Serialized Form

  • Package moss

    • Class moss.AtomTypeMgr

      class AtomTypeMgr extends TypeMgr implements Serializable
      serialVersionUID:
      65536L
    • Class moss.BondTypeMgr

      class BondTypeMgr extends TypeMgr implements Serializable
      serialVersionUID:
      65536L
    • Class moss.CanonicalForm

      class CanonicalForm extends Object implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • all
          long all
          all (remaining) ring flags of the current edge
        • cedge
          int cedge
          the edge type for chain extensions
        • chcnt
          int chcnt
          the number of variable length chains
        • cnode
          int cnode
          the node type for chain extensions
        • curr
          long curr
          the current ring flag
        • dir
          boolean dir
          whether the graphs are to be treated as directed
        • dst
          int dst
          the index of the current destination node
        • edgecnt
          int edgecnt
          the number of new edges
        • edges
          Edge[] edges
          (relevant) edges of the extension
        • emap
          int[] emap
          the edge map for making a graph canonic
        • emb
          Embedding emb
          the embedding that is extended (may be null)
        • fixed
          int fixed
          the number of fixed edges in a canonical form test
        • frag
          Fragment frag
          the fragment that is extended
        • idx
          int idx
          the current edge index in the source node
        • max
          int max
          the maximum fragment size (number of nodes)
        • mode
          int mode
          the extension mode (e.g. EDGE, RING)
        • nmap
          int[] nmap
          the node map for making a graph canonic
        • nodecnt
          int nodecnt
          the number of new nodes
        • nodes
          Node[] nodes
          (relevant) nodes of the extension
        • pmax
          int pmax
          the maximal position/position index of a ring edge
        • pmin
          int pmin
          the minimal position/current position index of a ring edge
        • pos1
          int pos1
          the current position 1 of equivalent edges for ring extensions
        • pos2
          int pos2
          the current position 2 of equivalent edges for ring extensions
        • rgmax
          int rgmax
          the maximum ring size (number of nodes/edges)
        • rgmin
          int rgmin
          the minimum ring size (number of nodes/edges)
        • size
          int size
          the number of nodes in a ring (positive) or chain (negative)
        • src
          int src
          the index of the current source node
        • sym
          boolean sym
          whether the current ring is locally symmetric
        • type
          int type
          the type of the extension edge (from EDGE.type)
        • word
          int[] word
          the code word for isCanonic/makeCanonic
        • xemgr
          ExtMgr xemgr
          the extension edge manager (for extensions without embeddings)
    • Class moss.CnFBreadth1

      class CnFBreadth1 extends CanonicalForm implements Serializable
      serialVersionUID:
      65536L
    • Class moss.CnFBreadth2

      class CnFBreadth2 extends CanonicalForm implements Serializable
      serialVersionUID:
      65536L
    • Class moss.CnFDepth

      class CnFDepth extends CanonicalForm implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • eqpos
          int[] eqpos
          the equivalent positions for a new ring edge
        • path
          int[] path
          the indices of the edges on the rightmost path
        • pei
          int pei
          the index of the next path edge
    • Class moss.Ctab

      class Ctab extends MoleculeNtn implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • buf
          int[] buf
          the buffer for number reading
    • Class moss.Edge

      class Edge extends Object implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • dst
          Node dst
          the destination node of the edge
        • flags
          long flags
          the flags for rings and bridges
        • mark
          int mark
          a marker for internal use (e.g. for a substructure)
        • src
          Node src
          the source node of the edge
        • type
          int type
          the type of the edge, e.g. SINGLE
    • Class moss.EdgePatternMgr

      class EdgePatternMgr extends Object implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • base
          int base
          the base support (largest possible support)
        • bins
          moss.EdgePattern[] bins
          the hash table of the extension edges
        • cnt
          int cnt
          the number of added edge patterns (full and partial)
        • dir
          boolean dir
          whether edges are to be treated as directed
        • supps
          int[] supps
          the support values for each edge type
    • Class moss.Embedding

      class Embedding extends Object implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • edges
          Edge[] edges
          the array of edges (only references to the underlying graph)
        • graph
          Graph graph
          the graph referred to
        • nodes
          Node[] nodes
          the array of nodes (only references to the underlying graph)
        • succ
          Embedding succ
          the next embedding in a list of embeddings
    • Class moss.ExtMgr

      class ExtMgr extends Object implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • bins
          moss.ExtEdge[] bins
          the hash table of the extension edges
        • cnt
          int cnt
          the number of added extension edges (with reversals)
        • curr
          moss.ExtEdge curr
          the current extension edge
        • dir
          boolean dir
          whether edges are to be treated as directed
        • exts
          moss.ExtEdge[] exts
          the table for access via the source node type
    • Class moss.Fragment

      class Fragment extends Object implements Serializable
      serialVersionUID:
      65541L
      • Serialized Fields

        • base
          Fragment base
          the base fragment (which was extended)
        • bemb
          Embedding bemb
          the current base embedding (which was extended)
        • chcnt
          int chcnt
          the number of variable length chains
        • cnt
          int cnt
          the number of embeddings/graphs for the current graph
        • cover
          NamedGraph[] cover
          the graph cover of the fragment
        • curr
          Embedding curr
          the current embedding (cursor)
        • dir
          boolean dir
          whether the fragment is directed
        • dst
          int dst
          the index of the destination node of the (first) new edge
        • flags
          int flags
          the property flags of the embedding (e.g. PERFECT)
        • graph
          Graph graph
          the fragment as a graph
        • hash
          int hash
          the hash code of the fragment (or -1 if not computed yet)
        • idx
          int idx
          the index of the (first) new edge
        • list
          Embedding list
          the list of embeddings of the fragment
        • max
          int max
          the maximal number of embeddings per graph
        • ris
          int[] ris
          the indices of the nodes of new ring edges
        • size
          int size
          the number of nodes in a ring or chain (positive: ring, negative: chain)
        • src
          int src
          the index of the source node of the (first) new edge
        • supp
          int[] supp
          the support and embedding counters for focus and complement
        • tail
          Embedding tail
          the tail of the embedding list
    • Class moss.FreeNtn

      class FreeNtn extends Notation implements Serializable
      serialVersionUID:
      65536L
    • Class moss.FreeTypeMgr

      class FreeTypeMgr extends TypeMgr implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • bins
          moss.Type[] bins
          the array of hash bins (name to code map)
        • imap
          moss.Type[] imap
          the inverse map (code to name map)
        • size
          int size
          the current number of types
    • Class moss.Graph

      class Graph extends Object implements Serializable
      serialVersionUID:
      65542L
      • Serialized Fields

        • coder
          Recoder coder
          an optional node type recoder
        • dir
          boolean dir
          whether the graph is directed
        • edgecnt
          int edgecnt
          the current number of edges (may be smaller than the array length)
        • edges
          Edge[] edges
          the array of edges (may be only partially used)
        • nodecnt
          int nodecnt
          the current number of nodes (may be smaller than the array length)
        • nodes
          Node[] nodes
          the array of nodes (may be only partially used)
        • ntn
          Notation ntn
          the notation for describing the graph
    • Class moss.GraphReader

      class GraphReader extends TableReader implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • cabs
          int cabs
          the absolute support in the complement
        • crel
          float crel
          the relative support in the complement
        • desc
          String desc
          the description of the current graph
        • edges
          int edges
          the number of edges of the current graph
        • graph
          Graph graph
          the current graph
        • mode
          int mode
          the read mode
        • name
          String name
          the name/identifier of the current graph
        • nodes
          int nodes
          the number of nodes of the current graph
        • ntn
          Notation ntn
          the notation for parsing graph descriptions
        • sabs
          int sabs
          the absolute support in the focus
        • srel
          float srel
          the relative support in the focus
        • value
          float value
          the value associated with the current graph
    • Class moss.GraphWriter

      class GraphWriter extends TableWriter implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • cabs
          int cabs
          the absolute support in the complement
        • crel
          float crel
          the relative support in the complement
        • desc
          String desc
          the description of the current graph
        • edges
          int edges
          the number of edges of the current graph
        • graph
          Graph graph
          the current graph
        • mode
          int mode
          the write mode
        • name
          String name
          the name of the current graph
        • nodes
          int nodes
          the number of nodes of the current graph
        • ntn
          Notation ntn
          the notation for the graphs
        • sabs
          int sabs
          the absolute support in the focus
        • srel
          float srel
          the relative support in the focus
        • value
          float value
          the value associated with the current graph
    • Class moss.LineReader

      class LineReader extends GraphReader implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • pbrec
          boolean pbrec
          whether there is a pushed back record
        • record
          String[] record
          the fields of a record
    • Class moss.LineWriter

      class LineWriter extends GraphWriter implements Serializable
      serialVersionUID:
      65536L
    • Class moss.LiNoG

      class LiNoG extends FreeNtn implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • buf
          StringBuilder buf
          the buffer for reading and creating node descriptions
        • coder
          Recoder coder
          the node type recoder for a graph to describe
        • desc
          StringBuilder desc
          the buffer for creating graph descriptions
        • graph
          Graph graph
          the parsed graph
        • labels
          int[] labels
          the label to node index map
    • Class moss.Miner

      class Miner extends Object implements Serializable
      serialVersionUID:
      524291L
      • Serialized Fields

        • bins
          moss.RepoElem[] bins
          the repository of processed substructures (hash table)
        • canonic
          long canonic
          for benchmarking: canonical form pruning counter
        • chains
          long chains
          for benchmarking: invalid chains counter
        • cnf
          CanonicalForm cnf
          the canonical form and restricted extension generator
        • cnts
          int[] cnts
          the numbers of graphs in focus and complement
        • coder
          Recoder coder
          the recoder for the node types
        • comp
          int comp
          the maximum support in the complement as an absolute value
        • conf
          double conf
          the minimum confidence of an association rule as a fraction
        • curr
          NamedGraph curr
          the current insertion point for the focus
        • duplic
          long duplic
          for benchmarking: duplicate fragments counter
        • embcmp
          long embcmp
          for benchmarking: the number of comparisons with embeddings
        • embcnt
          long embcnt
          for benchmarking: the number of created embeddings
        • emblvl
          int emblvl
          the level at which to switch to embeddings
        • epmgr
          EdgePatternMgr epmgr
          the edge pattern manager (if needed, for rule generation)
        • equiv
          long equiv
          for benchmarking: equivalent frag. pruning counter
        • error
          Throwable error
          the error status for the search process
        • exseed
          Graph exseed
          the node types that are excluded as seeds
        • extype
          Graph extype
          the excluded node types
        • fcomp
          double fcomp
          the maximum support in the complement as a fraction
        • frag
          Fragment frag
          the initial fragment (embedded seed structure)
        • fragcmp
          long fragcmp
          for benchmarking: the number of fragment comparisons
        • fragcnt
          long fragcnt
          for benchmarking: the number of created fragments
        • fsupp
          double fsupp
          the minimum support in the focus as a fraction
        • graphs
          NamedGraph graphs
          the list of graphs to mine (database)
        • group
          int group
          the group for graphs with a value below the threshold
        • invalid
          long invalid
          for benchmarking: invalid fragments counter
        • isocnt
          long isocnt
          for benchmarking: the number of isomorphism tests
        • lowsupp
          long lowsupp
          for benchmarking: insufficient support pruning counter
        • masks
          int[] masks
          the masks for nodes and edges
        • max
          int max
          the maximum size of substructures to report (number of nodes)
        • maxdepth
          int maxdepth
          for benchmarking: the maximum depth of the search tree
        • maxepg
          int maxepg
          the maximum number of embeddings per graph
        • min
          int min
          the minimum size of substructures to report (number of nodes)
        • mode
          int mode
          the search mode flags
        • nodecnt
          long nodecnt
          for benchmarking: the number of search tree nodes
        • nonclsd
          long nonclsd
          for benchmarking: non-closed fragments counter
        • norm
          CanonicalForm norm
          the canonical form for normalizing the output
        • openrgs
          long openrgs
          for benchmarking: open ring fragments counter
        • pats
          moss.GraphPattern pats
          the list of found patterns for rule generation
        • perfect
          long perfect
          for benchmarking: perfect extension pruning counter
        • reader
          GraphReader reader
          the graph data set file reader
        • recnt
          int recnt
          the size of the repository (number of substructures)
        • repcnt
          long repcnt
          for benchmarking: the number of repository accesses
        • rgmax
          int rgmax
          the maximum size of rings (number of nodes/edges)
        • rgmin
          int rgmin
          the minimum size of rings (number of nodes/edges)
        • ringord
          long ringord
          for benchmarking: ring order pruning counter
        • seed
          Graph seed
          the seed structure to start the search from
        • stop
          boolean stop
          whether to abort the search thread
        • subcnt
          int subcnt
          the number of reported substructures
        • supp
          int supp
          the minimum support in the focus as an absolute value
        • tail
          NamedGraph tail
          the tail of the list of graphs (insertion point for complement)
        • thresh
          double thresh
          the threshold for the split into focus and complement
        • type
          int type
          the type of support to use
        • vntn
          Notation vntn
          the notation for verbose output
        • writer
          GraphWriter writer
          the substructure file writer
    • Class moss.MoleculeNtn

      class MoleculeNtn extends Notation implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • desc
          StringBuilder desc
          the buffer for creating molecule descriptions
    • Class moss.MoSS

      class MoSS extends JFrame implements Serializable
      serialVersionUID:
      196608L
      • Serialized Fields

        • aborted
          boolean aborted
          whether the miner has been aborted
        • abssupp
          JCheckBox abssupp
          whether to interpret the support as absolute numbers
        • atarom
          JCheckBox atarom
          whether to match the atom aromaticity
        • attype
          JComboBox<String> attype
          whether to ignore the atom type
        • bdarom
          JComboBox<String> bdarom
          how to treat aromatic bonds
        • bdtype
          JComboBox<String> bdtype
          whether to ignore the bond type
        • buf
          StringBuilder buf
          the buffer for reading the configuration file
        • canonic
          JCheckBox canonic
          whether to do canonical form pruning
        • chains
          JCheckBox chains
          whether to find variable length carbon chains
        • charge
          JCheckBox charge
          whether to match the atom charge
        • chooser
          JFileChooser chooser
          the file chooser for selecting the input and output files
        • closed
          JCheckBox closed
          whether to restrict the output to closed substructures
        • equiv
          JCheckBox equiv
          whether to do equivalent sibling pruning
        • exec
          JButton exec
          the execute/abort button
        • exseed
          JTextField exseed
          the node types that are excluded for seeds
        • exttype
          JComboBox<String> exttype
          the extension type
        • extype
          JTextField extype
          the excluded node types
        • fn_data
          JTextField fn_data
          the name of the input file
        • fn_ids
          JTextField fn_ids
          the name of the graph identifier file
        • fn_sub
          JTextField fn_sub
          the name of the substructure output file
        • greedy
          JCheckBox greedy
          whether to use greedy algorithm for MIS computation
        • infmt
          JComboBox<String> infmt
          the input format for the graphs
        • invert
          JCheckBox invert
          whether to invert the split
        • isprog
          boolean isprog
          whether started as a stand-alone program
        • kekule
          JCheckBox kekule
          whether to convert Kekule representations
        • level
          JSpinner level
          the level from which to use embeddings
        • maxepg
          JSpinner maxepg
          the maximal number of embeddings per graph
        • maxring
          JSpinner maxring
          the maximal size of a ring
        • maxsize
          JSpinner maxsize
          the maximal size of a substructure
        • maxsupp
          JTextField maxsupp
          the maximal support in the complement
        • miner
          Miner miner
          the current substructure miner
        • minring
          JSpinner minring
          the minimal size of a ring
        • minsize
          JSpinner minsize
          the minimal size of a substructure
        • minsupp
          JTextField minsupp
          the minimal support in the focus
        • normal
          JCheckBox normal
          whether to normalize the output
        • orbits
          JCheckBox orbits
          whether to do filter with node orbits
        • owner
          Component owner
          the owner of this dialog box
        • pane
          JTabbedPane pane
          the pane for the parameter tabs
        • perfect
          JComboBox<String> perfect
          whether to do perfect extension pruning
        • rclbls
          JLabel[] rclbls
          the labels that can be disabled in the tab
        • ringext
          JComboBox<String> ringext
          the type of ring extensions
        • rings
          JCheckBox rings
          whether to mark rings
        • running
          boolean running
          whether the miner is currently running
        • seed
          JTextField seed
          the seed structure to start the search from
        • seedfmt
          JComboBox<String> seedfmt
          the seed format
        • splbls
          JLabel[] splbls
          the labels that can be disabled in the tab
        • start
          long start
          the start time for the miner thread
        • stat
          JTextField stat
          the status line
        • subfmt
          JComboBox<String> subfmt
          the output format for the substructures
        • supptype
          JComboBox<String> supptype
          the support type
        • thresh
          JTextField thresh
          the threshold for the split
        • timer
          Timer timer
          the timer for updating the progress information
        • unembed
          JCheckBox unembed
          whether to unembed siblings of the current search tree node
        • verbose
          JCheckBox verbose
          whether to do verbose message output
    • Class moss.MoSSPanel

      class MoSSPanel extends JPanel implements Serializable
      serialVersionUID:
      131079L
    • Class moss.MoSSTable

      class MoSSTable extends AbstractTableModel implements Serializable
      serialVersionUID:
      131079L
      • Serialized Fields

        • buf
          StringBuilder buf
          the buffer for reading input lines
        • format
          String format
          the format of the table
        • mode
          int mode
          the mode of the table
        • names
          String[] names
          the names of the columns of the table
        • rowcnt
          int rowcnt
          the number of rows of the table
    • Class moss.NamedGraph

      class NamedGraph extends Graph implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • group
          int group
          the marker for grouping (either 0 or 1, used as an array index)
        • name
          String name
          the graph name/identifier
        • succ
          NamedGraph succ
          the next graph in a list
        • value
          float value
          the value associated with the graph
    • Class moss.NEList

      class NEList extends FreeNtn implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • linog
          LiNoG linog
          linear notation for creating a description
    • Class moss.NEListReader

      class NEListReader extends GraphReader implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • buf
          StringBuilder buf
          the buffer for an input field
        • linog
          Notation linog
          the notation for line descriptions
    • Class moss.NEListWriter

      class NEListWriter extends GraphWriter implements Serializable
      serialVersionUID:
      65536L
    • Class moss.Node

      class Node extends Object implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • deg
          int deg
          the current number of incident edges (node degree)
        • edges
          Edge[] edges
          the array of incident edges (may not be fully used)
        • mark
          int mark
          a marker for internal use (e.g. for a substructure)
        • orbit
          int orbit
          the representative of the orbit of the node
        • type
          int type
          the type (attribute/label) of a node (including flags)
    • Class moss.Notation

      class Notation extends Object implements Serializable
      serialVersionUID:
      65538L
      • Serialized Fields

        • cnt
          int cnt
          the number of unread/pushed back characters
        • edgemgr
          TypeMgr edgemgr
          the manager for the edge types
        • nodemgr
          TypeMgr nodemgr
          the manager for the node types
        • stack
          int[] stack
          the stack of unread/pushed back characters
    • Class moss.Recoder

      class Recoder extends Object implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • bins
          moss.RcType[] bins
          the hash table for mapping types to codes (old codes to new)
        • idx
          int idx
          the index of the current graph (for frequency counting)
        • size
          int size
          the current number of types
        • types
          moss.RcType[] types
          the types and their frequencies, sorted by their code
    • Class moss.SDfileReader

      class SDfileReader extends GraphReader implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • buf
          StringBuilder buf
          the buffer for an input line
        • smiles
          Notation smiles
          the notation for line descriptions
    • Class moss.SDfileWriter

      class SDfileWriter extends GraphWriter implements Serializable
      serialVersionUID:
      65536L
    • Class moss.SLN

      class SLN extends MoleculeNtn implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • buf
          StringBuilder buf
          the buffer for creating atom descriptions
        • coder
          Recoder coder
          the atom type recoder for a molecule to describe
        • labels
          int[] labels
          the label to node index map
        • mol
          Graph mol
          the parsed molecule
    • Class moss.SMILES

      class SMILES extends MoleculeNtn implements Serializable
      serialVersionUID:
      65536L
      • Serialized Fields

        • bonds
          int[] bonds
          the bond types of forward references
        • buf
          StringBuilder buf
          the buffer for creating atom descriptions
        • coder
          Recoder coder
          the atom type recoder for a molecule to describe
        • labels
          int[] labels
          the label to node index map
        • mol
          Graph mol
          the parsed molecule
    • Class moss.TypeMgr

      class TypeMgr extends Object implements Serializable
      serialVersionUID:
      65536L