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

Class SBMLReactionHelper

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

  • Constructor Details

    • SBMLReactionHelper

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

  • Method Details

    • getReactionClones

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

    • getReactantClones

      public Map<ReactionIDSpeciesIDWrapper,​List<Edge>> getReactantClones()

    • getProductClones

      public Map<ReactionIDSpeciesIDWrapper,​List<Edge>> getProductClones()

    • getModifierClones

      public Map<ReactionIDSpeciesIDWrapper,​List<Edge>> getModifierClones()

    • getReactionNode

      public Node getReactionNode​(String layoutId, String reactionId)

    • addReactionCloneToList

      public void addReactionCloneToList​(String reactionId, Node reactionNode)

    • addReactantCloneToList

      public void addReactantCloneToList​(String reactionId, String speciesId, Edge reactantEdge)

    • addProductCloneToList

      public void addProductCloneToList​(String reactionId, String speciesId, Edge reactantEdge)

    • addModifierCloneToList

      public void addModifierCloneToList​(String reactionId, String speciesId, Edge reactantEdge)

    • isSetCompartment

      public Boolean isSetCompartment​(Node reactionNode)

    • isSetFast

      public Boolean isSetFast​(Node reactionNode)

    • isSetReversible

      public Boolean isSetReversible​(Node reactionNode)

    • isSetName

      public Boolean isSetName​(Node reactionNode)

    • isSetID

      public Boolean isSetID​(Node reactionNode)

    • getID

      public String getID​(Node reactionNode)

    • getName

      public String getName​(Node reactionNode)

    • getReversible

      public Boolean getReversible​(Node reactionNode)

    • getFast

      public Boolean getFast​(Node reactionNode)

    • getCompartment

      public String getCompartment​(Node reactionNode)

    • setID

      public void setID​(Node reactionNode, String ID)

    • setLabel

      public void setLabel​(Node reactionNode, String name, String id, PositionGridGenerator pgg)

    • setReversible

      public void setReversible​(Node reactionNode, Boolean reversible)

    • setFast

      public void setFast​(Node reactionNode, Boolean fast)

    • setCompartment

      public void setCompartment​(Node reactionNode, String compartment)

    • setMetaID

      public void setMetaID​(Node reactionNode, String metaID)

    • isSetMetaID

      public Boolean isSetMetaID​(Node reactionNode)

    • deleteMetaID

      public void deleteMetaID​(Node reactinNode)

    • getMetaID

      public String getMetaID​(Node reactionNode)

    • deleteSBOTerm

      public void deleteSBOTerm​(Node reactinNode)

    • setSBOTerm

      public void setSBOTerm​(Node reactionNode, String sboTerm)

    • isSetSBOTerm

      public Boolean isSetSBOTerm​(Node reactionNode)

    • getSBOTerm

      public String getSBOTerm​(Node reactionNode)

    • setAnnotation

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

    • getAnnotation

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

    • deleteAnnotation

      public void deleteAnnotation​(Node reactinNode)

    • isSetAnnotation

      public Boolean isSetAnnotation​(Node reactionNode)

    • setNonRDFAnnotation

      public void setNonRDFAnnotation​(Node reactionNode, org.sbml.jsbml.xml.XMLNode nonRDFAnnotation)

    • getNonRDFAnnotation

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

    • deleteNonRDFAnnotation

      public void deleteNonRDFAnnotation​(Node reactinNode)

    • isSetNonRDFAnnotation

      public Boolean isSetNonRDFAnnotation​(Node reactionNode)

    • setNotes

      public void setNotes​(Node reactionNode, String notes, org.sbml.jsbml.xml.XMLNode notesObj)

    • getNotes

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

    • isSetNotes

      public Boolean isSetNotes​(Node reactionNode)

    • deleteNotes

      public void deleteNotes​(Node reactinNode)

    • setSpecies

      public void setSpecies​(Edge reactionEdge, String species)

    • setID

      public void setID​(Edge reactionEdge, String ID)

    • setName

      public void setName​(Edge reactionEdge, String name)

    • isSetSpecies

      public Boolean isSetSpecies​(Edge reactionEdge)

    • isSetID

      public Boolean isSetID​(Edge reactionEdge)

    • isSetName

      public Boolean isSetName​(Edge reactionEdge)

    • getSpecies

      public String getSpecies​(Edge reactionEdge)

    • getName

      public String getName​(Edge reactionEdge)

    • getID

      public String getID​(Edge reactionEdge)

    • setMetaIDReactant

      public void setMetaIDReactant​(Edge reactionEdge, String metaID)

    • getMetaIDReactant

      public String getMetaIDReactant​(Edge edge)

    • deleteMetaIDReactant

      public void deleteMetaIDReactant​(Edge edge)

    • isSetMetaIDReactant

      public Boolean isSetMetaIDReactant​(Edge edge)

    • setMetaIDProduct

      public void setMetaIDProduct​(Edge reactionEdge, String metaID)

    • getMetaIDProduct

      public String getMetaIDProduct​(Edge edge)

    • deleteMetaIDProduct

      public void deleteMetaIDProduct​(Edge edge)

    • isSetMetaIDProduct

      public Boolean isSetMetaIDProduct​(Edge edge)

    • setMetaIDModifier

      public void setMetaIDModifier​(Edge reactionEdge, String metaID)

    • getMetaIDModifier

      public String getMetaIDModifier​(Edge edge)

    • deleteMetaIDModifier

      public void deleteMetaIDModifier​(Edge edge)

    • isSetMetaIDModifier

      public Boolean isSetMetaIDModifier​(Edge edge)

    • setSBOTermReactant

      public void setSBOTermReactant​(Edge reactionEdge, String sboTerm)

    • getSBOTermReactant

      public String getSBOTermReactant​(Edge edge)

    • deleteSBOTermReactant

      public void deleteSBOTermReactant​(Edge edge)

    • isSetSBOTermReactant

      public Boolean isSetSBOTermReactant​(Edge edge)

    • setSBOTermProduct

      public void setSBOTermProduct​(Edge reactionEdge, String sboTerm)

    • getSBOTermProduct

      public String getSBOTermProduct​(Edge edge)

    • deleteSBOTermProduct

      public void deleteSBOTermProduct​(Edge edge)

    • isSetSBOTermProduct

      public Boolean isSetSBOTermProduct​(Edge edge)

    • setSBOTermModifier

      public void setSBOTermModifier​(Edge reactionEdge, String sboTerm)

    • getSBOTermModifier

      public String getSBOTermModifier​(Edge edge)

    • deleteSBOTermModifier

      public void deleteSBOTermModifier​(Edge edge)

    • isSetSBOTermModifier

      public Boolean isSetSBOTermModifier​(Edge edge)

    • setAnnotationProduct

      public void setAnnotationProduct​(Edge reactionEdge, org.sbml.jsbml.Annotation annotation)

    • getAnnotationProduct

      public org.sbml.jsbml.Annotation getAnnotationProduct​(Edge edge)

    • deleteAnnotationProduct

      public void deleteAnnotationProduct​(Edge edge)

    • isSetAnnotationProduct

      public Boolean isSetAnnotationProduct​(Edge edge)

    • setNonRDFAnnotationProduct

      public void setNonRDFAnnotationProduct​(Edge reactionEdge, org.sbml.jsbml.xml.XMLNode xmlNode)

    • getNonRDFAnnotationProduct

      public org.sbml.jsbml.xml.XMLNode getNonRDFAnnotationProduct​(Edge edge)

    • deleteNonRDFAnnotationProduct

      public void deleteNonRDFAnnotationProduct​(Edge edge)

    • isSetNonRDFAnnotationProduct

      public Boolean isSetNonRDFAnnotationProduct​(Edge edge)

    • setAnnotationModifier

      public void setAnnotationModifier​(Edge reactionEdge, org.sbml.jsbml.Annotation annotation)

    • getAnnotationModifier

      public org.sbml.jsbml.Annotation getAnnotationModifier​(Edge edge)

    • deleteAnnotationModifier

      public void deleteAnnotationModifier​(Edge edge)

    • isSetAnnotationModifier

      public Boolean isSetAnnotationModifier​(Edge edge)

    • setNonRDFAnnotationModifier

      public void setNonRDFAnnotationModifier​(Edge reactionEdge, org.sbml.jsbml.xml.XMLNode xmlNode)

    • getNonRDFAnnotationModifier

      public org.sbml.jsbml.xml.XMLNode getNonRDFAnnotationModifier​(Edge edge)

    • deleteNonRDFAnnotationModifier

      public void deleteNonRDFAnnotationModifier​(Edge edge)

    • isSetNonRDFAnnotationModifier

      public Boolean isSetNonRDFAnnotationModifier​(Edge edge)

    • setAnnotationReactant

      public void setAnnotationReactant​(Edge reactionEdge, org.sbml.jsbml.Annotation annotation)

    • getAnnotationReactant

      public org.sbml.jsbml.Annotation getAnnotationReactant​(Edge edge)

    • deleteAnnotationReactant

      public void deleteAnnotationReactant​(Edge edge)

    • isSetAnnotationReactant

      public Boolean isSetAnnotationReactant​(Edge edge)

    • setNonRDFAnnotationReactant

      public void setNonRDFAnnotationReactant​(Edge reactionEdge, org.sbml.jsbml.xml.XMLNode xmlNode)

    • getNonRDFAnnotationReactant

      public org.sbml.jsbml.xml.XMLNode getNonRDFAnnotationReactant​(Edge edge)

    • deleteNonRDFAnnotationReactant

      public void deleteNonRDFAnnotationReactant​(Edge edge)

    • isSetNonRDFAnnotationReactant

      public Boolean isSetNonRDFAnnotationReactant​(Edge edge)

    • setNotesReactant

      public void setNotesReactant​(Edge reactionEdge, String notes, org.sbml.jsbml.xml.XMLNode notesObj)

    • getNotesReactant

      public Object getNotesReactant​(Edge edge)

    • deleteNotesReactant

      public void deleteNotesReactant​(Edge edge)

    • isSetNotesReactant

      public Boolean isSetNotesReactant​(Edge edge)

    • setNotesProduct

      public void setNotesProduct​(Edge reactionEdge, String notes, org.sbml.jsbml.xml.XMLNode notesObj)

    • getNotesProduct

      public Object getNotesProduct​(Edge edge)

    • deleteNotesProduct

      public void deleteNotesProduct​(Edge edge)

    • isSetNotesProduct

      public Boolean isSetNotesProduct​(Edge edge)

    • setNotesModifier

      public void setNotesModifier​(Edge reactionEdge, String notes, org.sbml.jsbml.xml.XMLNode notesObj)

    • getNotesModifier

      public Object getNotesModifier​(Edge edge)

    • deleteNotesModifier

      public void deleteNotesModifier​(Edge edge)

    • isSetNotesModifier

      public Boolean isSetNotesModifier​(Edge edge)

    • isSetStoichiometry

      public Boolean isSetStoichiometry​(Edge reactionEdge)

    • isSetConstant

      public Boolean isSetConstant​(Edge reactionEdge)

    • getStoichiometry

      public String getStoichiometry​(Edge reactionEdge)

    • getConstant

      public Boolean getConstant​(Edge reactionEdge)

    • setStoichiometry

      public void setStoichiometry​(Edge reactionEdge, Double stoichiometry)

    • setConstant

      public void setConstant​(Edge reactionEdge, Boolean constant)