Class PPNode

    • Constructor Detail

      • PPNode

        public PPNode()
      • PPNode

        public PPNode​(PPNode node)
    • Method Detail

      • add

        public void add​(int interactionType)
        Caution! After finishing all adding's realize() has to be called!
        Parameters:
        interactionType -
      • addAtoms

        public void addAtoms​(PPNode node)
        Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
        Parameters:
        node -
      • compareTo

        public int compareTo​(PPNode o)
        Specified by:
        compareTo in interface java.lang.Comparable<PPNode>
      • containsInteractionID

        public boolean containsInteractionID​(int interactid)
      • copy

        public void copy​(PPNode node)
        Copy of node into this.
        Parameters:
        node -
      • getCopy

        public PPNode getCopy()
        node deep copy.
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object
      • realize

        public void realize()
        May be called after finishing adding new interaction types.
      • equalAtoms

        public boolean equalAtoms​(PPNode node)
        realize() may be called first.
        Parameters:
        node -
        Returns:
      • get

        public byte[] get()
      • getInteractionTypeCount

        public int getInteractionTypeCount()
        realize() may be called first.
        Specified by:
        getInteractionTypeCount in interface IPPNode
        Returns:
      • getInteractionTypeFromByteArray

        protected static int getInteractionTypeFromByteArray​(byte low,
                                                             byte med,
                                                             byte high)
      • getAtomicNo

        public int getAtomicNo​(int i)
      • isAromatic

        public boolean isAromatic​(int i)
      • getAtomicNoFromInteractionType

        public static int getAtomicNoFromInteractionType​(int interactionType)
      • getDummy

        public static PPNode getDummy()
      • isCarbonExclusiveNode

        public boolean isCarbonExclusiveNode()
      • set

        public void set​(byte[] arrInteractionType,
                        byte size)
        Flat copy from node into this.
        Parameters:
        arrInteractionType -
        size -
      • getModeFlexophore

        public byte getModeFlexophore()
      • setModeFlexophore

        public void setModeFlexophore​(byte modeFlexophore)
      • sortInteractionTypes

        public void sortInteractionTypes()
      • getFractionCarbonInteractions

        public double getFractionCarbonInteractions()
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • getHeteroOnlyNode

        public static PPNode getHeteroOnlyNode​(PPNode node)
      • toStringLong

        public java.lang.String toStringLong()
      • toStringLongHardPPPoint

        public java.lang.String toStringLongHardPPPoint()
      • read

        public static PPNode read​(java.lang.String strNode)
        Parameters:
        strNode - i.e. 262,392,4358*2,8582,590088,598407
        Returns:
      • getNumBytesEntry

        public static int getNumBytesEntry()