Package de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml

Class SBMLSpeciesHelper

java.lang.Object
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLNodesNiceIdHelper
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper
public class SBMLSpeciesHelper
extends SBMLNodesNiceIdHelper

  • Field Details

  • Constructor Details

    • SBMLSpeciesHelper

      public SBMLSpeciesHelper​(Graph g)
      Constructor. Initializes the graph
      Parameters:
      g - the graph where the information is read from

  • Method Details

    • getSpeicesClones

      public Map<String,​List<Node>> getSpeicesClones()

    • getSpeciesNode

      public Node getSpeciesNode​(String layoutId, String speciesId)

    • addCloneToList

      public void addCloneToList​(String speciesId, Node speciesNode)

    • getCompartmentName

      public String getCompartmentName​(Node speciesNode)

    • getSpeciesNodes

      public List<Node> getSpeciesNodes()
      Returns all species nodes of the graph
      Returns:
      a list of all species nodes of the graph

    • getSpeciesNode

      public static Node getSpeciesNode​(String id)
      Returns the species with a distinct id
      Parameters:
      id - the id of the asked node
      Returns:
      the node with a certain id or null if no node has this id

    • isSetCompartment

      public Boolean isSetCompartment​(Node speciesNode)
      Indicates if the compartment id of a species is set
      Parameters:
      node - the node where the information is read from
      Returns:
      true if the compartment id is set else false

    • isSetID

      public Boolean isSetID​(Node speciesNode)
      Indicates if the id of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if the id is set else false

    • isSetName

      public Boolean isSetName​(Node speciesNode)
      Indicates if the name of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if the name is set else false

    • isSetInitialAmount

      public Boolean isSetInitialAmount​(Node speciesNode)
      Indicates if the initial amount of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if the initial amount is set else false

    • isSetInitialConcentration

      public Boolean isSetInitialConcentration​(Node speciesNode)
      Indicates if the initial concentration of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if the initial concentration is set else false

    • isSetSubstanceUnits

      public Boolean isSetSubstanceUnits​(Node speciesNode)
      Indicates if substance units of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if substance units is set else false

    • isSetHasOnlySubstanceUnits

      public Boolean isSetHasOnlySubstanceUnits​(Node speciesNode)
      Indicates if hasOnlySubstanceUnits of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if hasOnlySubstanceUnits is set else false

    • isSetBoundaryCondition

      public Boolean isSetBoundaryCondition​(Node speciesNode)
      Indicates if boundary condition of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if boundary condition is set else false

    • isSetConstant

      public Boolean isSetConstant​(Node speciesNode)
      Indicates if constant of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if constant is set else false

    • isSetConversionFactor

      public Boolean isSetConversionFactor​(Node speciesNode)
      Indicates if conversion factor of a species is set
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      true if conversion factor is set else false

    • getCompartment

      public String getCompartment​(Node speciesNode)
      Returns the compartment id of a species
      Parameters:
      Node - the node where the information is read from
      Returns:
      the compartment id if it is set else the empty string

    • getID

      public String getID​(Node speciesNode)
      Returns the id of the species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      the species id if it is set else the empty string

    • getName

      public String getName​(Node speciesNode)
      Returns the name of the species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      the species name if it is set else the empty string

    • getInitialAmount

      public Double getInitialAmount​(Node speciesNode)
      Returns the initial amount of a species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      initial amount if it is set else null

    • getInitialConcentration

      public Double getInitialConcentration​(Node speciesNode)
      Returns the initial concentration of a species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      initial concentration if it is set else null

    • getSubstanceUnits

      public String getSubstanceUnits​(Node speciesNode)
      Returns the substance units of a species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      substance Units if it is set else the empty string

    • getHasOnlySubstanceUnits

      public Boolean getHasOnlySubstanceUnits​(Node speciesNode)
      Returns the boolean value hasOnlySubstanceUnits of the species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      a boolean value if the attribute hasOnlySubstanceUnits is set else null

    • getBoundaryCondition

      public Boolean getBoundaryCondition​(Node speciesNode)
      Returns the boolean value boundaryCondition of the species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      a boolean value if the attribute boundaryCondition is set else null

    • getConstant

      public Boolean getConstant​(Node speciesNode)
      Returns the boolean value constant of the species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      a boolean value if the attribute constant is set else null

    • getConversionFactor

      public String getConversionFactor​(Node speciesNode)
      Returns the conversion factor units of a species
      Parameters:
      speciesNode - the node where the information is read from
      Returns:
      conversion factor if it is set else null

    • setID

      public void setID​(Node speciesNode, String id)
      Sets the id of a species node
      Parameters:
      speciesNode - where the information should be read in
      id - the id to set

    • setLabel

      public void setLabel​(Node speciesNode, String name, String id, PositionGridGenerator pgg)
      Sets the label of a node. The id string will be the label if name is not set
      Parameters:
      speciesNode - where the information should be read in
      name - the name to set
      id - will be set if name is empty
      pgg - helps to set the position of the node

    • setCompartment

      public void setCompartment​(Node speciesNode, String compartment)
      Sets the compartment of a node
      Parameters:
      speciesNode - the compartment belongs to this node
      compartment - the id of the compartment that will be set

    • setCompartmentName

      public void setCompartmentName​(Node speciesNode)

    • setInitialAmount

      public void setInitialAmount​(Node speciesNode, Double initialAmount)
      Sets the initial amount of a node
      Parameters:
      speciesNode - the initial amount belongs to this node
      initialAmount - the value that will be set

    • setInitialConcentration

      public void setInitialConcentration​(Node speciesNode, Double initialConcentration)
      Sets the initial concentration of a node
      Parameters:
      speciesNode - the initial concentration belongs to this node
      initialConcentration - the value that will be set

    • setSubstanceUnits

      public void setSubstanceUnits​(Node speciesNode, String substanceUnits)
      Sets the substance units of a species node
      Parameters:
      speciesNode - the substance units belong to this node
      substanceUnits - the substance units to set

    • setHasOnlySubstanceUnits

      public void setHasOnlySubstanceUnits​(Node speciesNode, Boolean hasOnlySubstanceUnits)
      Sets the attribute hasOnlySubstanceUnits of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      hasOnlySubstanceUnits - the value that will be set

    • setBoundaryConsition

      public void setBoundaryConsition​(Node speciesNode, Boolean boundaryCondition)
      Sets the attribute boundary condition of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      boundaryCondition - the value that will be set

    • setConstant

      public void setConstant​(Node speciesNode, Boolean constant)
      Sets the attribute constant of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      constant - the value that will be set

    • setConversionFactor

      public void setConversionFactor​(Node speciesNode, String conversionFactor)
      Sets the attribute conversion factor of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      conversionFactor - the value that will be set

    • setMetaID

      public void setMetaID​(Node speciesNode, String metaID)
      Sets the attribute meta id of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      metaID - the value that will be set

    • isSetMetaID

      public Boolean isSetMetaID​(Node speciesNode)

    • deleteMetaID

      public void deleteMetaID​(Node speciesNode)

    • getMetaID

      public String getMetaID​(Node speciesNode)

    • setAnnotation

      public void setAnnotation​(Node speciesNode, org.sbml.jsbml.Annotation annotation)

    • isSetAnnotation

      public Boolean isSetAnnotation​(Node speciesNode)

    • deleteAnnotation

      public void deleteAnnotation​(Node speciesNode)

    • getAnnotation

      public org.sbml.jsbml.Annotation getAnnotation​(Node speciesNode)

    • setNonRDFAnnotation

      public void setNonRDFAnnotation​(Node speciesNode, org.sbml.jsbml.xml.XMLNode xmlNode)

    • isSetNonRDFAnnotation

      public Boolean isSetNonRDFAnnotation​(Node speciesNode)

    • deleteNonRDFAnnotation

      public void deleteNonRDFAnnotation​(Node speciesNode)

    • getNonRDFAnnotation

      public org.sbml.jsbml.Annotation getNonRDFAnnotation​(Node speciesNode)

    • setSBOTerm

      public void setSBOTerm​(Node speciesNode, String sboTerm)
      Sets the attribute sboTerm of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      sboTerm - the value that will be set

    • isSetSBOTerm

      public Boolean isSetSBOTerm​(Node speciesNode)

    • deleteSBOTerm

      public void deleteSBOTerm​(Node speciesNode)

    • getSBOTerm

      public String getSBOTerm​(Node speciesNode)

    • setNotes

      public void setNotes​(Node speciesNode, String notes, org.sbml.jsbml.xml.XMLNode notesObj)
      Sets the attribute notes of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      notes - the value that will be set
      notesObj - the Object that will be set

    • isSetNotes

      public Boolean isSetNotes​(Node speciesNode)

    • deleteNotes

      public void deleteNotes​(Node speciesNode)

    • getNotes

      public org.sbml.jsbml.xml.XMLNode getNotes​(Node speciesNode)

    • setCharge

      public void setCharge​(Node speciesNode, Integer charge)
      Sets the deprecated attribute charge of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      charge - the value that will be set

    • setHiddenLabel

      public void setHiddenLabel​(Node speciesNode, String id)
      Sets the hidden label of a species node
      Parameters:
      speciesNode - where the attribute is going to be added
      id - the value that will be set