pappso::MsRunDataSetTreeNode::toString

(

)

const

Definition at line 448 of file msrundatasettreenode.cpp.

{
  return 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());
}

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

Friends And Related Function Documentation

MsRunDataSetTree

friend class MsRunDataSetTree

friend

Definition at line 34 of file msrundatasettreenode.h.

Member Data Documentation

m_children

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

private

Definition at line 95 of file msrundatasettreenode.h.

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

mcsp_massSpectrum

QualifiedMassSpectrumCstSPtr pappso::MsRunDataSetTreeNode::mcsp_massSpectrum = nullptr

private

Definition at line 91 of file msrundatasettreenode.h.

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

---

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

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