- abort() - Method in class moss.Miner
-
Abort the miner (if running as a thread).
- ACTINIUM - Static variable in class moss.AtomTypeMgr
-
- adapt(CanonicalForm, boolean) - Method in class moss.Fragment
-
Adapt the fragment (limited reordering of the edges and nodes).
- ADAPTED - Static variable in class moss.Fragment
-
flag for an adapted fragment; this flag is set when a fragment
gets adapted, so that the adaptation is not repeated
- adaptRing(Fragment, boolean) - Method in class moss.CanonicalForm
-
Reorder the edges of a fragment with a ring extension.
- adaptRing(Fragment, boolean) - Method in class moss.CnFBreadth1
-
Reorder the edges of a fragment with a ring extension.
- adaptRing(Fragment, boolean) - Method in class moss.CnFBreadth2
-
Reorder the edges of a fragment with a ring extension.
- adaptRing(Fragment, boolean) - Method in class moss.CnFDepth
-
Reorder the edges of a fragment with a ring extension.
- add(String) - Method in class moss.AtomTypeMgr
-
Add an atom type.
- add(String) - Method in class moss.BondTypeMgr
-
Add a bond type.
- add(Edge) - Method in class moss.ExtMgr
-
Add an extension edge.
- add(String) - Method in class moss.FreeTypeMgr
-
Add a type to the type map.
- add(Component, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a component.
- add(Embedding) - Method in class moss.OverlapGraph
-
Add an embedding to the overlap graph.
- add(int) - Method in class moss.Recoder
-
Add a type to the recoder.
- add(String) - Method in class moss.TypeMgr
-
Add a type to the type manager.
- addButton(String) - Method in class moss.MoSSPanel
-
Add a button to a tab.
- addButton(String, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a button to a tab.
- addCheckBox(boolean) - Method in class moss.MoSSPanel
-
Add a check box to a tab.
- addCheckBox(boolean, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a check box to a tab.
- addComboBox(String[]) - Method in class moss.MoSSPanel
-
Add a combo box to a tab.
- addComboBox(String[], GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a combo box to a tab.
- addEdge(int, int, int) - Method in class moss.Graph
-
Add an edge to the graph.
- addEdge(Edge) - Method in class moss.Node
-
Add an edge to a node.
- addEmb(Embedding) - Method in class moss.Fragment
-
Add an embedding (list) to the fragment.
- addEmb(CanonicalForm) - Method in class moss.Fragment
-
Add an extension (as an embedding) to the fragment.
- addFileInput(String) - Method in class moss.MoSSPanel
-
Add a file input field to a tab.
- addFileInput(String, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a text input field to a tab.
- addFiller(int) - Method in class moss.MoSSPanel
-
Add a filler.
- addGraph(NamedGraph) - Method in class moss.Fragment
-
Add a graph to the cover of the fragment.
- addGraph(NamedGraph) - Method in class moss.Miner
-
Add a graph to the database.
- addHelp(String) - Method in class moss.MoSSPanel
-
Add a help text.
- addLabel(String) - Method in class moss.MoSSPanel
-
Add a label to a tab.
- addLabel(String, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a label to a tab.
- addNode(int) - Method in class moss.Graph
-
Add a node to the graph, encode type if needed.
- addNodeRaw(int) - Method in class moss.Graph
-
Add a node to the graph, do not encode the type.
- addNumberInput(String) - Method in class moss.MoSSPanel
-
Add a text input field to a tab.
- addNumberInput(String, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a text input field to a tab.
- addSpinner(int, int, int, int) - Method in class moss.MoSSPanel
-
Add a spinner to a tab.
- addSpinner(int, int, int, int, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a combo box to a tab.
- addTextInput(String) - Method in class moss.MoSSPanel
-
Add a text input field to a tab.
- addTextInput(String, GridBagConstraints) - Method in class moss.MoSSPanel
-
Add a text input field to a tab.
- all - Variable in class moss.CanonicalForm
-
all (remaining) ring flags of the current edge
- ALLEXTS - Static variable in class moss.CanonicalForm
-
extension mode flag: generate all extensions
- ALLEXTS - Static variable in class moss.Miner
-
flag for generating all extensions
- ALLORBS - Static variable in class moss.CanonicalForm
-
extension mode flag: use node orbits for all extensions;
not only those leading to a new node
- ALUMINUM - Static variable in class moss.AtomTypeMgr
-
- AMERICUM - Static variable in class moss.AtomTypeMgr
-
- ANTIMONY - Static variable in class moss.AtomTypeMgr
-
- ARGON - Static variable in class moss.AtomTypeMgr
-
- AROMATIC - Static variable in class moss.AtomTypeMgr
-
the flag indicating whether an atom is part of an aromatic ring
- AROMATIC - Static variable in class moss.BondTypeMgr
-
bond type: aromatic
- aromatize(Graph) - Static method in class moss.BondTypeMgr
-
Convert Kekulé representations to true aromatic rings.
- AROMATIZE - Static variable in class moss.Miner
-
flag for converting Kekulé representations
- ARSENIC - Static variable in class moss.AtomTypeMgr
-
- ASTATINE - Static variable in class moss.AtomTypeMgr
-
- AtomTypeMgr - Class in moss
-
Class for an atom type manager.
- AtomTypeMgr() - Constructor for class moss.AtomTypeMgr
-
Create an atom type manager.
- cabs - Variable in class moss.GraphReader
-
the absolute support in the complement
- cabs - Variable in class moss.GraphWriter
-
the absolute support in the complement
- CADMIUM - Static variable in class moss.AtomTypeMgr
-
- CALCIUM - Static variable in class moss.AtomTypeMgr
-
- CALIFORNIUM - Static variable in class moss.AtomTypeMgr
-
- canonic - Variable in class moss.Miner
-
for benchmarking: canonical form pruning counter
- CanonicalForm - Class in moss
-
Class for canonical forms of graphs and their restricted extensions.
- CanonicalForm() - Constructor for class moss.CanonicalForm
-
Create a canonical form object.
- CARBON - Static variable in class moss.AtomTypeMgr
-
- cedge - Variable in class moss.CanonicalForm
-
the edge type for chain extensions
- CERIUM - Static variable in class moss.AtomTypeMgr
-
- CESIUM - Static variable in class moss.AtomTypeMgr
-
- CHAIN - Static variable in class moss.CanonicalForm
-
extension mode flag: variable length chain
- chain() - Method in class moss.CanonicalForm
-
Create a variable length chain extension.
- CHAIN - Static variable in class moss.Fragment
-
flag for the result of an extension that is a chain start
- CHAIN - Static variable in class moss.Node
-
the flag for a chain node (representing several equal nodes)
- CHAINEXT - Static variable in class moss.Miner
-
flag for extensions by chains
- chains - Variable in class moss.Miner
-
for benchmarking: invalid chains counter
- chainsValid() - Method in class moss.Fragment
-
Check whether all variable length chains are valid.
- CHARGEMASK - Static variable in class moss.AtomTypeMgr
-
the mask for extracting the charge from an atom type
- CHARGESHIFT - Static variable in class moss.AtomTypeMgr
-
the shift value for extracting the charge from an atom type
- chcnt - Variable in class moss.CanonicalForm
-
the number of variable length chains
- chcnt - Variable in class moss.Fragment
-
the number of variable length chains
- CHLORINE - Static variable in class moss.AtomTypeMgr
-
- CHROMIUM - Static variable in class moss.AtomTypeMgr
-
- CLASSES - Static variable in class moss.CanonicalForm
-
extension mode flag: use node equivalence classes
- CLASSES - Static variable in class moss.Miner
-
flag for using node equivalence classes
- clear() - Method in class moss.FreeTypeMgr
-
Clear the type map (remove all types).
- clear() - Method in class moss.Graph
-
Clear a graph (remove all nodes and edges).
- clear() - Method in class moss.OverlapGraph
-
Clear an overlap graph (remove all embeddings).
- clear(int) - Method in class moss.Recoder
-
Clear the frequency and support of a type.
- clearRings() - Method in class moss.Edge
-
Clear the ring flags of the edge.
- clone() - Method in class moss.Graph
-
Create a clone of the graph.
- clone() - Method in class moss.NamedGraph
-
Create a clone of this named graph.
- CLOSED - Static variable in class moss.Fragment
-
flag for a closed fragment
(no super-fragment has the same support)
- CLOSED - Static variable in class moss.Miner
-
flag for restriction to closed fragments
- CLOSERINGS - Static variable in class moss.Miner
-
flag for filtering open rings
- cnf - Variable in class moss.Miner
-
the canonical form and restricted extension generator
- CnFBreadth1 - Class in moss
-
Class for breadth-first search spanning tree canonical form
and the corresponding maximum source extensions.
- CnFBreadth1() - Constructor for class moss.CnFBreadth1
-
Create a breadth-first search spanning tree canonical form.
- CnFBreadth2 - Class in moss
-
Class for breadth-first search spanning tree canonical form
and the corresponding maximum source extensions.
- CnFBreadth2() - Constructor for class moss.CnFBreadth2
-
Create a breadth-first search spanning tree canonical form.
- CnFDepth - Class in moss
-
Class for a depth-first search spanning tree canonical form
and the corresponding rightmost path extensions.
- CnFDepth() - Constructor for class moss.CnFDepth
-
Create a depth-first search spanning tree canonical form.
- cnode - Variable in class moss.CanonicalForm
-
the node type for chain extensions
- cnt - Variable in class moss.ExtMgr
-
the number of extension edges
- cnt - Variable in class moss.Fragment
-
the number of embeddings/graphs for the current graph
- cnt - Variable in class moss.Notation
-
the number of unread/pushed back characters
- cnts - Variable in class moss.Miner
-
the numbers of graphs in focus and complement
- COBALT - Static variable in class moss.AtomTypeMgr
-
- codeCharge(int) - Static method in class moss.AtomTypeMgr
-
Encode a charge for addition to an atom type.
- codeHydros(int) - Static method in class moss.AtomTypeMgr
-
Encode hydrogens for addition to an atom type.
- coder - Variable in class moss.Graph
-
an optional node type recoder
- coder - Variable in class moss.Miner
-
the recoder for the node types
- COMMENT - Static variable in class moss.TableReader
-
class/type flag: comment character
- commit() - Method in class moss.Recoder
-
Commit a type code counting.
- common(Embedding) - Method in class moss.Embedding
-
Find the (maximum) length of a common edge array prefix.
- comp - Variable in class moss.Miner
-
the maximum support in the complement as an absolute value
- compareEdge(Edge, Edge, int) - Method in class moss.CanonicalForm
-
Compare two edges with the precedence order of the canonical form.
- compareEdge(Edge, Edge, int) - Method in class moss.CnFBreadth1
-
Compare two edges with the precedence order of the canonical form.
- compareEdge(Edge, Edge, int) - Method in class moss.CnFBreadth2
-
Compare two edges with the precedence order of the canonical form.
- compareEdge(Edge, Edge, int) - Method in class moss.CnFDepth
-
Compare two edges with the precedence order of the canonical form.
- compareRing(Fragment) - Method in class moss.CanonicalForm
-
Compare the current ring extension to a fragment.
- compareTo(Edge) - Method in class moss.Edge
-
Compare two edges (w.r.t.
- compareTo(ExtList) - Method in class moss.ExtList
-
Compare to another extension list element.
- compareTo(Node) - Method in class moss.Node
-
Compare two nodes (w.r.t.
- compareToFrag(Fragment) - Method in class moss.CanonicalForm
-
Compare the current extension to a given fragment.
- compareToFrag(Fragment) - Method in class moss.CnFBreadth1
-
Compare the current extension to a given fragment.
- compareToFrag(Fragment) - Method in class moss.CnFBreadth2
-
Compare the current extension to a given fragment.
- compareToFrag(Fragment) - Method in class moss.CnFDepth
-
Compare the current extension to a given fragment.
- compareWord(Graph) - Method in class moss.CanonicalForm
-
Compare the current code word to the one of the given graph.
- compareWord(Graph, int) - Method in class moss.CanonicalForm
-
Compare the current code word to the one of the given graph.
- compareWord(Edge[], int) - Method in class moss.CanonicalForm
-
Compare the current code word to the one of the given edge array.
- compareWord(Edge[], int) - Method in class moss.CnFBreadth1
-
Compare the current code word to the one of the given edge array.
- compareWord(Edge[], int) - Method in class moss.CnFBreadth2
-
Compare the current code word to the one of the given edge array.
- compareWord(Edge[], int) - Method in class moss.CnFDepth
-
Compare the current code word to the one of the given edge array.
- COMPL - Static variable in class moss.Fragment
-
group identifier: complement
- COMPL - Static variable in class moss.NamedGraph
-
group identifier: complement
- computeSupport(int) - Method in class moss.Fragment
-
Compute the support of the fragment.
- contains(int) - Method in class moss.Graph
-
Check whether a node type is contained in this graph.
- contains(Graph) - Method in class moss.Graph
-
Check whether a graph is contained in this graph.
- COPERNICIUM - Static variable in class moss.AtomTypeMgr
-
- COPPER - Static variable in class moss.AtomTypeMgr
-
- COPYRIGHT - Static variable in class moss.Miner
-
the copyright information for this program
- costs - Variable in class moss.MaxComSub
-
the costs of the best sequence of edit operations transforming
graph 1 into graph 2
- count(int) - Method in class moss.Recoder
-
Count a type code.
- cover - Variable in class moss.Fragment
-
the graph cover of the fragment
- createCnF(String) - Static method in class moss.CanonicalForm
-
Create an extension object corresponding to a given name.
- createNotation(String) - Static method in class moss.Notation
-
Create a graph notation corresponding to a given name.
- createNumberInput(String) - Static method in class moss.MoSSPanel
-
Create a number input field.
- createReader(Reader, int, String) - Static method in class moss.GraphReader
-
Create a graph reader for a given format and mode.
- createWriter(Writer, int, String) - Static method in class moss.GraphWriter
-
Create a graph writer for a given format and mode.
- crel - Variable in class moss.GraphReader
-
the relative support in the complement
- crel - Variable in class moss.GraphWriter
-
the relative support in the complement
- Ctab - Class in moss
-
Class for the connection table notation (Ctab, Elsevier MDL).
- Ctab() - Constructor for class moss.Ctab
-
Create a connection table notation.
- CURIUM - Static variable in class moss.AtomTypeMgr
-
- curr - Variable in class moss.CanonicalForm
-
the current ring flag
- curr - Variable in class moss.ExtMgr
-
the current extension edge
- curr - Variable in class moss.Fragment
-
the current embedding (cursor)
- curr - Variable in class moss.Miner
-
the current insertion point for the focus
- DARMSTADTIUM - Static variable in class moss.AtomTypeMgr
-
- decode() - Method in class moss.Graph
-
Decode the node types.
- decode(Recoder) - Method in class moss.Node
-
Decode the node type.
- decode(int) - Method in class moss.Recoder
-
Decode a type code, that is, retrieve the original type value.
- DEFAULT - Static variable in class moss.Fragment
-
default flags that are set when a fragment is created
- DEFAULT - Static variable in class moss.Miner
-
default search mode flags: edge extensions, embeddings,
canonical form and full perfect extension pruning
- deg - Variable in class moss.Node
-
the current number of incident edges (node degree)
- desc - Variable in class moss.GraphReader
-
the description of the current graph
- desc - Variable in class moss.GraphWriter
-
the description of the current graph
- desc - Variable in class moss.MoleculeNtn
-
the buffer for creating molecule descriptions
- describe(Graph) - Method in class moss.CanonicalForm
-
Create the code word for a given graph as a string.
- describe(Graph, boolean) - Method in class moss.CanonicalForm
-
Create the code word for a given graph as a string.
- describe(Graph, boolean) - Method in class moss.CnFBreadth1
-
Create the code word for a given graph as a string.
- describe(Graph, boolean) - Method in class moss.CnFBreadth2
-
Create the code word for a given graph as a string.
- describe(Graph, boolean) - Method in class moss.CnFDepth
-
Create the code word for a given graph as a string.
- describe(Graph) - Method in class moss.Ctab
-
Create a description of a given molecule.
- describe(Graph) - Method in class moss.LiNoG
-
Create a description of a given attributed graph.
- describe(Graph) - Method in class moss.NEList
-
Create a string description of a graph.
- describe(Graph) - Method in class moss.Notation
-
Create a string description of a graph.
- describe(Graph) - Method in class moss.SLN
-
Create a description of a given molecule.
- describe(Graph) - Method in class moss.SMILES
-
Create a string description of a molecule.
- DESCRIPTION - Static variable in class moss.Miner
-
the program description
- DOUBLE - Static variable in class moss.BondTypeMgr
-
bond type: double
- DOWNGRADE - Static variable in class moss.BondTypeMgr
-
a mask, to be anded (bitwise &) with a bond type
in order to downgrade an aromatic bond to a single bond
- dst - Variable in class moss.CanonicalForm
-
the index of the current destination node
- dst - Variable in class moss.Edge
-
the destination node of the edge
- dst - Variable in class moss.ExtList
-
the index of the destination node
- dst - Variable in class moss.Fragment
-
the index of the destination node of the (first) new edge
- DUBNIUM - Static variable in class moss.AtomTypeMgr
-
- duplic - Variable in class moss.Miner
-
for benchmarking: duplicate fragments counter
- DYSPROSIUM - Static variable in class moss.AtomTypeMgr
-
- EDGE - Static variable in class moss.CanonicalForm
-
extension mode flag: single edge
- Edge - Class in moss
-
Class for edges of an attributed (labeled/typed) graph.
- Edge(Node, Node, int) - Constructor for class moss.Edge
-
Create an edge of a given type between two nodes.
- Edge(Node, Node, int, long) - Constructor for class moss.Edge
-
Create an edge of a given type between two nodes.
- edge - Variable in class moss.ExtList
-
the type of the extension edge
- edgecnt - Variable in class moss.CanonicalForm
-
the number of new edges
- edgecnt - Variable in class moss.Graph
-
the current number of edges
(may be smaller than the array length)
- EDGEEXT - Static variable in class moss.Miner
-
flag for extensions by single edges
- edgemap - Variable in class moss.MaxComSub
-
the mapping of the edges of graph 1 to graph 2
- edgemgr - Variable in class moss.Notation
-
the manager for the edge types
- edges - Variable in class moss.CanonicalForm
-
(relevant) edges of the extension
- edges - Variable in class moss.Embedding
-
the array of edges (only references to the underlying graph)
- edges - Variable in class moss.Graph
-
the array of edges (may be only partially used)
- edges - Variable in class moss.GraphReader
-
the number of edges of the current graph
- edges - Variable in class moss.GraphWriter
-
the number of edges of the current graph
- edges - Variable in class moss.Node
-
the array of incident edges (may not be fully used)
- EINSTEINIUM - Static variable in class moss.AtomTypeMgr
-
- ELEMCNT - Static variable in class moss.AtomTypeMgr
-
the number of chemical elements (not all actually exist)
- ELEMENTS - Static variable in class moss.AtomTypeMgr
-
the periodic table of elements; using the chemical element as
an index for this table yields a printable element name
- ELEMMASK - Static variable in class moss.AtomTypeMgr
-
the mask for the chemical element of an atom
- emap - Variable in class moss.CanonicalForm
-
the edge map for making a graph canonic
- emb - Variable in class moss.CanonicalForm
-
the embedding that is extended (may be null
)
- embcmp - Variable in class moss.Miner
-
for benchmarking: the number of comparisons with embeddings
- embcnt - Variable in class moss.Miner
-
for benchmarking: the number of created embeddings
- embed(int) - Method in class moss.Graph
-
Embed a single node into the graph.
- embed(Graph) - Method in class moss.Graph
-
Embed a graph structure (find all its embeddings).
- embed() - Method in class moss.Miner
-
Embed the seed structure into all graphs.
- Embedding - Class in moss
-
Class for embeddings of substructures into graphs.
- Embedding() - Constructor for class moss.Embedding
-
Dummy constructor.
- Embedding(Graph, int) - Constructor for class moss.Embedding
-
Create a single node embedding.
- Embedding(Graph, Node[], Edge[]) - Constructor for class moss.Embedding
-
Create an embedding from node and edge references.
- Embedding(CanonicalForm) - Constructor for class moss.Embedding
-
Create an embedding from a canonical form.
- Embedding(Embedding, Edge) - Constructor for class moss.Embedding
-
Extend a given embedding with a given edge.
- emblvl - Variable in class moss.Miner
-
the level at which to switch to embeddings
- encode(Recoder) - Method in class moss.Graph
-
Encode the node types with the given type recoder.
- encode(Recoder) - Method in class moss.Node
-
Encode the node type.
- encode(int) - Method in class moss.Recoder
-
Encode a type, that is, retrieve its code.
- equals(Object) - Method in class moss.Edge
-
Check whether two edges are equal.
- equals(Object) - Method in class moss.Embedding
-
Check whether two embeddings are equal.
- equals(Object) - Method in class moss.Fragment
-
Check whether two fragments are equal.
- equals(Object) - Method in class moss.Graph
-
Check whether another graph is equal to this graph.
- equalsCanonic(Fragment) - Method in class moss.Fragment
-
Compare the (canonical) code words of two fragments.
- equalsCanonic(Graph) - Method in class moss.Graph
-
Compare the (canonical) code words of two graphs.
- equiv - Variable in class moss.Miner
-
for benchmarking: equivalent frag.
- equivClasses(Graph) - Method in class moss.CanonicalForm
-
Find the node equivalence classes for a given graph.
- equivSiblings() - Method in class moss.Fragment
-
Check whether a fragments can have equivalent siblings.
- EQVARS - Static variable in class moss.CanonicalForm
-
extension mode flag: equivalent ring variants
- EQVARS - Static variable in class moss.Miner
-
flag for extensions by equivalent variants of rings
- ERBIUM - Static variable in class moss.AtomTypeMgr
-
- EUROPIUM - Static variable in class moss.AtomTypeMgr
-
- exclude(int) - Method in class moss.Recoder
-
Mark a type as excluded.
- execute() - Method in class moss.MoSS
-
Execute the substructure search, that is, start a miner.
- exseed - Variable in class moss.Miner
-
the node types that are excluded as seeds
- extend(int, int, int, int) - Method in class moss.Embedding
-
Create all extensions of a given type of this embedding.
- ExtList - Class in moss
-
Class for managing extension lists and their elements.
- ExtList(int, int, int, int) - Constructor for class moss.ExtList
-
Create an extension list element for a single edge extension.
- ExtList(int, int, int, int, int[], int) - Constructor for class moss.ExtList
-
Create an extension list element for a ring extension.
- ExtMgr - Class in moss
-
Class for an extension edge manager.
- ExtMgr(int, int) - Constructor for class moss.ExtMgr
-
Create an extension edge manager.
- ExtMgr(int) - Constructor for class moss.ExtMgr
-
Create an extension edge manager.
- exts - Variable in class moss.ExtMgr
-
the table for access via the source node type
- extype - Variable in class moss.Miner
-
the excluded node types
- fcomp - Variable in class moss.Miner
-
the maximum support in the complement as a fraction
- FERMIUM - Static variable in class moss.AtomTypeMgr
-
- FILL - Static variable in class moss.MoSSPanel
-
the grid bag constraints for fillers
- first(int) - Method in class moss.ExtMgr
-
Initialize the traversal of extension edges.
- firstEmb() - Method in class moss.Fragment
-
Get the first embedding of the fragment.
- firstGraph() - Method in class moss.Fragment
-
Get the first graph containing the fragment.
- FIXED - Static variable in class moss.CanonicalForm
-
flag for a fixed edge in the ring order test
- fixed - Variable in class moss.CanonicalForm
-
the number of fixed edges in a canonical form test
- FLAGMASK - Static variable in class moss.Edge
-
the mask for the edge flags (wildcard and ring)
- FLAGMASK - Static variable in class moss.Node
-
the mask for the node flags (wildcard and chain)
- FLAGMASK - Static variable in class moss.TypeMgr
-
the mask for the type flags
- flags - Variable in class moss.Edge
-
the flags for rings and bridges
- flags - Variable in class moss.Fragment
-
the property flags of the embedding (e.g.
- FLDSEP - Static variable in class moss.TableReader
-
class/type flag: field separator
- FLOURINE - Static variable in class moss.AtomTypeMgr
-
- FOCUS - Static variable in class moss.Fragment
-
group identifier: focus
- FOCUS - Static variable in class moss.NamedGraph
-
group identifier: focus
- frag - Variable in class moss.CanonicalForm
-
the fragment that is extended
- frag - Variable in class moss.Miner
-
the initial fragment (embedded seed structure)
- fragcmp - Variable in class moss.Miner
-
for benchmarking: the number of fragment comparisons
- fragcnt - Variable in class moss.Miner
-
for benchmarking: the number of created fragments
- Fragment - Class in moss
-
Class for graph fragments (subgraphs and their embeddings).
- Fragment() - Constructor for class moss.Fragment
-
Create an empty fragment.
- Fragment(Graph) - Constructor for class moss.Fragment
-
Create a fragment from a graph.
- Fragment(int) - Constructor for class moss.Fragment
-
Create an empty fragment with an embedding limit.
- Fragment(Graph, int) - Constructor for class moss.Fragment
-
Create a fragment with an embedding limit from a graph.
- Fragment(Graph, Graph) - Constructor for class moss.Fragment
-
Create a fragment from a graph and a subgraph.
- Fragment(Graph, Graph, int) - Constructor for class moss.Fragment
-
Create a fragment from a graph and a subgraph.
- Fragment(Fragment, int, int, int, int) - Constructor for class moss.Fragment
-
Create an extended fragment.
- Fragment(CanonicalForm) - Constructor for class moss.Fragment
-
Create a fragment from an extension.
- FRANCIUM - Static variable in class moss.AtomTypeMgr
-
- FreeNtn - Class in moss
-
Class for free graph notations (with dynamic type managers).
- FreeNtn() - Constructor for class moss.FreeNtn
-
- FreeTypeMgr - Class in moss
-
Class for a node or edge type map.
- FreeTypeMgr() - Constructor for class moss.FreeTypeMgr
-
Create a type map.
- fsupp - Variable in class moss.Miner
-
the minimum support in the focus as a fraction
- g1 - Variable in class moss.MaxComSub
-
the first graph of the pair
for which to find the maximum common subgraph
- g2 - Variable in class moss.MaxComSub
-
the second graph of the pair
for which to find the maximum common subgraph
- GADOLINIUM - Static variable in class moss.AtomTypeMgr
-
- GALLIUM - Static variable in class moss.AtomTypeMgr
-
- GERMANIUM - Static variable in class moss.AtomTypeMgr
-
- getAbsCompl() - Method in class moss.GraphReader
-
Get the absolute complement support of the current substructure.
- getAbsSupp() - Method in class moss.GraphReader
-
Get the absolute focus support of the current substructure.
- getBase(int) - Static method in class moss.TypeMgr
-
Get the base type (remove flags).
- getBaseType() - Method in class moss.Edge
-
Get the base type (attribute/label) of an edge.
- getBaseType() - Method in class moss.Node
-
Get the base type (attribute/label) of a node.
- getBond(int) - Static method in class moss.BondTypeMgr
-
Extract the raw bond type from a bond type.
- getBondName(int) - Static method in class moss.BondTypeMgr
-
Get the name of the bond type.
- getChainName() - Static method in class moss.AtomTypeMgr
-
Get the name of a chain atom.
- getCharge(int) - Static method in class moss.AtomTypeMgr
-
Extract the charge from an atom type.
- getChooser() - Method in class moss.MoSS
-
Get the file chooser (create if necessary).
- getCode(String) - Method in class moss.AtomTypeMgr
-
Map an atom name to the corresponding code.
- getCode(String) - Method in class moss.BondTypeMgr
-
Map a bond name to the corresponding code.
- getCode(String) - Method in class moss.FreeTypeMgr
-
Map a type name to the corresponding type code.
- getCode(String) - Method in class moss.TypeMgr
-
Map a type name to the corresponding type code.
- getColumnCount() - Method in class moss.MoSSTable
-
Get the number of columns of the data table.
- getColumnName(int) - Method in class moss.MoSSTable
-
Get the name of a column given its index.
- getComplEmbCount() - Method in class moss.Fragment
-
Get the number of embeddings in the complement.
- getComplSupport() - Method in class moss.Fragment
-
Get the complement support of a fragment.
- getCosts() - Method in class moss.MaxComSub
-
Get the costs of the best sequence of edit operations.
- getCurrent() - Method in class moss.Miner
-
Get the substructures that have been found up to now.
- getDegree() - Method in class moss.ExtMgr
-
Get the maximum source node degree of the current extension edge.
- getDegree() - Method in class moss.Node
-
Get the degree of the node.
- getDelim() - Method in class moss.Notation
-
Get the delimiter character.
- getDesc() - Method in class moss.GraphReader
-
Get a line description of the current graph.
- getDesc() - Method in class moss.NEListReader
-
Get a (line) description of the current graph.
- getDesc() - Method in class moss.SDfileReader
-
Get a (line) description of the current graph.
- getDest() - Method in class moss.Edge
-
Get the destination node of the edge.
- getDest() - Method in class moss.ExtMgr
-
Get the destination node type of the current extension edge.
- getEdge(int) - Method in class moss.Graph
-
Get an edge by its index.
- getEdge(int) - Method in class moss.Node
-
Get an edge of the node.
- getEdgeCount() - Method in class moss.Graph
-
Get the number of edges of the graph.
- getEdgeCount() - Method in class moss.GraphReader
-
Get the number of edges of the current graph.
- getEdgeMap() - Method in class moss.MaxComSub
-
Get the mapping of the edges of graph 1 to the edges of graph 2.
- getEdgeMgr() - Method in class moss.FreeNtn
-
Get the edge type manager.
- getEdgeMgr() - Method in class moss.Graph
-
Get the edge type manager of the graph.
- getEdgeMgr() - Method in class moss.Notation
-
Get the edge type manager.
- getEdgeType(int) - Method in class moss.Graph
-
Get the type of an edge.
- getElem(int) - Static method in class moss.AtomTypeMgr
-
Extract the chemical element from an atom type.
- getElemName(int) - Static method in class moss.AtomTypeMgr
-
Extract the name of a chemical element from an atom type.
- getEmbCount() - Method in class moss.Fragment
-
Get the number of embeddings (in both groups together).
- getEmbCount(int) - Method in class moss.Fragment
-
Get the number of embeddings in the given group.
- getError() - Method in class moss.Miner
-
Get the error status of the search process.
- getFileName(String, JTextField) - Method in class moss.MoSS
-
Get a file name and store it in a text field.
- getFocusEmbCount() - Method in class moss.Fragment
-
Get the number of embeddings in the focus.
- getFocusSupport() - Method in class moss.Fragment
-
Get the focus support of a fragment.
- getFreq(int) - Method in class moss.Recoder
-
Get the frequency of a type (number of occurrences).
- getGraph() - Method in class moss.Fragment
-
Get the fragment as a (sub-)graph.
- getGraph() - Method in class moss.GraphReader
-
Get the current graph or substructure.
- getGraph() - Method in class moss.MaxComSub
-
Get the mapping of the edges of graph 1 to the edges of graph 2.
- getGraph() - Method in class moss.TableReader
-
Get the current graph or substructure.
- getGroup() - Method in class moss.Embedding
-
Get the group of the underlying graph.
- getGroup() - Method in class moss.NamedGraph
-
Get the group of this graph.
- getHydros(int) - Static method in class moss.AtomTypeMgr
-
Extract the hydrogens from an atom type.
- getHydros() - Method in class moss.MoleculeNtn
-
Read shorthand hydrogen atoms.
- getHydros(Node, Recoder) - Static method in class moss.MoleculeNtn
-
Get the number of adjacent hydrogen atoms (and mark them).
- getMISExact() - Method in class moss.OverlapGraph
-
Find the size of a maximum independent node set (MIS).
- getMISGreedy() - Method in class moss.OverlapGraph
-
Find the size of a maximum independent node set (MIS).
- getMISSize() - Method in class moss.OverlapGraph
-
Find the size of a maximum independent node set (MIS).
- getMISSize(boolean) - Method in class moss.OverlapGraph
-
Find the size of a maximum independent node set (MIS).
- getMode() - Method in class moss.GraphReader
-
Get the mode of the graph reader.
- getMode() - Method in class moss.GraphWriter
-
Get the mode of the graph writer.
- getName(int) - Method in class moss.AtomTypeMgr
-
Map a code to the corresponding atom name.
- getName(int) - Method in class moss.BondTypeMgr
-
Map a code to the corresponding bond name.
- getName(int) - Method in class moss.FreeTypeMgr
-
Map a type code to the corresponding type name.
- getName() - Method in class moss.GraphReader
-
Get the name of the current graph.
- getName() - Method in class moss.NamedGraph
-
Get the name of this graph.
- getName(int) - Method in class moss.TypeMgr
-
Map a type code to the corresponding type name.
- getNode(int) - Method in class moss.Graph
-
Get a node by its index.
- getNodeCount() - Method in class moss.Graph
-
Get the number of nodes of the graph.
- getNodeCount() - Method in class moss.GraphReader
-
Get the number of nodes of the current graph.
- getNodeMap() - Method in class moss.MaxComSub
-
Get the mapping of the nodes of graph 1 to the nodes of graph 2.
- getNodeMgr() - Method in class moss.FreeNtn
-
Get the node type manager.
- getNodeMgr() - Method in class moss.Graph
-
Get the node type manager of the graph.
- getNodeMgr() - Method in class moss.Notation
-
Get the node type manager.
- getNodeType(int) - Method in class moss.Graph
-
Get the type of a node.
- getNodeTypeRaw(int) - Method in class moss.Graph
-
Get the type of a node.
- getNotation() - Method in class moss.Graph
-
Get the notation of the graph.
- getNotation() - Method in class moss.GraphReader
-
Get the notation of the graph reader.
- getNotation() - Method in class moss.GraphWriter
-
Get the notation of the graph writer.
- getRecoder() - Method in class moss.Graph
-
Get the recoder for the node types.
- getRelCompl() - Method in class moss.GraphReader
-
Get the relative support of the current substructure.
- getRelSupp() - Method in class moss.GraphReader
-
Get the relative focus support of the current substructure.
- getRings() - Method in class moss.Edge
-
Get the ring flags of the edge.
- getRowCount() - Method in class moss.MoSSTable
-
Get the number of rows of the table.
- getSource() - Method in class moss.Edge
-
Get the source node of the edge.
- getSupp(int) - Method in class moss.Recoder
-
Get the support of a type (number of containing graphs).
- getSupport() - Method in class moss.Fragment
-
Get the support of a fragment (in both groups together).
- getSupport(int) - Method in class moss.Fragment
-
Get the support of a fragment in the given group.
- getType() - Method in class moss.Edge
-
Get the full type (attribute/label) of an edge.
- getType() - Method in class moss.ExtMgr
-
Get the edge type of the current extension edge.
- getType() - Method in class moss.Node
-
Get the full type (attribute/label) of a node.
- getTypes(char) - Method in class moss.TableReader
-
Get the classes/types of a given character.
- getValue() - Method in class moss.GraphReader
-
Get the value associated with the current graph.
- getValue() - Method in class moss.NamedGraph
-
Get the value of this graph.
- getValueAt(int, int) - Method in class moss.MoSSTable
-
Get the value of a table cell as an object.
- getWildcard() - Static method in class moss.AtomTypeMgr
-
Get the name of a wildcard atom.
- GOLD - Static variable in class moss.AtomTypeMgr
-
- graph - Variable in class moss.Embedding
-
the graph referred to
- graph - Variable in class moss.Fragment
-
the fragment as a graph
- Graph - Class in moss
-
Class to represent attributed graphs for substructure mining.
- Graph() - Constructor for class moss.Graph
-
Create/Initialize an empty graph.
- Graph(Notation) - Constructor for class moss.Graph
-
Create a (empty) graph with default array sizes.
- Graph(Notation, Recoder) - Constructor for class moss.Graph
-
Create a (empty) graph with default array sizes.
- Graph(Notation, int, int) - Constructor for class moss.Graph
-
Create a (empty) graph with the given array sizes.
- Graph(Notation, Recoder, int, int) - Constructor for class moss.Graph
-
Create a (empty) graph with the given array sizes.
- Graph(Graph) - Constructor for class moss.Graph
-
Create a clone of a graph.
- Graph(Graph, int, int, int, int) - Constructor for class moss.Graph
-
Create an extended graph (extended by one edge).
- Graph(Fragment) - Constructor for class moss.Graph
-
Turn a fragment into a graph.
- graph - Variable in class moss.GraphReader
-
the current graph
- graph - Variable in class moss.GraphWriter
-
the current graph
- GraphReader - Class in moss
-
Class for a reader for graph data sets.
- GraphReader(Reader, int) - Constructor for class moss.GraphReader
-
Create a reader for a graph data set.
- GRAPHS - Static variable in class moss.Fragment
-
support type: number of graphs that contain an embedding
- GRAPHS - Static variable in class moss.GraphReader
-
read mode: graphs
- GRAPHS - Static variable in class moss.GraphWriter
-
write mode: graphs
- graphs - Variable in class moss.Miner
-
the list of graphs to mine (database)
- GRAPHS - Static variable in class moss.MoSSTable
-
mode: graphs
- GraphWriter - Class in moss
-
Class for a writer for graph data sets.
- GraphWriter(Writer, int) - Constructor for class moss.GraphWriter
-
Create a writer for a graph data set.
- GREEDY - Static variable in class moss.Fragment
-
support type flag: whether to use the greedy MIS algorithm
- group - Variable in class moss.Miner
-
the group for graphs with a value below the threshold
- group - Variable in class moss.NamedGraph
-
the marker for grouping (either 0 or 1, used as an array index)
- IDS - Static variable in class moss.MoSSTable
-
mode: identifiers
- idx - Variable in class moss.CanonicalForm
-
the current edge index in the source node
- idx - Variable in class moss.Fragment
-
the index of the (first) new edge
- index() - Method in class moss.Embedding
-
Mark all nodes and edges with their index.
- index() - Method in class moss.Graph
-
Mark all nodes and edges with their index.
- INDIUM - Static variable in class moss.AtomTypeMgr
-
- init(Fragment, Embedding) - Method in class moss.CanonicalForm
-
Initialize the extension generation process.
- init(Fragment) - Method in class moss.CanonicalForm
-
Initialize the extension generation process.
- init(Fragment, Embedding) - Method in class moss.CnFBreadth1
-
Initialize the extension generation process.
- init(Fragment, Embedding) - Method in class moss.CnFBreadth2
-
Initialize the extension generation process.
- init(Fragment, Embedding) - Method in class moss.CnFDepth
-
Initialize the extension generation process.
- init(String[]) - Method in class moss.Miner
-
Initialize the miner from command line arguments.
- initCanonic(Graph, int) - Method in class moss.CanonicalForm
-
Initialize a canonical form test or generation.
- initFrag(Fragment) - Method in class moss.CanonicalForm
-
Initialize the extension generation process.
- initVars() - Method in class moss.CanonicalForm
-
Initialize the generation of equivalent ring extension variants.
- initVars() - Method in class moss.CnFBreadth1
-
Initialize the generation of equivalent ring extension variants.
- initVars() - Method in class moss.CnFBreadth2
-
Initialize the generation of equivalent ring extension variants.
- initVars() - Method in class moss.CnFDepth
-
Initialize the generation of equivalent ring extension variants.
- invalid - Variable in class moss.Miner
-
for benchmarking: invalid fragments counter
- IODINE - Static variable in class moss.AtomTypeMgr
-
- IRIDIUM - Static variable in class moss.AtomTypeMgr
-
- IRON - Static variable in class moss.AtomTypeMgr
-
- isAromatic(int) - Static method in class moss.AtomTypeMgr
-
Check whether an atom type specifies an aromatic atom.
- isAromatic(int) - Static method in class moss.BondTypeMgr
-
Check whether a bond type is aromatic.
- isBridge() - Method in class moss.Edge
-
Check whether the edge is a bridge.
- isCanExt(Graph) - Method in class moss.CanonicalForm
-
Check whether a given graph is a canonic extension of its base.
- isCanonic(int, int, int) - Method in class moss.CanonicalForm
-
Internal recursive function for the canonical form test.
- isCanonic(Graph, int) - Method in class moss.CanonicalForm
-
Check whether a given graph is canonic.
- isCanonic(Graph) - Method in class moss.CanonicalForm
-
Check whether a given graph is canonic.
- isCanonic(int, int, int) - Method in class moss.CnFBreadth1
-
Internal recursive function for the canonical form test.
- isCanonic(int, int, int) - Method in class moss.CnFBreadth2
-
Internal recursive function for the canonical form test.
- isCanonic(int, int, int) - Method in class moss.CnFDepth
-
Internal recursive function for the canonical form test.
- isCanonic(CanonicalForm) - Method in class moss.Fragment
-
Check whether the fragment is in canonical form.
- isCanonic(CanonicalForm, boolean) - Method in class moss.Fragment
-
Check whether the fragment is in canonical form.
- isCanonic(CanonicalForm) - Method in class moss.Graph
-
Check whether a graph is canonic w.r.t.
- isCanonic(CanonicalForm, int) - Method in class moss.Graph
-
Check whether a graph is canonic w.r.t.
- isCellEditable(int, int) - Method in class moss.MoSSTable
-
Returns whether a table cell is editable.
- isChain(int) - Static method in class moss.AtomTypeMgr
-
Check whether an atom type specifies a chain atom.
- isChain() - Method in class moss.Node
-
Check whether this is a chain node.
- isClosed(CanonicalForm) - Method in class moss.Fragment
-
Check whether the fragment is closed.
- isConnected() - Method in class moss.Graph
-
Check whether the graph is connected.
- isDouble(int) - Static method in class moss.BondTypeMgr
-
Check whether a bond type is double.
- isEquivTo(Fragment) - Method in class moss.Fragment
-
Check whether two fragments are equivalent.
- isExcluded(int) - Method in class moss.Recoder
-
Check whether a type is excluded.
- isFixed() - Method in class moss.AtomTypeMgr
-
Check whether a type manager is fixed (is not extendable).
- isFixed() - Method in class moss.BondTypeMgr
-
Check whether a type manager is fixed (is not extendable).
- isFixed() - Method in class moss.FreeTypeMgr
-
Check whether a type manager is fixed (is not extendable).
- isFixed() - Method in class moss.TypeMgr
-
Check whether a type manager is fixed (is not extendable).
- isHarmful() - Method in class moss.OverlapGraph
-
Check whether this is a harmful overlap graph.
- isInRing() - Method in class moss.Edge
-
Check whether the edge is part of a ring.
- isLine() - Method in class moss.Ctab
-
Whether this is a line notation (single line description).
- isLine() - Method in class moss.LiNoG
-
Whether this is a line notation (single line description).
- isLine() - Method in class moss.NEList
-
Whether this is a line notation (single line description).
- isLine() - Method in class moss.Notation
-
Whether this is a line notation (single line description).
- isLine() - Method in class moss.SLN
-
Whether this is a line notation (single line description).
- isLine() - Method in class moss.SMILES
-
Whether this is a line notation (single line description).
- isMaximal(int) - Method in class moss.Recoder
-
Check whether a code has maximal frequency.
- isocnt - Variable in class moss.Miner
-
for benchmarking: the number of isomorphism tests
- isPerfect(boolean) - Method in class moss.Fragment
-
Check whether an extension is perfect.
- isRing(int) - Static method in class moss.BondTypeMgr
-
Check whether a bond type specifies a ring bond.
- isRingEdgeExt() - Method in class moss.Fragment
-
Check whether the fragment is the result of an extension
by a ring edge.
- isRingExt() - Method in class moss.Fragment
-
Check whether the fragment is the result of a ring extension.
- isRingKey(Graph, Edge) - Method in class moss.CanonicalForm
-
Check whether a prefix is a ring key.
- isSingle(int) - Static method in class moss.BondTypeMgr
-
Check whether a bond type is single.
- isSpecial() - Method in class moss.Edge
-
Check whether this is a special edge (wildcard or ring).
- isSpecial() - Method in class moss.Node
-
Check whether this is a special node (wildcard or chain).
- isSpecial(int) - Static method in class moss.TypeMgr
-
Check whether a type code specifies a special type.
- isTriple(int) - Static method in class moss.BondTypeMgr
-
Check whether a bond type is triple.
- isType(int, char) - Method in class moss.TableReader
-
Check whether a given character is in a given class
or of a given type.
- isValid() - Method in class moss.Fragment
-
Check whether the valid flag is set.
- isWildcard() - Method in class moss.Edge
-
Check whether this is a wildcard edge.
- isWildcard() - Method in class moss.Node
-
Check whether this is a wildcard node.
- isWildcard(int) - Static method in class moss.TypeMgr
-
Check whether a type code specifies a wildcard.
- itemStateChanged(ItemEvent) - Method in class moss.MoSS
-
Handle the state change of the support type combo box.
- MAGNESIUM - Static variable in class moss.AtomTypeMgr
-
- main(String[]) - Static method in class moss.AtomTypeMgr
-
Main function for testing some basic functionality.
- main(String[]) - Static method in class moss.BondTypeMgr
-
Main function for testing some basic functionality.
- main(String[]) - Static method in class moss.Ctab
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.Embedding
-
Main function for testing the overlap functions.
- main(String[]) - Static method in class moss.Fragment
-
Main function for testing some basic functionality.
- main(String[]) - Static method in class moss.Graph
-
Main function for testing some basic functionality.
- main(String[]) - Static method in class moss.LiNoG
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.MaxComSub
-
Main function for basic testing basic functionality.
- main(String[]) - Static method in class moss.Miner
-
Command line invocation of the molecular substructure miner.
- main(String[]) - Static method in class moss.MoSS
-
Main function to invoke the user interface
as a stand-alone program.
- main(String[]) - Static method in class moss.NamedGraph
-
Main function for testing some basic functionality.
- main(String[]) - Static method in class moss.NEList
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.NEListReader
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.OverlapGraph
-
Main function for testing some basic functionality.
- main(String[]) - Static method in class moss.SDfileReader
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.SLN
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.SMILES
-
Main function for testing basic functionality.
- main(String[]) - Static method in class moss.TableReader
-
Main function for testing basic functionality.
- makeCanonic(int, int, int) - Method in class moss.CanonicalForm
-
Internal recursive function for making a given graph canonic.
- makeCanonic(Graph, int) - Method in class moss.CanonicalForm
-
Make a given graph canonic.
- makeCanonic(Graph) - Method in class moss.CanonicalForm
-
Make a given graph canonic.
- makeCanonic(int, int, int) - Method in class moss.CnFBreadth1
-
Internal recursive function for making a given graph canonic.
- makeCanonic(int, int, int) - Method in class moss.CnFBreadth2
-
Internal recursive function for making a given graph canonic.
- makeCanonic(int, int, int) - Method in class moss.CnFDepth
-
Internal recursive function for making a given graph canonic.
- makeCanonic(CanonicalForm) - Method in class moss.Fragment
-
Make the fragment canonic (minimize the code word).
- makeCanonic(CanonicalForm, int) - Method in class moss.Fragment
-
Make the fragment canonic (minimize the code word).
- makeCanonic(CanonicalForm) - Method in class moss.Graph
-
Make a graph canonic w.r.t.
- makeCanonic(CanonicalForm, int) - Method in class moss.Graph
-
Make a graph canonic w.r.t.
- makeEmbedding() - Method in class moss.CanonicalForm
-
Create an embedding from the current extension.
- makeFragment() - Method in class moss.CanonicalForm
-
Create a fragment from the current extension.
- makeMap(Graph, int) - Method in class moss.CanonicalForm
-
Build a map for reordering the nodes and edges.
- makeWord(Graph) - Method in class moss.CanonicalForm
-
Create the code word for a given graph.
- makeWord(Graph, int) - Method in class moss.CanonicalForm
-
Create the code word for the first edges of a given graph.
- makeWord(Edge[], int) - Method in class moss.CanonicalForm
-
Create the (prefix of a) code word for a given edge array.
- makeWord(Edge[], int) - Method in class moss.CnFBreadth1
-
Create the (prefix of a) code word for a given edge array.
- makeWord(Edge[], int) - Method in class moss.CnFBreadth2
-
Create the (prefix of a) code word for a given edge array.
- makeWord(Edge[], int) - Method in class moss.CnFDepth
-
Create the (prefix of a) code word for a given edge array.
- MANGANESE - Static variable in class moss.AtomTypeMgr
-
- map - Static variable in class moss.AtomTypeMgr
-
the map from element names (character pairs) to element codes
- map(CanonicalForm) - Method in class moss.Fragment
-
Reorganize the fragment with a map from a canonical form.
- map(CanonicalForm) - Method in class moss.Graph
-
Reorganize a graph with a map from a canonical form.
- mark - Variable in class moss.Edge
-
a marker for internal use (e.g.
- mark(int) - Method in class moss.Embedding
-
Mark all nodes and edges with a given value.
- mark(int) - Method in class moss.Graph
-
Mark all nodes and edges with a given value.
- mark - Variable in class moss.Node
-
a marker for internal use (e.g.
- mark(int) - Method in class moss.Node
-
Recursive function to mark a connected component.
- mark(Node) - Static method in class moss.Notation
-
Mark the visits of each node.
- markBridge(boolean) - Method in class moss.Edge
-
Set or clear the bridge flag of the edge.
- markBridges() - Method in class moss.Graph
-
Mark all edges that are bridges.
- markPseudo(int) - Method in class moss.Graph
-
Mark pseudo-rings up to a given size.
- markRing(boolean) - Method in class moss.Edge
-
Set or clear the ring type flag of the edge.
- markRings(int, int) - Method in class moss.Graph
-
Mark rings in a given size range.
- markRings(int, int, int) - Method in class moss.Graph
-
Mark rings in a given size range with a given type flag.
- masks - Variable in class moss.Miner
-
the masks for nodes and edges
- maskType(int) - Method in class moss.Edge
-
Mask the edge type with the given mask.
- maskType(int) - Method in class moss.Node
-
Mask the edge type with the given mask.
- maskTypes(int[]) - Method in class moss.Graph
-
Mask the node and edge types.
- max - Variable in class moss.CanonicalForm
-
the maximum fragment size (number of nodes)
- max - Variable in class moss.Fragment
-
the maximal number of embeddings per graph
- max - Variable in class moss.Miner
-
the maximum size of substructures to report (number of nodes)
- MaxComSub - Class in moss
-
Class for finding maximum common subgraphs.
- MaxComSub(Graph, Graph) - Constructor for class moss.MaxComSub
-
Find the maximum common subgraph of two given graphs.
- MaxComSub(Graph, Graph, boolean) - Constructor for class moss.MaxComSub
-
Find the maximum common subgraph of two given graphs.
- maxdep - Variable in class moss.Miner
-
for benchmarking: the maximum depth of the search tree
- maxepg - Variable in class moss.Miner
-
the maximum number of embeddings per graph
- maximize(int) - Method in class moss.Recoder
-
Set frequency and support to a maximal value.
- mcs - Variable in class moss.MaxComSub
-
the found maximum common subgraph (created on demand)
- MEITNERIUM - Static variable in class moss.AtomTypeMgr
-
- MENDELEVIUM - Static variable in class moss.AtomTypeMgr
-
- MERCURY - Static variable in class moss.AtomTypeMgr
-
- merge(ExtList, ExtList) - Static method in class moss.ExtList
-
Merge two sorted extension lists (and remove duplicates).
- mergeExts(Fragment[], int) - Method in class moss.Fragment
-
Merge ring extensions that have the same initial edge.
- MERGERINGS - Static variable in class moss.Miner
-
flag for merging ring extensions with the same first edge
- MIDDLE - Static variable in class moss.MoSSPanel
-
the grid bag constraints for middle input fields
- min - Variable in class moss.Miner
-
the minimum size of substructures to report (number of nodes)
- MIN_IMAGE - Static variable in class moss.Fragment
-
support type: minimum number of different nodes mapped to
- mine() - Method in class moss.Miner
-
Preprocess the graphs, embed the seed, and start the search.
- Miner - Class in moss
-
Class for the molecular substructure miner.
- Miner() - Constructor for class moss.Miner
-
Create an empty miner with default parameter settings.
- MIS_HARM - Static variable in class moss.Fragment
-
support type: maximum independent set of harmful overlap graph
- MIS_OLAP - Static variable in class moss.Fragment
-
support type: maximum independent set of normal overlap graph
- mode - Variable in class moss.CanonicalForm
-
the extension mode (e.g.
- mode - Variable in class moss.GraphReader
-
the read mode
- mode - Variable in class moss.GraphWriter
-
the write mode
- mode - Variable in class moss.Miner
-
the search mode flags
- MoleculeNtn - Class in moss
-
Class for (linear) notations for molecules.
- MoleculeNtn() - Constructor for class moss.MoleculeNtn
-
- MOLYBDENUM - Static variable in class moss.AtomTypeMgr
-
- moss - package moss
-
- MoSS - Class in moss
-
Graphical user interface for the molecular substructure miner.
- MoSS() - Constructor for class moss.MoSS
-
Create a user interface dialog box.
- MoSS(Component) - Constructor for class moss.MoSS
-
Create a user interface for the molecular substructure miner.
- MoSS(Component, boolean) - Constructor for class moss.MoSS
-
Create a user interface for the molecular substructure miner.
- MoSSPanel - Class in moss
-
Class for a tab panel for the MoSS graphical user interface.
- MoSSPanel() - Constructor for class moss.MoSSPanel
-
Create a MoSS tab panel.
- MoSSTable - Class in moss
-
Class for data tables for molecular substructure mining.
- MoSSTable(int, String) - Constructor for class moss.MoSSTable
-
Create a data table.
- name - Variable in class moss.GraphReader
-
the name/identifier of the current graph
- name - Variable in class moss.GraphWriter
-
the name of the current graph
- name - Variable in class moss.NamedGraph
-
the graph name/identifier
- NamedGraph - Class in moss
-
Class for attributed graphs with a name and a group.
- NamedGraph(Notation) - Constructor for class moss.NamedGraph
-
Create a graph with an empty name and value and group 0.
- NamedGraph(Notation, String) - Constructor for class moss.NamedGraph
-
Create a graph with value and group 0.
- NamedGraph(Notation, String, float, int) - Constructor for class moss.NamedGraph
-
Create a graph of default size with a given name and group.
- NamedGraph(Notation, int, int, String, float, int) - Constructor for class moss.NamedGraph
-
Create a graph with a given name, group and size.
- NamedGraph(Graph) - Constructor for class moss.NamedGraph
-
Turn a graph into a named graph.
- NamedGraph(Graph, String) - Constructor for class moss.NamedGraph
-
Turn a graph into a named graph.
- NamedGraph(Graph, String, float, int) - Constructor for class moss.NamedGraph
-
Turn a graph into a named graph.
- NamedGraph(NamedGraph) - Constructor for class moss.NamedGraph
-
Clone a named graph.
- names - Static variable in class moss.BondTypeMgr
-
the table of bond names; using the bond type as an index
for this table yields a printable bond description
- NEList - Class in moss
-
Class for a simple node/edge list notation.
- NEList() - Constructor for class moss.NEList
-
Create a list notation with empty type managers.
- NEList(TypeMgr, TypeMgr) - Constructor for class moss.NEList
-
Create a list notation with given type managers.
- NEListReader - Class in moss
-
Class for readers for a simple node/edge list format.
- NEListReader(Reader, int) - Constructor for class moss.NEListReader
-
Create a reader for a simple node/edge list format.
- NEListWriter - Class in moss
-
Class for writers for a simple node/edge list format.
- NEListWriter(Writer, int) - Constructor for class moss.NEListWriter
-
Create a writer for a simple node/edge list format.
- NEODYMIUM - Static variable in class moss.AtomTypeMgr
-
- NEON - Static variable in class moss.AtomTypeMgr
-
- NEPTUNIUM - Static variable in class moss.AtomTypeMgr
-
- next() - Method in class moss.CanonicalForm
-
Create the next (restricted) extension of an embedding.
- next() - Method in class moss.CnFBreadth1
-
Create the next extension.
- next() - Method in class moss.CnFBreadth2
-
Create the next extension.
- next() - Method in class moss.CnFDepth
-
Create the next extension.
- next() - Method in class moss.ExtMgr
-
Get the next extension edge.
- nextEmb() - Method in class moss.Fragment
-
Get the next embedding of the fragment.
- nextFrag() - Method in class moss.CanonicalForm
-
Create the next (restricted) extension of a fragment.
- nextFrag() - Method in class moss.CnFBreadth1
-
Create the next extended fragment.
- nextFrag() - Method in class moss.CnFBreadth2
-
Create the next extended fragment.
- nextFrag() - Method in class moss.CnFDepth
-
Create the next extended fragment.
- nextGraph() - Method in class moss.Fragment
-
Get the next graph containing the fragment.
- NICKEL - Static variable in class moss.AtomTypeMgr
-
- NIOBIUM - Static variable in class moss.AtomTypeMgr
-
- NITROGEN - Static variable in class moss.AtomTypeMgr
-
- nmap - Variable in class moss.CanonicalForm
-
the node map for making a graph canonic
- NOBELIUM - Static variable in class moss.AtomTypeMgr
-
- node - Variable in class moss.ExtList
-
the type of the destination node
- Node - Class in moss
-
Class for nodes of an attributed (labeled/typed) graph.
- Node(int) - Constructor for class moss.Node
-
Create a node with a given type (attribute/label).
- Node(int, int) - Constructor for class moss.Node
-
Create a node of a given type and given edge array size.
- nodecnt - Variable in class moss.CanonicalForm
-
the number of new nodes
- nodecnt - Variable in class moss.Graph
-
the current number of nodes
(may be smaller than the array length)
- nodecnt - Variable in class moss.Miner
-
for benchmarking: the number of search tree nodes
- nodemap - Variable in class moss.MaxComSub
-
the mapping of the nodes of graph 1 to graph 2
- nodemgr - Variable in class moss.Notation
-
the manager for the node types
- nodes - Variable in class moss.CanonicalForm
-
(relevant) nodes of the extension
- nodes - Variable in class moss.Embedding
-
the array of nodes (only references to the underlying graph)
- nodes - Variable in class moss.Graph
-
the array of nodes (may be only partially used)
- nodes - Variable in class moss.GraphReader
-
the number of nodes of the current graph
- nodes - Variable in class moss.GraphWriter
-
the number of nodes of the current graph
- nonclsd - Variable in class moss.Miner
-
for benchmarking: non-closed fragments counter
- norm - Variable in class moss.Miner
-
the canonical form for normalizing the output
- normalize(CanonicalForm) - Method in class moss.Graph
-
Normalize a graph w.r.t.
- NORMFORM - Static variable in class moss.Miner
-
flag for normalized substructure output
- NOSTATS - Static variable in class moss.Miner
-
flag for no search statistics output
- Notation - Class in moss
-
Class for notations for attributed graphs.
- Notation() - Constructor for class moss.Notation
-
- ntn - Variable in class moss.Graph
-
the notation for describing the graph
- ntn - Variable in class moss.GraphReader
-
the notation for parsing graph descriptions
- ntn - Variable in class moss.GraphWriter
-
the notation for the graphs
- NULL - Static variable in class moss.AtomTypeMgr
-
- NULL - Static variable in class moss.BondTypeMgr
-
bond type: null bond, that is,
a bond that does not actually connect two atoms
- pack() - Method in class moss.Fragment
-
Pack the list of embeddings.
- pack(int) - Method in class moss.Fragment
-
Pack the list of embeddings.
- PACKED - Static variable in class moss.Fragment
-
flag for a packed list of embeddings
- PALLADIUM - Static variable in class moss.AtomTypeMgr
-
- parse(Reader) - Method in class moss.Ctab
-
Parse the description of a molecule.
- parse(Reader) - Method in class moss.LiNoG
-
Parse a description of an attributed graph.
- parse(Reader) - Method in class moss.NEList
-
Parse a description of an attributed graph.
- parse(Reader) - Method in class moss.Notation
-
Parse a description of an attributed graph.
- parse(Reader) - Method in class moss.SLN
-
Parse a description of a molecule.
- parse(Reader) - Method in class moss.SMILES
-
Parse the description of a molecule.
- parseGraph(Reader) - Static method in class moss.OverlapGraph
-
Parse a graph description.
- PERFECT - Static variable in class moss.Fragment
-
flag for a perfect extension; set if the fragment was created
by a perfect extension of its base fragment
- perfect - Variable in class moss.Miner
-
for benchmarking: perfect extension pruning counter
- PHOSPHORUS - Static variable in class moss.AtomTypeMgr
-
- PLATINUM - Static variable in class moss.AtomTypeMgr
-
- PLUTONIUM - Static variable in class moss.AtomTypeMgr
-
- pmax - Variable in class moss.CanonicalForm
-
the maximal position/position index of a ring edge
- pmin - Variable in class moss.CanonicalForm
-
the minimal position/current position index of a ring edge
- POLONIUM - Static variable in class moss.AtomTypeMgr
-
- pos1 - Variable in class moss.CanonicalForm
-
the current position 1 of equivalent edges for ring extensions
- pos2 - Variable in class moss.CanonicalForm
-
the current position 2 of equivalent edges for ring extensions
- POTASSIUM - Static variable in class moss.AtomTypeMgr
-
- PR_CANONIC - Static variable in class moss.Miner
-
flag for canonical form pruning
- PR_EQUIV - Static variable in class moss.Miner
-
flag for equivalent sibling extension pruning
- PR_PARTIAL - Static variable in class moss.Miner
-
flag for partial perfect extension pruning
- PR_PERFECT - Static variable in class moss.Miner
-
flag for full perfect extension pruning
- PR_UNCLOSE - Static variable in class moss.Miner
-
flag for pruning fragments with unclosable rings
- PRASEODYMIUM - Static variable in class moss.AtomTypeMgr
-
- prepare(Fragment) - Method in class moss.CanonicalForm
-
Prepare the rings of a fragment for adaptation and order test.
- prepare() - Method in class moss.Graph
-
Prepare a graph for frequent substructure mining.
- prepareEmbed() - Method in class moss.Graph
-
Prepare a graph for embedding it into another.
- PROMETHIUM - Static variable in class moss.AtomTypeMgr
-
- PROTACTINIUM - Static variable in class moss.AtomTypeMgr
-
- RADIUM - Static variable in class moss.AtomTypeMgr
-
- RADON - Static variable in class moss.AtomTypeMgr
-
- read(File) - Method in class moss.MoSSTable
-
Read table from an input stream.
- read() - Method in class moss.Notation
-
Read the next character.
- reader - Variable in class moss.Miner
-
the graph data set file reader
- reader - Variable in class moss.Notation
-
the reader from which to read the graph description
- readGraph() - Method in class moss.GraphReader
-
Read a graph.
- readGraph() - Method in class moss.NEListReader
-
Read a graph.
- readGraph() - Method in class moss.SDfileReader
-
Get the next graph description.
- readGraph() - Method in class moss.TableReader
-
Read the next graph description.
- readHeader() - Method in class moss.GraphReader
-
Read an (optional) header.
- readHeader() - Method in class moss.NEListReader
-
Read an (optional) header.
- readHeader() - Method in class moss.SDfileReader
-
Read an (optional) header.
- readHeader() - Method in class moss.TableReader
-
Read an (optional) table header.
- readLine() - Method in class moss.SDfileReader
-
Read the next input line.
- recnt - Variable in class moss.Miner
-
the size of the repository (number of substructures)
- Recoder - Class in moss
-
Class for recoders for node types.
- Recoder() - Constructor for class moss.Recoder
-
Create a recoder of default size.
- RECSEP - Static variable in class moss.TableReader
-
class/type flag: record separator
- reembed() - Method in class moss.Fragment
-
Reembed a fragment, that is, recreate its embedding list.
- removeCharge(int) - Static method in class moss.AtomTypeMgr
-
Remove the charge from an atom type.
- removeExts(int) - Static method in class moss.AtomTypeMgr
-
Remove the extended information from an atom type.
- removeHydros(int) - Static method in class moss.AtomTypeMgr
-
Remove the hydrogens from an atom type.
- removeRings(Edge) - Static method in class moss.CanonicalForm
-
Remove the flags of all rings an edge is contained in.
- repcnt - Variable in class moss.Miner
-
for benchmarking: the number of repository accesses
- report(Fragment) - Method in class moss.Miner
-
Check and report a found fragment/substructure.
- revert() - Method in class moss.Fragment
-
Revert the extension information of the fragment.
- REVERTED - Static variable in class moss.Fragment
-
flag for reverted extension information
- rgmax - Variable in class moss.CanonicalForm
-
the maximum ring size (number of nodes/edges)
- rgmax - Variable in class moss.Miner
-
the maximum size of rings (number of nodes/edges)
- rgmin - Variable in class moss.CanonicalForm
-
the minimum ring size (number of nodes/edges)
- rgmin - Variable in class moss.Miner
-
the minimum size of rings (number of nodes/edges)
- RHENIUM - Static variable in class moss.AtomTypeMgr
-
- RHODIUM - Static variable in class moss.AtomTypeMgr
-
- RIGHT - Static variable in class moss.MoSSPanel
-
the grid bag constraints for right input fields
- RING - Static variable in class moss.CanonicalForm
-
extension mode flag: ring (must be marked)
- ring() - Method in class moss.CanonicalForm
-
Create a ring extension.
- RING - Static variable in class moss.Edge
-
the flag for the edge type to distinguish ring edges
- ring - Variable in class moss.ExtList
-
the ring information (if needed)
- RINGEXT - Static variable in class moss.Miner
-
flag for extensions by rings
- RINGMASK - Static variable in class moss.Edge
-
the mask to extract the ring flags
- ringord - Variable in class moss.Miner
-
for benchmarking: ring order pruning counter
- ris - Variable in class moss.Fragment
-
the indices of the nodes of new ring edges
- rno() - Method in class moss.TableReader
-
Get a string stating the current record number.
- rno(int) - Method in class moss.TableReader
-
Get a string stating the current record number.
- ROENTGENIUM - Static variable in class moss.AtomTypeMgr
-
- RUBIDIUM - Static variable in class moss.AtomTypeMgr
-
- run() - Method in class moss.Miner
-
Run the miner and clean up after the search finished.
- run() - Method in class moss.MoSS
-
Create the user interface dialog box.
- RUTHENIUM - Static variable in class moss.AtomTypeMgr
-
- RUTHERFORDIUM - Static variable in class moss.AtomTypeMgr
-
- sabs - Variable in class moss.GraphReader
-
the absolute support in the focus
- sabs - Variable in class moss.GraphWriter
-
the absolute support in the focus
- SAMARIUM - Static variable in class moss.AtomTypeMgr
-
- SAMETYPE - Static variable in class moss.BondTypeMgr
-
a mask, to be anded (bitwise &) with a bond type
in order to remove any distinction of bond types
- SCANDIUM - Static variable in class moss.AtomTypeMgr
-
- SDfileReader - Class in moss
-
Class for readers for structure-data files (SDfile, Elsevier MDL).
- SDfileReader(Reader, int) - Constructor for class moss.SDfileReader
-
Create a reader for SDfiles.
- SDfileWriter - Class in moss
-
Class for writers for structure-data files (SDfile, Elsevier MDL).
- SDfileWriter(Writer, int) - Constructor for class moss.SDfileWriter
-
Create a writer for SDfiles.
- SEABORGIUM - Static variable in class moss.AtomTypeMgr
-
- seed - Variable in class moss.Miner
-
the seed structure to start the search from
- SELENIUM - Static variable in class moss.AtomTypeMgr
-
- setAbsCompl(int) - Method in class moss.GraphWriter
-
Set the absolute complement support of the current substructure.
- setAbsSupp(int) - Method in class moss.GraphWriter
-
Set the absolute focus support of the current substructure.
- setChainTypes(int, int) - Method in class moss.CanonicalForm
-
Set the node and edge type for chain extensions.
- setChars(int, String) - Method in class moss.TableReader
-
Set the characters for a specific type/class.
- setChars(String, String, String, String) - Method in class moss.TableReader
-
Set the characters for all types.
- setChars(char, char) - Method in class moss.TableWriter
-
Set the record and field separators.
- setClosed(boolean) - Method in class moss.Fragment
-
Set the flag for a closed fragment.
- setCnF(CanonicalForm) - Method in class moss.Miner
-
Set the canonical form.
- setEdgeMgr(TypeMgr) - Method in class moss.FreeNtn
-
Set the edge type manager.
- setEdgeMgr(TypeMgr) - Method in class moss.MoleculeNtn
-
Set the edge type manager.
- setEdgeMgr(TypeMgr) - Method in class moss.Notation
-
Set the edge type manager.
- setEmbed(int, int) - Method in class moss.Miner
-
Set the embeddings parameters.
- setExcluded(Graph, Graph) - Method in class moss.Miner
-
Set the excluded nodes and excluded seeds.
- setExcluded(String, String, String) - Method in class moss.Miner
-
Set the excluded nodes and excluded seeds.
- setExtMgr(ExtMgr) - Method in class moss.CanonicalForm
-
Set the extension edge manager.
- setExtMode(int) - Method in class moss.CanonicalForm
-
Set the extension mode.
- setGraph(Graph) - Method in class moss.GraphWriter
-
Set the current graph or substructure.
- setGroup(int) - Method in class moss.NamedGraph
-
Set the group of this graph.
- setGrouping(double, boolean) - Method in class moss.Miner
-
Set the grouping parameters.
- setInput(GraphReader) - Method in class moss.Miner
-
Set the input reader.
- setInput(String, String) - Method in class moss.Miner
-
Set the input reader.
- setLimits(double, double) - Method in class moss.Miner
-
Set the support limits.
- setLog(PrintStream) - Method in class moss.Miner
-
Sets the stream to which progress messages are written.
- setMasks(int, int, int, int) - Method in class moss.Miner
-
Set the node and edge masks.
- setMaxSize(int) - Method in class moss.CanonicalForm
-
Set the maximum fragment size (to limit extensions).
- setMode(int) - Method in class moss.Miner
-
Set the search mode.
- setName(String) - Method in class moss.GraphWriter
-
Set the name of the current graph.
- setName(String) - Method in class moss.NamedGraph
-
Set the name of this graph.
- setNodeMgr(TypeMgr) - Method in class moss.FreeNtn
-
Set the node type manager.
- setNodeMgr(TypeMgr) - Method in class moss.MoleculeNtn
-
Set the node type manager.
- setNodeMgr(TypeMgr) - Method in class moss.Notation
-
Set the node type manager.
- setOutput(GraphWriter) - Method in class moss.Miner
-
Set the output writer.
- setOutput(GraphWriter, Writer) - Method in class moss.Miner
-
Set the output writers.
- setOutput(String, String) - Method in class moss.Miner
-
Set the output writer.
- setOutput(String, String, String) - Method in class moss.Miner
-
Set the output writers.
- setReader(Reader) - Method in class moss.Notation
-
Set the reader to read from.
- setRelCompl(float) - Method in class moss.GraphWriter
-
Set the relative complement support of the current substructure.
- setRelSupp(float) - Method in class moss.GraphWriter
-
Set the relative focus support of the current substructure.
- setRingSizes(int, int) - Method in class moss.CanonicalForm
-
Set the ring sizes for ring extensions.
- setRingSizes(int, int) - Method in class moss.Miner
-
Set the minimum and maximum ring size.
- setSeed(Graph) - Method in class moss.Miner
-
Set the seed structure to start the search from.
- setSeed(String, String) - Method in class moss.Miner
-
Set the seed structure to start the search from.
- setSizes(int, int) - Method in class moss.Miner
-
Set the minimum and maximum fragment size.
- setType(int) - Method in class moss.Miner
-
Set the support type.
- setTypeMgrs(Notation) - Method in class moss.Notation
-
Set the type managers from another notation.
- setValid(boolean) - Method in class moss.Fragment
-
Set or clear the valid flag.
- setValue(float) - Method in class moss.GraphWriter
-
Set the value associated with the current graph.
- setValue(float) - Method in class moss.NamedGraph
-
Set the value of this graph.
- setValueAt(Object, int, int) - Method in class moss.MoSSTable
-
Set the value of a table cell from an object.
- SIBLINGS - Static variable in class moss.Fragment
-
flag for possible equivalent siblings
- SILICON - Static variable in class moss.AtomTypeMgr
-
- SILVER - Static variable in class moss.AtomTypeMgr
-
- SINGLE - Static variable in class moss.BondTypeMgr
-
bond type: single
- size - Variable in class moss.CanonicalForm
-
the number of nodes in a ring (positive) or chain (negative)
- size - Variable in class moss.Fragment
-
the number of nodes in a ring or chain
(positive: ring, negative: chain)
- size() - Method in class moss.Fragment
-
Get the size of the fragment.
- size() - Method in class moss.FreeTypeMgr
-
Get the current number of types.
- size() - Method in class moss.OverlapGraph
-
Get the size of the overlap graph (number of nodes).
- size() - Method in class moss.Recoder
-
Get the size of the recoder.
- SLN - Class in moss
-
Class for the SYBYL line notation (SLN, Tripos, Inc.).
- SLN() - Constructor for class moss.SLN
-
Create a SYBYL line notation object.
- SMALL - Static variable in class moss.MoSSPanel
-
the font for help text fields
- SMILES - Class in moss
-
Class for the Simplified Molecular Input Line Entry System
(SMILES, Daylight, Inc.).
- SMILES() - Constructor for class moss.SMILES
-
Create a SMILES notation object.
- SODIUM - Static variable in class moss.AtomTypeMgr
-
- sort(ExtList) - Static method in class moss.ExtList
-
Sort an extension list (and remove duplicates).
- sort() - Method in class moss.ExtMgr
-
Sort the extension edges lexicographically.
- sort() - Method in class moss.Recoder
-
Sort types w.r.t. their frequency.
- sortEdges() - Method in class moss.Node
-
Sort the edges that are incident to the node.
- sortvec() - Method in class moss.ExtMgr
-
Sort the extension edges lexicographically.
- SPECIAL - Static variable in class moss.TypeMgr
-
the flag for a special type
- split() - Method in class moss.NamedGraph
-
Split a graph into its connected components.
- src - Variable in class moss.CanonicalForm
-
the index of the current source node
- src - Variable in class moss.Edge
-
the source node of the edge
- src - Variable in class moss.ExtList
-
the index of the source node
- src - Variable in class moss.Fragment
-
the index of the source node of the (first) new edge
- srel - Variable in class moss.GraphReader
-
the relative support in the focus
- srel - Variable in class moss.GraphWriter
-
the relative support in the focus
- stack - Variable in class moss.Notation
-
the stack of unread/pushed back characters
- stateChanged(ChangeEvent) - Method in class moss.MoSS
-
Handle the state change of the ring marking check box.
- stats() - Method in class moss.Miner
-
Print statistics about the search.
- STRONTIUM - Static variable in class moss.AtomTypeMgr
-
- subcnt - Variable in class moss.Miner
-
the number of reported substructures
- SUBS - Static variable in class moss.GraphReader
-
read mode: substructures
- SUBS - Static variable in class moss.GraphWriter
-
write mode: substructures
- SUBS - Static variable in class moss.MoSSTable
-
mode: substructures
- succ - Variable in class moss.Embedding
-
the next embedding in a list of embeddings
- succ - Variable in class moss.ExtList
-
the successor in a list
- succ - Variable in class moss.NamedGraph
-
the next graph in a list
- SULFUR - Static variable in class moss.AtomTypeMgr
-
- supp - Variable in class moss.Fragment
-
the support and embedding counters for focus and complement
- supp - Variable in class moss.Miner
-
the minimum support in the focus as an absolute value
- SUPPMASK - Static variable in class moss.Fragment
-
the support type mask
- sym - Variable in class moss.CanonicalForm
-
whether the current ring is locally symmetric
- TableReader - Class in moss
-
Class for readers for simple table formats for graph data sets.
- TableReader(Reader, int, Notation) - Constructor for class moss.TableReader
-
Create a table reader with default character flags.
- TableWriter - Class in moss
-
Class for writers for simple table formats for graph data sets.
- TableWriter(Writer, int, Notation) - Constructor for class moss.TableWriter
-
Create a simple table format writer.
- tail - Variable in class moss.Fragment
-
the tail of the embedding list
- tail - Variable in class moss.Miner
-
the tail of the list of graphs (insertion point for complement)
- TANTALUM - Static variable in class moss.AtomTypeMgr
-
- TECHNETIUM - Static variable in class moss.AtomTypeMgr
-
- TELLURIUM - Static variable in class moss.AtomTypeMgr
-
- TERBIUM - Static variable in class moss.AtomTypeMgr
-
- term() - Method in class moss.Miner
-
Clean up after the search finished or was aborted.
- THALLIUM - Static variable in class moss.AtomTypeMgr
-
- THORIUM - Static variable in class moss.AtomTypeMgr
-
- thresh - Variable in class moss.Miner
-
the threshold for the split into focus and complement
- THULIUM - Static variable in class moss.AtomTypeMgr
-
- TIN - Static variable in class moss.AtomTypeMgr
-
- TITANIUM - Static variable in class moss.AtomTypeMgr
-
- toLogic() - Method in class moss.NamedGraph
-
Create a Prolog description of this graph.
- toString() - Method in class moss.Fragment
-
Create a string description of the fragment.
- toString(Notation) - Method in class moss.Fragment
-
Create a string description of the fragment.
- toString(CanonicalForm) - Method in class moss.Fragment
-
Create the code word of the fragment.
- toString() - Method in class moss.Graph
-
Create a string description of the graph.
- toString(Notation) - Method in class moss.Graph
-
Create a string description in the given notation.
- toString(CanonicalForm) - Method in class moss.Graph
-
Create a code word for a given canonical form.
- TRANSFORM - Static variable in class moss.Miner
-
flag for conversion to another description format
- trim(Recoder) - Method in class moss.ExtMgr
-
Trim the extension edges.
- trim(boolean) - Method in class moss.Graph
-
Trim a graph based on its encoding recoder.
- trim(boolean, int) - Method in class moss.Recoder
-
Trim the recoder with a minimum support or frequency.
- trim(int) - Method in class moss.Recoder
-
Trim the recoder with a minimum support.
- trimFreq(int) - Method in class moss.Recoder
-
Trim the recoder with a minimum frequency.
- trimSupp(int) - Method in class moss.Recoder
-
Trim the recoder with a minimum support.
- TRIPLE - Static variable in class moss.BondTypeMgr
-
bond type: triple
- TUNGSTEN - Static variable in class moss.AtomTypeMgr
-
- type - Variable in class moss.CanonicalForm
-
the type of the extension edge (from EDGE.type
)
- type - Variable in class moss.Edge
-
the type of the edge, e.g.
- type - Variable in class moss.Miner
-
the type of support to use
- type - Variable in class moss.Node
-
the type (attribute/label) of a node (including flags)
- TYPEMASK - Static variable in class moss.Edge
-
the mask for the base type
- TYPEMASK - Static variable in class moss.Node
-
the mask for the base type
- TypeMgr - Class in moss
-
Class for a node or edge type manager.
- TypeMgr() - Constructor for class moss.TypeMgr
-