Ejemplo n.º 1
0
        public void ContractChains()
        {
            HasseNodeCollection VisitedNodes = new HasseNodeCollection();
            // identify vertices with one edge in and one edge out, put them on remove list
            List <HasseNode> ToBeRemoved = new List <HasseNode>();

            foreach (HasseNode Node in HasseDiagramNodes.Values)
            {
                if (!VisitedNodes.ContainsKey(Node.KeyString))
                {
                    if (Node.EdgesToCovered.Count == 1 && Node.EdgesToCovering.Count == 1)
                    {
                        ToBeRemoved.Add(Node);
                    }
                    VisitedNodes.Add(Node.KeyString, Node);
                }
            }

            //now contract nodes A-B-C to form A-C, then throw away B
            foreach (HasseNode Node in ToBeRemoved)
            {
                HasseNode Node1 = Node.EdgesToCovered[0].LowerNode;
                HasseNode Node2 = Node.EdgesToCovering[0].UpperNode;
                this.MakeEdge(Node1, Node2);
                this.RemoveEdge(Node.EdgesToCovered[0]);
                this.RemoveEdge(Node.EdgesToCovering[0]);
                HasseDiagramNodes.Remove(Node.KeyString);
            }
        }
Ejemplo n.º 2
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        private void WriteEdge(HasseEdge E)
        {
            HasseNode Node1 = E.LowerNode;
            HasseNode Node2 = E.UpperNode;

            if ((Node1.KeyString.Contains("\"")) || (Node2.KeyString.Contains("\"")))
            {
                throw new Exception("disallowed character: double quote");
            }

            DotFile.Write(DoubleQuoted(Node2.KeyString)); // node 2 key

            DotFile.Write(" -> ");                        // arrow

            DotFile.Write(DoubleQuoted(Node1.KeyString)); // node 1 key

            DotFile.Write("[dir=back ");
            if (Node1.DrawingColor != "")
            {
                DotFile.Write(" color=" + Node1.DrawingColor + " ");
            }
            DotFile.Write(" shape=vee ");
            if (this.WriteEdgeLabels)
            {
                DotFile.Write("label=");
                DotFile.Write(DoubleQuoted(E.LabelText));
            }
            DotFile.Write("]");

            DotFile.WriteLine(";");
        }
Ejemplo n.º 3
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 public override bool GetMaxCommonFragments(
     HasseNode Node1, HasseNode Node2,
     bool dbg, HasseFragmentInsertionQueue NewFragmentList,
     int MinimumOverlap)
 {
     return(ChemObject.GetMaxCommonFragments(this, Node1, Node2, dbg, NewFragmentList, MinimumOverlap));
 }
Ejemplo n.º 4
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 public override string[] GetDifferenceString(HasseNode LargerNode)
 {
     List<string> DiffList = new List<string>() ;
     string SmallString = this.KeyString.Replace("*", "");
     int MatchPosFirst = GetNextMatch(0, SmallString, LargerNode.KeyString);
     int MatchposLast = MatchPosFirst + SmallString.Length-1;
                 while (MatchPosFirst > -1)
                 {
                     string strL = LargerNode.KeyString.Substring(0, MatchPosFirst );
                     if (strL.Length > 0 && (!strL.Equals("*")))
                     {
                         // last char in small string matches (non-star) character ?
                         if (LargerNode.KeyString.Length > strL.Length && (!LargerNode.KeyString.Substring(strL.Length, 1).Equals("*")))
                             strL = strL + "*" ;
                             DiffList.Add(strL);
                     }
                     string strR = LargerNode.KeyString.Substring(MatchPosFirst + SmallString.Length);
                     if (strR.Length > 0 && (!strR.Equals("*")))
                     {
                         if ((MatchPosFirst + SmallString.Length) > 0 && (!LargerNode.KeyString.Substring(MatchPosFirst + SmallString.Length - 1, 1).Equals("*")))
                             strR = "*" + strR;
                         DiffList.Add(strR);
                     }
                     MatchPosFirst = GetNextMatch(MatchPosFirst + 1, SmallString, LargerNode.KeyString);
                 }
     //return new string[]{};
     string[] s = DiffList.ToArray();
     return s;
 }
Ejemplo n.º 5
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        public void RemoveNodeFromHasseDiagram(HasseNode Node)
        {
            HasseEdge[] CoveredEdges  = Node.EdgesToCovered.ToArray();
            HasseEdge[] CoveringEdges = Node.EdgesToCovering.ToArray();

            // form the new edges;
            foreach (HasseEdge CoveredEdge in CoveredEdges)
            {
                foreach (HasseEdge CoveringEdge in CoveringEdges)
                {
                    MakeEdge(CoveredEdge.LowerNode, CoveringEdge.UpperNode);
                }
            }
            // remove all edges involving Node
            foreach (HasseEdge CoveredEdge in CoveredEdges)
            {
                RemoveEdge(CoveredEdge);
            }
            foreach (HasseEdge CoveringEdge in CoveringEdges)
            {
                RemoveEdge(CoveringEdge);
            }
            // remove Node from Node dictionary
            HasseDiagramNodes.Remove(Node.KeyString);
        }
        public override string[] GetDifferenceString(HasseNode LargerNode)
        {
            List <string> DiffList      = new List <string>();
            string        SmallString   = this.KeyString.Replace("*", "");
            int           MatchPosFirst = GetNextMatch(0, SmallString, LargerNode.KeyString);
            int           MatchposLast  = MatchPosFirst + SmallString.Length - 1;

            while (MatchPosFirst > -1)
            {
                string strL = LargerNode.KeyString.Substring(0, MatchPosFirst);
                if (strL.Length > 0 && (!strL.Equals("*")))
                {
                    // last char in small string matches (non-star) character ?
                    if (LargerNode.KeyString.Length > strL.Length && (!LargerNode.KeyString.Substring(strL.Length, 1).Equals("*")))
                    {
                        strL = strL + "*";
                    }
                    DiffList.Add(strL);
                }
                string strR = LargerNode.KeyString.Substring(MatchPosFirst + SmallString.Length);
                if (strR.Length > 0 && (!strR.Equals("*")))
                {
                    if ((MatchPosFirst + SmallString.Length) > 0 && (!LargerNode.KeyString.Substring(MatchPosFirst + SmallString.Length - 1, 1).Equals("*")))
                    {
                        strR = "*" + strR;
                    }
                    DiffList.Add(strR);
                }
                MatchPosFirst = GetNextMatch(MatchPosFirst + 1, SmallString, LargerNode.KeyString);
            }
            //return new string[]{};
            string[] s = DiffList.ToArray();
            return(s);
        }
Ejemplo n.º 7
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        public override bool GetMaxCommonFragments(
            HasseNode Node1, HasseNode Node2,
            bool dbg, HasseFragmentInsertionQueue NewFragmentList,
            int MinimumOverlap)
        {
            string           debugInfo = "";
            HasseFingerprint fp1       = ((FingerprintChemHasseNode)Node1).hFingerprint;
            HasseFingerprint fp1_clone = fp1.CloneHasseFingerprint();
            HasseFingerprint fp2       = ((FingerprintChemHasseNode)Node2).hFingerprint;

            fp1_clone.AndBits(fp2);
            if (fp1_clone.bitCount >= MinimumOverlap)
            {
                string strMCS = fp1_clone.ToHex();

                HasseFingerprint test = new HasseFingerprint();
                test.FromHex(strMCS);

                NewFragmentList.Add(
                    new HasseNode[1] {
                    this
                },                                    // this is lower than new frag
                    new HasseNode[2] {
                    Node1, Node2
                },                                                                                               // those are higher than new frag
                    strMCS,                                                                                      // string to use for new node creation later
                    debugInfo, HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT, // type of frag
                    null                                                                                         // this new frag is not associated with a single edge
                    );
                return(true);
            }
            return(false);
        }
Ejemplo n.º 8
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        public static String Report(HasseNodeCollection nodes, HasseNode rootNode)
        {
            int countLeaves = 0;
            int countReals = 0;
            foreach (HasseNode node in nodes.Values)
            {
                if (node.IsLeafNode()) countLeaves++;
                if (node.HasNodeType (HasseNode.HasseNodeTypes.REAL)) countReals ++;
            }

            StringBuilder sb = new StringBuilder();

            sb.AppendLine("Leaf count: " + countLeaves.ToString () );
            sb.AppendLine("REAL count: " + countReals.ToString () );

            // how selective are the root nodes?
            // the average root node, how many parents, of all?

            List<HasseNodeCollection> NodesInLevel = new List<HasseNodeCollection>();
            int CountUpwardEdges = 0;
            int CountLeafNodes = 0;
            int countAllLeaves = 0;
            HasseNodeCollection NodesOnThisLevel = new HasseNodeCollection();
            NodesOnThisLevel.Add(rootNode.KeyString , rootNode);

            HasseNodeCollection NodesOnThisLevelPlusOne = new HasseNodeCollection();

            for (int level = 1; ;level++ )
            {
                CountUpwardEdges = 0;
                CountLeafNodes = 0;
                foreach (HasseNode node in NodesOnThisLevel.Values)
                {
                    node.LevelFromRoot = level;
                    foreach (HasseEdge EdgeUpToParent in node.EdgesToCovering )
                    {
                        HasseNode Parent = EdgeUpToParent.UpperNode;
                        CountUpwardEdges++;
                        if (!NodesOnThisLevelPlusOne.ContainsKey(Parent.KeyString))
                        {
                            NodesOnThisLevelPlusOne.Add(Parent.KeyString, Parent);
                        }
                    }
                    if (node.EdgesToCovering.Count == 0)
                    { CountLeafNodes++; countAllLeaves++; }
                }

                sb.AppendLine("at level " + level.ToString() + ";\tnodes: " + NodesOnThisLevel.Count.ToString() + "\tsum upward edges: " +  CountUpwardEdges.ToString() + "\t count leaf nodes: " +  CountLeafNodes.ToString());

                NodesInLevel.Add(NodesOnThisLevel);
               if (NodesOnThisLevelPlusOne.Count ==0) {break;}
                NodesOnThisLevel = NodesOnThisLevelPlusOne;
                NodesOnThisLevelPlusOne = new  HasseNodeCollection();
            }
            sb.AppendLine("total node count: " + nodes.Count.ToString());
            sb.AppendLine("total leaves count: " + countAllLeaves.ToString());

            return sb.ToString ();
        }
Ejemplo n.º 9
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        public override string[] GetDifferenceString(HasseNode LargerNode)
        {
            if (this.NodeType == HasseNodeTypes.ROOT)
            {
                return(new string[] { }); //TODO - is this right?
            }

            return(ChemObject.GetDifferenceString(LargerNode));
        }
Ejemplo n.º 10
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 void InsertFragmentsInQueue()
 {
     while (FragmentInsertionQueue.Count > 0)
     {
         FragmentToBeInserted F    = FragmentInsertionQueue.Dequeue();
         HasseNode            Frag = this.diagramNodeFactory.NewNode(F.NewNodeContent, HasseNode.HasseNodeTypes.FRAGMENT, "frag from " + F.Origin);
         bool NodeWasInserted      = addNode(Frag, null, null);
     }
 }
Ejemplo n.º 11
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        public HasseNode  AddNode(string NodeContentString)
        {
            HasseNode newNode = CreateNewNode(NodeContentString);

            //HasseNode newNode=  this.diagramNodeFactory.NewNode (NodeContentString, HasseNode.HasseNodeTypes.REAL ,  "");
            addNode(newNode, null, null);
            InsertFragmentsInQueue();
            return(newNode);
        }
Ejemplo n.º 12
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        public void FindLUBAndGLB(HasseNode newNode, ref HasseNodeCollection lub, ref HasseNodeCollection glb)
        {
            bool dbgTimings     = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_TIMINGS);
            bool dbgComparisons = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_COMPARISON_COUNTS);

            //glb = BruteForceFindGlb(newNode, HasseDiagramNodes);
            //lub = BruteForceFindLub(newNode, HasseDiagramNodes);
            glb = FindGlb(newNode, HasseDiagramNodes);
            lub = FindLub(newNode, HasseDiagramNodes);
        }
Ejemplo n.º 13
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 private bool ExistsEdge(HasseNode N1, HasseNode N2)
 {
     foreach (HasseEdge E in N1.EdgesToCovering)
     {
         if (E.UpperNode == N2)
         {
             return(true);
         }
     }
     return(false);
 }
Ejemplo n.º 14
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        private void DrawCoveringNodes(int level, HasseNode Node)
        {
            string spaces = new string('-', level * 2);

            //if (Node.NodesCovering().Values.Count >5  )
            System.Diagnostics.Debug.WriteLine(Node.Weight().ToString() + "\t" + spaces + Node.KeyString);

            foreach (HasseEdge e in Node.EdgesToCovering)
            {
                DrawCoveringNodes(level + 1, e.UpperNode);
            }
        }
Ejemplo n.º 15
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 private void MakeEdgeIfNotExists(HasseNode N1, HasseNode N2)
 {
     // Todo for max efficiency check if count covered from N2 is lower
     foreach (HasseEdge E in N1.EdgesToCovering)
     {
         if (E.UpperNode == N2)
         {
             return;
         }
     }
     MakeEdge(N1, N2);
 }
Ejemplo n.º 16
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        public static HasseNodeCollection FindLub(HasseNode ReferenceNode, HasseNodeCollection AllNodes)
        {
            bool dbg = Convert.ToBoolean(DEBUGLEVEL & LOG_DEBUG_MAKE_LUB);
            HasseNodeCollection lub = new HasseNodeCollection();
            //List<string> ToBeRemoved = new List<string>();
            HashSet <string> ToBeRemoved = new HashSet <string>();

            foreach (HasseNode Node in AllNodes.Values)
            {
                if (!ToBeRemoved.Contains(Node.KeyString))
                {
                    System.Diagnostics.Debug.WriteLineIf(dbg, "test if " + Node.KeyString + " is larger than " + ReferenceNode.KeyString);


                    // debug:
                    //HasseNode[] subobj = ReferenceNode.getElementarySubobjects().Values.ToArray();
                    //if (!Node.HasElements(subobj) &&
                    //    (Node.IsLargerThan(ReferenceNode)))
                    //{
                    //    System.Diagnostics.Debugger.Break();
                    //}


                    if (Node.IsLargerThan(ReferenceNode))
                    {
                        System.Diagnostics.Debug.WriteLineIf(dbg, " yes - is lub candidate, delete above...");
                        lub.Add(Node.KeyString, Node);
                        FindNodesAbove(Node, ToBeRemoved, 0);
                    }

                    /*
                     * else if (ReferenceNode.IsLargerThan(Node))
                     * {
                     *  DeleteNodesBelow(Node, ToBeRemoved, 0);
                     * }
                     */
                    else
                    {
                        ToBeRemoved.Add(Node.KeyString);
                    }
                }
            }

            foreach (string key in ToBeRemoved)
            {
                lub.Remove(key);
            }

            return(lub);
        }
Ejemplo n.º 17
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 private static void FindNodesAbove(HasseNode Node, HashSet <string> NodeKeys, int level)
 {
     foreach (HasseEdge EdgeToCovering in Node.EdgesToCovering)
     {
         if (!NodeKeys.Contains(EdgeToCovering.UpperNode.KeyString))
         {
             FindNodesAbove(EdgeToCovering.UpperNode, NodeKeys, level + 1);
         }
     }
     if (level > 0)
     {
         NodeKeys.Add(Node.KeyString);
     }
 }
Ejemplo n.º 18
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 private static void FindNodesBelow(HasseNode Node, HashSet <string> NodeKeys, int level)
 {
     foreach (HasseEdge E in Node.EdgesToCovered)
     {
         if (!NodeKeys.Contains(E.LowerNode.KeyString))
         {
             FindNodesBelow(E.LowerNode, NodeKeys, level + 1);
         }
     }
     if (level > 0)
     {
         NodeKeys.Add(Node.KeyString);
     }
 }
Ejemplo n.º 19
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        private List <HasseEdge> InsertNodeBetweenGlbAndLub(
            HasseNode newNode,
            HasseNodeCollection collectionLUB,
            HasseNodeCollection collectionGLB, bool debug)
        {
            bool             dbg        = Convert.ToBoolean(DEBUGLEVEL & LOG_INSERTIONS);
            List <HasseEdge> AddedEdges = new List <HasseEdge>();
            // break any existing relations between LUBs and GLBs
            // first make list of edges to delete
            List <HasseEdge> EdgesToBeDeleted = new List <HasseEdge>();

            foreach (HasseNode v_low in collectionGLB.Values)
            {
                foreach (HasseNode v_high in collectionLUB.Values)
                {
                    System.Diagnostics.Debug.WriteLineIf(dbg, "cut " + v_low.KeyString + " - " + v_high.KeyString);
                    foreach (HasseEdge E in v_low.EdgesToCovering)
                    {
                        if (E.UpperNode == v_high)
                        {
                            EdgesToBeDeleted.Add(E);
                        }
                    }
                }
            }

            foreach (HasseEdge E in EdgesToBeDeleted)
            {
                RemoveEdge(E);
            }



            //make differences between elements and new
            foreach (HasseNode v_low in collectionGLB.Values)
            {
                System.Diagnostics.Debug.WriteLineIf(dbg, "cover (I)  " + v_low.KeyString + " with " + newNode.KeyString);
                HasseEdge NewEdge = MakeEdge(v_low, newNode);
                AddedEdges.Add(NewEdge);
            }

            //make relations between new and LUBs
            foreach (HasseNode v_high in collectionLUB.Values)
            {
                System.Diagnostics.Debug.WriteLineIf(dbg, "cover (II) " + newNode.KeyString + " with " + v_high.KeyString);
                MakeEdge(newNode, v_high);
            }

            return(AddedEdges);
        }
Ejemplo n.º 20
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        public override bool IsLargerThan(HasseNode smallobj)
        {
            if (this.HasNodeType(HasseNodeTypes.ROOT))
            {
                return(false);
            }
            if (smallobj.HasNodeType(HasseNodeTypes.ROOT))
            {
                return(true);
            }
            bool retval = this.hFingerprint.IsLargerThan(((FingerprintChemHasseNode )smallobj).hFingerprint);

            // if (retval == true) System.Diagnostics.Debugger.Break();
            return(retval);
        }
Ejemplo n.º 21
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        public void ContractChains2()
        {
            // identify vertices with one edge out, put them on remove list
            HasseNodeCollection VisitedNodes = new HasseNodeCollection();
            List <HasseNode>    ToBeRemoved  = new List <HasseNode>();

            foreach (HasseNode Node in HasseDiagramNodes.Values)
            {
                if (!VisitedNodes.ContainsKey(Node.KeyString))
                {
                    if (Node.EdgesToCovering.Count == 1)
                    {
                        foreach (HasseEdge TheCoveringEdge in Node.EdgesToCovering)
                        {
                            if (TheCoveringEdge.UpperNode.EdgesToCovered.Count == 1)
                            {
                                ToBeRemoved.Add(Node);
                            }
                        }
                    }
                    VisitedNodes.Add(Node.KeyString, Node);
                }
            }

            //now contract nodes A-B to form B
            // B must inherit innodes as into A, then throw away A
            foreach (HasseNode Node in ToBeRemoved)
            {
                HasseEdge EdgeUpToCovering = Node.EdgesToCovering[0];
                HasseNode NodeCovering     = EdgeUpToCovering.UpperNode;
                //HasseNode Node2 = null;

                System.Diagnostics.Debug.WriteLine("contract  [" + Node.KeyString + "]-[" + NodeCovering.KeyString + "]");
                RemoveEdge(EdgeUpToCovering);

                // make list of edges to covered
                HasseEdge[] EdgesToCovered = Node.EdgesToCovered.ToArray();

                foreach (HasseEdge E2 in EdgesToCovered)
                {
                    HasseNode Node2 = E2.LowerNode;
                    // inherit edges from those that Node covers
                    this.MakeEdge(Node2, NodeCovering);
                    this.RemoveEdge(E2);
                }
                HasseDiagramNodes.Remove(Node.KeyString);
            }
        }
Ejemplo n.º 22
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        public List <HasseNode> GetSiblings()
        {
            List <HasseNode> L = new List <HasseNode>();

            foreach (HasseEdge EdgeDown in this.EdgesToCovered)
            {
                HasseNode LowerNode = EdgeDown.LowerNode;
                foreach (HasseEdge EdgeUp in LowerNode.EdgesToCovering)
                {
                    if (this != EdgeUp.UpperNode)
                    {
                        L.Add(EdgeUp.UpperNode);
                    }
                }
            }
            return(L);
        }
Ejemplo n.º 23
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        public override bool IsLargerThan(HasseNode smallobj)
        {
            if (smallobj.HasNodeType(HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT))
            {
                System.Diagnostics.Debugger.Break();
            }

            if (smallobj.NodeType == HasseNode.HasseNodeTypes.ROOT)
            {
                return(true);
            }
            if (this.NodeType == HasseNode.HasseNodeTypes.ROOT)
            {
                return(false);
            }
            bool IsPossiblyLargerThanByFingerprint = ContainsFingerprintOf(((ChemHasseNode)smallobj).fingerprint());

            if (TrustFingerprints)
            {
                if (IsPossiblyLargerThanByFingerprint)
                {
                    ;
                } // is likely to be larger, but we are not sure, needs to be checked
                else
                {
                    return(false); // if fingerprints work as they should we are guaranteed that IsLargerThan must be false
                }
            }
            // todo take a away those checks that fingerprints work
            if (IsPossiblyLargerThanByFingerprint)
            { // can be a substructure match but need not be
              //if (matcher.countMatches(smallMol) == 0)
              //{
              //    System.Diagnostics.Debug.WriteLine("a fingerprint contained in b fingerprint - but a was not substruc of b");
              //    System.Diagnostics.Debug.WriteLine("a\t" + smallMol.smiles());
              //    System.Diagnostics.Debug.WriteLine("b\t" + molecule.smiles());
              //}
            }
            else
            {
                //if (matcher.countMatches(smallMol) != 0)
                //  System.Diagnostics.Debugger.Break(); //we have a match where fp says we certainly have not!
            }

            return(ChemObject.IsLargerThan(smallobj));
        }
Ejemplo n.º 24
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 // make node based on string
 public HasseNode NewNode(string s, HasseNode.HasseNodeTypes e, string debugInfo)
 {
     switch (nType)
     {
         case NodeType.STRING  :
             StringHasseNode SN = new StringHasseNode(s, e, debugInfo);
             return SN;
         case NodeType.CHEM  :
             ChemHasseNode CN = new ChemHasseNode(s, e,  debugInfo);
             return CN;
         case  NodeType.FINGERPRINTCHEM :
             FingerprintChemHasseNode FPC = new FingerprintChemHasseNode(s, e,  debugInfo);
             return FPC;
         default :
             throw new Exception ("HasseNodeFactory: unhandled NodeType");
     }
 }
Ejemplo n.º 25
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        public override string[] GetDifferenceString(HasseNode LargerNode)
        {
            if (this.NodeType == HasseNodeTypes.ROOT)
            {
                return(new string[] { });
            }
            else
            {
                string           buf;
                HasseFingerprint fp      = this.hFingerprint;
                HasseFingerprint fpclone = fp.CloneHasseFingerprint();
                fpclone.Minus(((FingerprintChemHasseNode )LargerNode).hFingerprint);
                buf = fpclone.ToHex();
                return(new string[] { buf });
            }

            return(ChemObject.GetDifferenceString(LargerNode));
        }
Ejemplo n.º 26
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        // ==========================================


        public HasseDiagram(HasseNodeFactory.NodeType t)
        {
            // construct new HasseDiagram
            HasseDiagramNodes = new HasseNodeCollection();  //collection nodes in diagram
            DifferenceNodes   = new HasseNodeCollection();  //collection of objects expressing difference
            //ElementaryHasseNodes = new HasseNodeCollection(); // collection of elements

            // factory for nodes, set its nodetype and let it have access to global elements collection
            diagramNodeFactory    = new HasseNodeFactory(t);
            differenceNodeFactory = new HasseNodeFactory(t);

            // a queue for nodes to be created after current node is fully processed
            FragmentInsertionQueue = new HasseFragmentInsertionQueue(HasseDiagramNodes);

            // create the root node as part of construction
            RootNode = diagramNodeFactory.NewNode("", HasseNode.HasseNodeTypes.ROOT, "");
            HasseDiagramNodes.Add("{}", RootNode);
        }
        public override string[] GetDifferenceString(HasseNode LargerNode)
        {
            if (this.NodeType == HasseNodeTypes.ROOT)
            {
                return new string[] { };
            }
            else
            {
                string buf;
                HasseFingerprint fp = this.hFingerprint;
                HasseFingerprint fpclone = fp.CloneHasseFingerprint();
                fpclone.Minus(((FingerprintChemHasseNode )LargerNode).hFingerprint );
                buf = fpclone.ToHex();
                return new string[] {buf };
            }

            return ChemObject.GetDifferenceString(LargerNode);
        }
Ejemplo n.º 28
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 public HasseNode NewNode(object  o, HasseNode.HasseNodeTypes e, string debugInfo)
 {
     // make node based on object of a class that the node implementing class knows about
     switch (nType)
     {
         case NodeType.STRING:
             StringHasseNode SN = new StringHasseNode((string) o, e, debugInfo);
             return SN;
         case NodeType.CHEM:
             ChemHasseNode CN = new ChemHasseNode((IndigoChemistry )o, e,  debugInfo);
             return CN;
         case NodeType.FINGERPRINTCHEM:
             FingerprintChemHasseNode FPC = new FingerprintChemHasseNode((IndigoChemistry)o, e,  debugInfo);
             return FPC;
         default:
             throw new Exception("HasseNodeFactory: unhandled NodeType");
     }
 }
Ejemplo n.º 29
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        public bool GetMaxCommonFragmentsNotUsed(HasseNode Node1, HasseNode Node2, bool dbg,
                                                 HasseFragmentInsertionQueue NewFragmentList, int MinimumOverlap)
        {
            // this Node is directly below both Node1 and Node2
            // it can match several places
            CountMCS++;
            string strSeed  = this.KeyString.Replace("*", "");
            string str1     = Node1.KeyString;
            string str2     = Node2.KeyString;
            bool   FoundMCS = false;

            // we are only interested in matches strictly larger than seed
            if (strSeed.Length + 1 > MinimumOverlap)
            {
                MinimumOverlap = strSeed.Length + 1;
            }

            int MatchPosA = GetNextMatch(0, strSeed, str1);

            while (MatchPosA > -1)
            {
                int MatchPosB = GetNextMatch(0, strSeed, str2);
                while (MatchPosB > -1)
                {
                    Match M = new Match(strSeed, MatchPosA, 0, str1, MatchPosB, 0, str2);
                    M.ExpandMCSMatch();
                    //MatchPosA= M.LastPosInA;
                    //MatchPosB = M.LastPosInB;
                    string debugInfo = "MCS " + Node1.GetID().ToString() + " " + Node2.GetID().ToString();
                    if (true == ProcessMatch(M, MinimumOverlap, NewFragmentList, new HasseNode[2] {
                        Node1, Node2
                    }, debugInfo))
                    {
                        FoundMCS = true;
                    }
                    MatchPosB = GetNextMatch(MatchPosB + 1, strSeed, str2);
                }
                MatchPosA = GetNextMatch(MatchPosA + 1, strSeed, str1);
            }

            return(FoundMCS);
        }
Ejemplo n.º 30
0
        public void ContractNodeWithCover(HasseNode Node)
        {
            // Node should have exactly one cover.
            // Edges from covered are moved to go to the cover = (break and form)
            // Finally Node is deleted


            HasseEdge[] EdgesDownToCovered = Node.EdgesToCovered.ToArray();
            HasseNode   TopNode            = Node.EdgesToCovering[0].UpperNode;

            System.Diagnostics.Debug.WriteLine("ContractNodeWithCover: " + Node.KeyString);
            System.Diagnostics.Debug.WriteLine("Covered by: " + TopNode.KeyString);

            foreach (HasseEdge EdgeToCovered in EdgesDownToCovered)
            {
                System.Diagnostics.Debug.WriteLine("Moving edge from : " + EdgeToCovered.LowerNode.KeyString);
                MakeEdgeIfNotExists(EdgeToCovered.LowerNode, TopNode);
                RemoveEdge(EdgeToCovered);
            }
            HasseDiagramNodes.Remove(Node.KeyString);
        }
Ejemplo n.º 31
0
        public static HasseNodeCollection BruteForceFindGlb(HasseNode @ref, HasseNodeCollection AllNodes)
        {
            if (@ref.KeyString.Equals("x"))
            {
                System.Diagnostics.Debugger.Break();
            }

            HasseNodeCollection glb         = new HasseNodeCollection();
            List <string>       ToBeRemoved = new List <string>();

            foreach (HasseNode Node in AllNodes.Values)
            {
                if (@ref.IsLargerThan(Node))
                {
                    glb.Add(Node.KeyString, Node);
                }
            }


            foreach (HasseNode Node in glb.Values)
            {
                foreach (HasseNode Node2 in glb.Values)
                {
                    if (Node != Node2)
                    {
                        if (Node.IsLargerThan(Node2))
                        {
                            ToBeRemoved.Add(Node2.KeyString);
                        }
                        //           break;
                    }
                }
            }
            foreach (string key in ToBeRemoved)
            {
                glb.Remove(key);
            }

            return(glb);
        }
Ejemplo n.º 32
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        public static HasseNodeCollection FindGlb(HasseNode ReferenceNode, HasseNodeCollection AllNodes)
        {
            bool dbg = Convert.ToBoolean(DEBUGLEVEL & LOG_DEBUG_MAKE_GLB);
            HasseNodeCollection glb = new HasseNodeCollection();
            //List<string> ToBeRemoved = new List<string>();
            HashSet <string> ToBeRemoved = new HashSet <string>();

            foreach (HasseNode Node in AllNodes.Values)
            {
                if (!ToBeRemoved.Contains(Node.KeyString))
                {
                    System.Diagnostics.Debug.WriteLineIf(dbg, "test if " + ReferenceNode.KeyString + " is larger than " + Node.KeyString);
                    if (ReferenceNode.IsLargerThan(Node))
                    {
                        System.Diagnostics.Debug.WriteLineIf(dbg, " yes - is glb candidate, delete below...");
                        glb.Add(Node.KeyString, Node);
                        FindNodesBelow(Node, ToBeRemoved, 0);
                    }

                    /*   else if (Node.IsLargerThan(ReferenceNode))
                     * {
                     *     DeleteNodesAbove(Node, ToBeRemoved, 0);
                     * }
                     */
                    else
                    {
                        ToBeRemoved.Add(Node.KeyString);
                    }
                }
            }

            foreach (string key in ToBeRemoved)
            {
                glb.Remove(key);
            }

            return(glb);
        }
Ejemplo n.º 33
0
        public static HasseNodeCollection BruteForceFindLub(HasseNode @ref, HasseNodeCollection AllNodes)
        {
#if DEBUG
            // if (@ref.UniqueString.Equals("*B*")) {
            //    System.Diagnostics.Debugger.Break();
            // }
#endif

            HasseNodeCollection lub         = new HasseNodeCollection();
            List <string>       ToBeRemoved = new List <string>();
            foreach (HasseNode Node in AllNodes.Values)
            {
                if (Node.IsLargerThan(@ref))
                {
                    lub.Add(Node.KeyString, Node);
                }
            }

            foreach (HasseNode Node in lub.Values)
            {
                foreach (HasseNode Node2 in lub.Values)
                {
                    if (Node2.IsLargerThan(Node))
                    {
                        ToBeRemoved.Add(Node2.KeyString);
                        //break;
                    }
                }
            }
            foreach (string key in ToBeRemoved)
            {
                lub.Remove(key);
            }

            return(lub);
        }
Ejemplo n.º 34
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        public override bool GetMaxCommonFragments(HasseNode Node1, HasseNode Node2, bool dbg,
                                                   HasseFragmentInsertionQueue NewFragmentList, int MinimumOverlap)
        {
            CountMCS++;
            string str1     = Node1.KeyString;
            string str2     = Node2.KeyString;
            bool   FoundMCS = false;

            StringMatcher sm = new StringMatcher();

            sm.Initialise(str1, str2);
            Match m = null;

            do
            {
                m = sm.nextMatch();
                if (m == null)
                {
                    break;
                }
                if (m.LastPosInA - m.FirstPosInA < MinimumOverlap - 1)
                {
                    continue;
                }
                //System.Diagnostics.Debug.WriteLine(m.StrA.Substring(m.FirstPosInA, m.LastPosInA - m.FirstPosInA + 1));
                //System.Diagnostics.Debug.WriteLine(m.StrB.Substring(m.FirstPosInB, m.LastPosInB - m.FirstPosInB + 1));
                string debugInfo = "MCS " + Node1.GetID().ToString() + " " + Node2.GetID().ToString();
                if (true == ProcessMatch(m, MinimumOverlap, NewFragmentList, new HasseNode[2] {
                    Node1, Node2
                }, debugInfo))
                {
                    FoundMCS = true;
                }
            } while (true);
            return(FoundMCS);
        }
Ejemplo n.º 35
0
 public void AddLinkedNode(HasseNode LinkedNode)
 {
     linkedNodes.Add(LinkedNode);
 }
Ejemplo n.º 36
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        private void WriteNode(HasseNode N)
        {
            //System.Diagnostics.Debug.WriteLine(((ChemHasseNode)N).GetName());
            //DotFile.WriteLine("node[shape = rounded];");
            DotFile.Write(DoubleQuoted(N.KeyString));
            DotFile.Write(" ["); // start node attributes

            switch (LabelMode)
            {
                case labelMode.NO_LABELS:
                    DotFile.Write(" label=\"\" "); //empty label
                    break;
                case labelMode.USE_NODE_ID:
                    DotFile.Write(" label=" + DoubleQuoted(N.GetID().ToString()));
                    break;

                case labelMode.USE_MOLNAME:
                    if (((ChemHasseNode)N).GetName() != "")
                    {
                        DotFile.Write(" label=" + DoubleQuoted(((ChemHasseNode)N).GetName()));
                    }
                    else
                    {
                        DotFile.Write(" label=" + DoubleQuoted(N.GetID().ToString()));
                    }
                    break;

                case labelMode.USE_NODE_KEY:
                    // need not do anything, the node key is shown by default
                    break;

                case labelMode.USE_NODE_LABEL:
                    DotFile.Write(" label=" + DoubleQuoted(N.LabelText));
                    break;

                default:
                    throw new Exception("unhandled labelmode");
            }

            if (N.DrawingColor!="" ) DotFile.Write(" color=" + N.DrawingColor + " ");

            if (UseImage && N.ImageFileName.Length > 0)
            {
                DotFile.Write(" image=\"" + N.ImageFileName + "\"");
            }

            if (N.HasNodeType (HasseNode.HasseNodeTypes.REAL) || N.NodeType == HasseNode.HasseNodeTypes.ROOT )
            { DotFile.Write(" shape=ellipse "); }
            else
            { DotFile.Write(" shape=none "); }

            DotFile.Write("] "); // end node attributes
            DotFile.WriteLine(";");
        }
Ejemplo n.º 37
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 private void MakeEdgeIfNotExists(HasseNode N1, HasseNode N2)
 {
     // Todo for max efficiency check if count covered from N2 is lower
     foreach (HasseEdge E in N1.EdgesToCovering)
     {
         if (E.UpperNode == N2) return;
     }
     MakeEdge(N1, N2);
 }
Ejemplo n.º 38
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        public static HasseNodeCollection BruteForceFindLub(HasseNode @ref, HasseNodeCollection AllNodes)
        {
            #if DEBUG
            // if (@ref.UniqueString.Equals("*B*")) {
            //    System.Diagnostics.Debugger.Break();
            // }
            #endif

            HasseNodeCollection lub = new HasseNodeCollection();
            List<string> ToBeRemoved = new List<string>();
            foreach (HasseNode Node in AllNodes.Values)
            {
                if (Node.IsLargerThan(@ref))
                {
                    lub.Add(Node.KeyString, Node);
                }
            }

            foreach (HasseNode Node in lub.Values)
            {
                foreach (HasseNode Node2 in lub.Values)
                {
                    if (Node2.IsLargerThan(Node))
                    {
                        ToBeRemoved.Add(Node2.KeyString);
                        //break;
                    }
                }
            }
            foreach (string key in ToBeRemoved)
            {
                lub.Remove(key);
            }

            return (lub);
        }
Ejemplo n.º 39
0
        public static HasseNodeCollection BruteForceFindGlb(HasseNode @ref, HasseNodeCollection AllNodes)
        {
            if (@ref.KeyString.Equals("x")) { System.Diagnostics.Debugger.Break(); }

            HasseNodeCollection glb = new HasseNodeCollection();
            List<string> ToBeRemoved = new List<string>();
            foreach (HasseNode Node in AllNodes.Values)
            {
                if (@ref.IsLargerThan(Node))
                {
                    glb.Add(Node.KeyString, Node);
                }
            }

            foreach (HasseNode Node in glb.Values)
            {
                foreach (HasseNode Node2 in glb.Values)
                {
                    if (Node != Node2)
                    {
                        if (Node.IsLargerThan(Node2))
                        { ToBeRemoved.Add(Node2.KeyString); }
                        //           break;
                    }
                }
            }
            foreach (string key in ToBeRemoved)
            {
                glb.Remove(key);
            }

            return (glb);
        }
Ejemplo n.º 40
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 public abstract string[] GetDifferenceString(HasseNode LargerNode);
Ejemplo n.º 41
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 // public abstract int elementCount();
 public abstract bool IsLargerThan(HasseNode smallobj);
Ejemplo n.º 42
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 private static void FindNodesBelow(HasseNode Node, HashSet<string> NodeKeys, int level)
 {
     foreach (HasseEdge E in Node.EdgesToCovered)
     {
         if (!NodeKeys.Contains(E.LowerNode.KeyString))
             FindNodesBelow(E.LowerNode, NodeKeys, level + 1);
     }
     if (level > 0) NodeKeys.Add(Node.KeyString);
 }
Ejemplo n.º 43
0
        private bool addNode(HasseNode newNode, HasseNode[] AboveTheseNodes, HasseNode[] BelowTheseNodes)
        {
            // should return true if node was inserted
            // or false if corresponding node already exist

            bool debug = Convert.ToBoolean(DEBUGLEVEL & LOG_INSERTIONS);
            bool dbgTimings = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_TIMINGS);
            sw.Reset();
            sw.Start();

            if (newNode.Size() < MINIMUM_FRAGMENT_SIZE) return false;

            // do not add identical objects
            if (HasseDiagramNodes.ContainsKey(newNode.KeyString))
            {
                // is already there - we will update type, set name, redraw image, then return.
                HasseDiagramNodes[newNode.KeyString].AddNodeType(newNode.NodeType);
                if(newNode.HasNodeType ( HasseNode.HasseNodeTypes.REAL )){
                    string n = newNode.GetName();
                    HasseDiagramNodes[newNode.KeyString].SetName(n);
                    //if (CREATE_NODE_IMAGE) HasseDiagramNodes[newNode.KeyString].CreateImage();
                System.Diagnostics.Debug.WriteLineIf(debug, " Skipping add of " + newNode.KeyString);
                }
                return false;
            }
            //if (CREATE_NODE_IMAGE) newNode.CreateImage();
            CountAdditions += 1;

            if (DEBUGLEVEL > 0)
            {
                System.Diagnostics.Debug.WriteLine("Add Node " + newNode.KeyString + " " + CountAdditions.ToString());
            }

                // loop elements of new object
               /*
            foreach (HasseNode Element in newNode.getElementarySubobjects().Values)
                {
                    if (USE_ELEMENTS)
                    {
                        // add to diagram nodes list if not already there
                        if (!HasseDiagramNodes.ContainsKey(Element.KeyString))
                        {
                            HasseDiagramNodes.Add(Element.KeyString, Element);
                            //Element.CreateImage();
                            this.MakeEdge(RootNode, Element);
                        }
                    }
                    // add to elements collection if not there already
                    if (!ElementaryHasseNodes.ContainsKey(Element.KeyString))
                        ElementaryHasseNodes.Add(Element.KeyString, Element);
                }
            */

            System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks add 1 (init) " + sw.ElapsedTicks.ToString());
            sw.Reset();
            sw.Start();

            System.Diagnostics.Debug.WriteLineIf(debug, "=== Start LUB and GLB for " + newNode.KeyString + " ===");

            if (CountAdditions == -1)
                System.Diagnostics.Debugger.Break();

            HasseNodeCollection NodesInGreatestLowerBound = null;
            HasseNodeCollection NodesInLeastUpperBound = null;

            FindLUBAndGLB(newNode, ref NodesInLeastUpperBound, ref NodesInGreatestLowerBound);

            System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 2 (got lub and glb) " + sw.ElapsedTicks.ToString());
            sw.Reset();
            sw.Start();
            System.Diagnostics.Debug.WriteLineIf(debug, "=== Done LUB and GLB =======");

            List<HasseEdge> NewlyFormedEdges = InsertNodeBetweenGlbAndLub(
                newNode, NodesInLeastUpperBound, NodesInGreatestLowerBound, debug);

            System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 3 (inserted new) " + sw.ElapsedTicks.ToString());
            sw.Reset();
            sw.Start();

            if (Convert.ToBoolean(CHECK_LEVEL & CHECK_ALL))
                newNode.validate();

            if (MAKE_MCS_AT_ONCE) { FindCommonFragments(newNode); }

            System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 4 (made MCS)" + sw.ElapsedTicks.ToString());
            // The node may be there already, just added, as element if it is both element and real
               // if (!newNode.HasNodeType(HasseNode.HasseNodeTypes.ELEMENT))
                HasseDiagramNodes.Add(newNode.KeyString, newNode);
            return true;
        }
Ejemplo n.º 44
0
        public void RemoveNodeFromHasseDiagram(HasseNode Node)
        {
            HasseEdge[] CoveredEdges = Node.EdgesToCovered.ToArray();
            HasseEdge[] CoveringEdges = Node.EdgesToCovering.ToArray();

            // form the new edges;
            foreach (HasseEdge CoveredEdge in CoveredEdges)
            {
                foreach (HasseEdge CoveringEdge in CoveringEdges)
                {
                    MakeEdge(CoveredEdge.LowerNode, CoveringEdge.UpperNode);
                }
            }
            // remove all edges involving Node
            foreach (HasseEdge CoveredEdge in CoveredEdges)
                RemoveEdge(CoveredEdge);
            foreach (HasseEdge CoveringEdge in CoveringEdges)
                RemoveEdge(CoveringEdge);
            // remove Node from Node dictionary
            HasseDiagramNodes.Remove(Node.KeyString);
        }
Ejemplo n.º 45
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 private static void FindNodesAbove(HasseNode Node, HashSet<string> NodeKeys, int level)
 {
     foreach (HasseEdge EdgeToCovering in Node.EdgesToCovering)
     {
         if (!NodeKeys.Contains(EdgeToCovering.UpperNode.KeyString))
             FindNodesAbove(EdgeToCovering.UpperNode, NodeKeys, level + 1);
     }
     if (level > 0) NodeKeys.Add(Node.KeyString);
 }
Ejemplo n.º 46
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 public void FindLUBAndGLB(HasseNode newNode, ref HasseNodeCollection lub, ref HasseNodeCollection glb)
 {
     bool dbgTimings = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_TIMINGS);
     bool dbgComparisons = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_COMPARISON_COUNTS);
     //glb = BruteForceFindGlb(newNode, HasseDiagramNodes);
     //lub = BruteForceFindLub(newNode, HasseDiagramNodes);
     glb = FindGlb(newNode, HasseDiagramNodes);
     lub = FindLub(newNode, HasseDiagramNodes);
 }
Ejemplo n.º 47
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        public void FindCommonFragments(HasseNode newNode)
        {
            bool CompareToAll = false;
            bool CompareToSiblings = false;
            if (newNode.NodeType == HasseNode.HasseNodeTypes.ROOT) return;

            /*
            List<HasseNode> DifferenceNodes = new List<HasseNode>();
            foreach (HasseEdge E in newNode.EdgesToCovered)
            {
                foreach (HasseNode N in E.LinkedNodes)
                {
                    DifferenceNodes.Add(N);
                }
            }
            */
            if (newNode.IsLeafNode())
            {
                CompareToAll = true;

            }
            else
            {
                CompareToSiblings = true;
            }
            //CompareToAll = true;

            /*
            if (DifferenceNodes.Count() == 0)
            {
                CompareToAll = true;
                System.Diagnostics.Debug.WriteLine("Zero differencenodes! ");
            }
            else
            {
                System.Diagnostics.Debug.WriteLine( DifferenceNodes.Count().ToString () + " differencenodes ");
            }
            */

            List<HasseNode> MCSPartners = new List<HasseNode>();

            // loop all diagram nodes to see if at least one element is in common
            // one, because it can repeat and be involved in a match, like AXXY to BXXZ
            //foreach (HasseNode N in HasseDiagramNodes.NodesWithOneOfElements(Elements))
            foreach (HasseNode N in HasseDiagramNodes.Values )
            {
                    if (N.NodeType != HasseNode.HasseNodeTypes.ROOT  )
                    {
            //                        System.Diagnostics.Debug.WriteLine("each N " + ((ChemHasseNode)N).Molecule().smiles());
                        if (CompareToAll == true)
                        {
                            MCSPartners.Add(N);
                            continue;
                        }
                    }
            }

            if (CompareToSiblings)
            {
                foreach (HasseNode N in newNode.GetSiblings())
                {
                    if (!MCSPartners.Contains(N))
                        MCSPartners.Add(N);
                }

            }
            float selectivity = (float)MCSPartners.Count / (float)HasseDiagramNodes.Count;
               // if (selectivity < 0.01) System.Diagnostics.Debugger.Break();
               // System.Diagnostics.Debug.WriteLine(selectivity);

            foreach (HasseNode N in MCSPartners)
            {

                System.Diagnostics.Stopwatch sw = new Stopwatch() ;
                sw.Start();
                bool debugMCS = Convert.ToBoolean(DEBUGLEVEL & DEBUG_MCS );
                bool FoundMCS = newNode.GetMaxCommonFragments(newNode, N, debugMCS, FragmentInsertionQueue, MINIMUM_FRAGMENT_SIZE);

                    long elapsed = sw.ElapsedMilliseconds;
                if (elapsed > 5000) System.Diagnostics.Debugger.Break();
            }
        }
Ejemplo n.º 48
0
        public void ContractNodeWithCover(HasseNode Node)
        {
            // Node should have exactly one cover.
            // Edges from covered are moved to go to the cover = (break and form)
            // Finally Node is deleted

            HasseEdge[] EdgesDownToCovered = Node.EdgesToCovered.ToArray();
            HasseNode TopNode = Node.EdgesToCovering[0].UpperNode;

            System.Diagnostics.Debug.WriteLine("ContractNodeWithCover: " + Node.KeyString);
            System.Diagnostics.Debug.WriteLine("Covered by: " + TopNode.KeyString);

            foreach (HasseEdge EdgeToCovered in EdgesDownToCovered)
            {
                System.Diagnostics.Debug.WriteLine("Moving edge from : " + EdgeToCovered.LowerNode.KeyString);
                MakeEdgeIfNotExists(EdgeToCovered.LowerNode, TopNode);
                RemoveEdge(EdgeToCovered);
            }
            HasseDiagramNodes.Remove(Node.KeyString);
        }
Ejemplo n.º 49
0
        // Implement IComparable CompareTo method - provide default sort order.
        int IComparable.CompareTo(object node)
        {
            HasseNode Node = (HasseNode)node;

            return(String.Compare(this.KeyString, Node.KeyString));
        }
Ejemplo n.º 50
0
        private void DrawCoveringNodes(int level, HasseNode Node)
        {
            string spaces = new string('-', level * 2);
            //if (Node.NodesCovering().Values.Count >5  )
            System.Diagnostics.Debug.WriteLine(Node.Weight().ToString() + "\t" + spaces + Node.KeyString);

            foreach (HasseEdge e in Node.EdgesToCovering)
            {
                DrawCoveringNodes(level + 1, e.UpperNode);
            }
        }
Ejemplo n.º 51
0
        public static HasseNodeCollection FindGlb(HasseNode ReferenceNode, HasseNodeCollection AllNodes)
        {
            bool dbg = Convert.ToBoolean(DEBUGLEVEL & LOG_DEBUG_MAKE_GLB);
            HasseNodeCollection glb = new HasseNodeCollection();
            //List<string> ToBeRemoved = new List<string>();
            HashSet<string> ToBeRemoved = new HashSet<string>();
            foreach (HasseNode Node in AllNodes.Values)
            {
                if (!ToBeRemoved.Contains(Node.KeyString))
                {
                    System.Diagnostics.Debug.WriteLineIf(dbg, "test if " + ReferenceNode.KeyString + " is larger than " + Node.KeyString);
                    if ( ReferenceNode.IsLargerThan(Node))
                    {
                        System.Diagnostics.Debug.WriteLineIf(dbg, " yes - is glb candidate, delete below...");
                        glb.Add(Node.KeyString, Node);
                        FindNodesBelow(Node, ToBeRemoved, 0);
                    }
                    /*   else if (Node.IsLargerThan(ReferenceNode))
                       {
                           DeleteNodesAbove(Node, ToBeRemoved, 0);
                       }
                     */
                    else ToBeRemoved.Add(Node.KeyString);
                }

            }

            foreach (string key in ToBeRemoved)
            {
                glb.Remove(key);
            }

            return (glb);
        }
Ejemplo n.º 52
0
 private bool ExistsEdge(HasseNode N1, HasseNode N2)
 {
     foreach (HasseEdge E in N1.EdgesToCovering)
     {
         if (E.UpperNode == N2)
         {
             return true;
         }
     }
     return false;
 }
Ejemplo n.º 53
0
 public abstract bool GetMaxCommonFragments(HasseNode Node1, HasseNode Node2, bool dbg, HasseFragmentInsertionQueue NewFragmentList, int MinimumOverlap);
Ejemplo n.º 54
0
        private List<HasseEdge> InsertNodeBetweenGlbAndLub(
            HasseNode newNode,
            HasseNodeCollection collectionLUB,
            HasseNodeCollection collectionGLB, bool debug)
        {
            bool dbg = Convert.ToBoolean(DEBUGLEVEL & LOG_INSERTIONS);
            List<HasseEdge> AddedEdges = new List<HasseEdge>();
            // break any existing relations between LUBs and GLBs
            // first make list of edges to delete
            List<HasseEdge> EdgesToBeDeleted = new List<HasseEdge>();
            foreach (HasseNode v_low in collectionGLB.Values)
            {
                foreach (HasseNode v_high in collectionLUB.Values)
                {
                    System.Diagnostics.Debug.WriteLineIf(dbg, "cut " + v_low.KeyString + " - " + v_high.KeyString);
                    foreach (HasseEdge E in v_low.EdgesToCovering)
                    {
                        if (E.UpperNode == v_high)
                            EdgesToBeDeleted.Add(E);
                    }
                }
            }

            foreach (HasseEdge E in EdgesToBeDeleted)
            {
                RemoveEdge(E);
            }

            //make differences between elements and new
            foreach (HasseNode v_low in collectionGLB.Values)
            {
                System.Diagnostics.Debug.WriteLineIf(dbg, "cover (I)  " + v_low.KeyString + " with " + newNode.KeyString);
                HasseEdge NewEdge = MakeEdge(v_low, newNode);
                AddedEdges.Add(NewEdge);
            }

            //make relations between new and LUBs
            foreach (HasseNode v_high in collectionLUB.Values)
            {
                System.Diagnostics.Debug.WriteLineIf(dbg, "cover (II) " + newNode.KeyString + " with " + v_high.KeyString);
                MakeEdge(newNode, v_high);
            }

            return AddedEdges;
        }
 public override bool IsLargerThan(HasseNode smallobj)
 {
     if (this.HasNodeType(HasseNodeTypes.ROOT)) { return false; }
     if (smallobj.HasNodeType(HasseNodeTypes.ROOT)) { return true; }
     bool retval= this.hFingerprint.IsLargerThan(((FingerprintChemHasseNode )smallobj).hFingerprint );
        // if (retval == true) System.Diagnostics.Debugger.Break();
     return retval;
 }
Ejemplo n.º 56
0
        private HasseEdge MakeEdge(HasseNode N1, HasseNode N2)
        {
            // returns new edge. If already exists, returns null
            if ((N1 == null) || (N2 == null)) { throw new Exception("MakeEdge with null argument"); }
            if (ExistsEdge(N1, N2)) return null;

            HasseEdge E = new HasseEdge();
            E.LowerNode = N1;
            E.UpperNode = N2;
            N1.EdgesToCovering.Add(E);
            N2.EdgesToCovered.Add(E);

            // analyse difference between smaller and larger.
            // output can be the *-marked smaller node + all difference fragments
            // or can be partial
            if ((LABEL_EDGES_WITH_DIFFERENCE) && (N1 != RootNode)   )
            {
                string[] EdgeLabels = N1.GetDifferenceString(N2);
                E.LabelText = String.Join(", ", EdgeLabels);

                foreach (string s in EdgeLabels)
                {
                    if (E.LabelText.Contains("~~~")) //for debug
                    {
                        System.Diagnostics.Debugger.Break();
                    }

                    // For difference fragments, add link between fragment and those
                    // edges giving this Node as difference.
                    // The link is for efficient updates of difference items, it is not an edge in hasse diagram

                    //if (N1 != RootNode) // do not make difference here
                    //{
                        HasseNode DifferenceNode = null;
                        if (DifferenceNodes.ContainsKey(s))  // if such node already exists in differenc nodes
                        {
                            DifferenceNode = DifferenceNodes[s]; //  get that node
                        }
                        else
                            if (HasseDiagramNodes.ContainsKey(s))  // if already exists in diagram nodes
                            {
                                DifferenceNode = HasseDiagramNodes[s]; // get reference
                                // add difference type
                                DifferenceNode.AddNodeType(HasseNode.HasseNodeTypes.DIFFERENCE_FRAGMENT);
                                // and add to difference catalog
                                DifferenceNodes.Add(DifferenceNode.KeyString, DifferenceNode);
                            }
                            else // not exist anywhere
                            {
                                // create and add to differene node catalog

                                // need to create to get keystring - not same as s!
                                DifferenceNode = this.differenceNodeFactory.NewNode(s, HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.DIFFERENCE_FRAGMENT,"diff");
                                if (DifferenceNodes.ContainsKey(DifferenceNode.KeyString  ))
                                {
                                    DifferenceNode = DifferenceNodes[DifferenceNode.KeyString];
                                }
                                else
                                {
                                    DifferenceNodes.Add(DifferenceNode.KeyString, DifferenceNode);
                                }
                               // DifferenceNode = new StringHasseNode(HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.DIFFERENCE_FRAGMENT,this.ElementaryHasseNodes);
                              //      s, HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.DIFFERENCE_FRAGMENT,
                              //      this.ElementaryHasseNodes);
                            }

                        DifferenceNode.AddLinkToEdge(E); // create the link
                    //}
                }
            }
            return E;
        }
        public override bool GetMaxCommonFragments(
        HasseNode Node1, HasseNode Node2,
        bool dbg, HasseFragmentInsertionQueue NewFragmentList,
        int MinimumOverlap)
        {
            string debugInfo = "";
            HasseFingerprint fp1 = ((FingerprintChemHasseNode)Node1).hFingerprint;
            HasseFingerprint fp1_clone = fp1.CloneHasseFingerprint();
            HasseFingerprint fp2 = ((FingerprintChemHasseNode)Node2).hFingerprint;
            fp1_clone.AndBits(fp2);
            if(fp1_clone.bitCount >= MinimumOverlap ){
                string strMCS = fp1_clone.ToHex();

                HasseFingerprint test = new HasseFingerprint();
                test.FromHex(strMCS);

            NewFragmentList.Add(
                           new HasseNode[1] { this }, // this is lower than new frag
                           new HasseNode[2] { Node1, Node2 }, // those are higher than new frag
                           strMCS, // string to use for new node creation later
                           debugInfo, HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT, // type of frag
                           null // this new frag is not associated with a single edge
                           );
                return true;
            }
            return false;
        }
Ejemplo n.º 58
0
        // ==========================================
        public HasseDiagram(HasseNodeFactory.NodeType t )
        {
            // construct new HasseDiagram
            HasseDiagramNodes = new HasseNodeCollection();  //collection nodes in diagram
            DifferenceNodes = new HasseNodeCollection();    //collection of objects expressing difference
            //ElementaryHasseNodes = new HasseNodeCollection(); // collection of elements

            // factory for nodes, set its nodetype and let it have access to global elements collection
            diagramNodeFactory = new HasseNodeFactory(t);
            differenceNodeFactory = new HasseNodeFactory(t);

            // a queue for nodes to be created after current node is fully processed
            FragmentInsertionQueue = new HasseFragmentInsertionQueue(HasseDiagramNodes);

            // create the root node as part of construction
            RootNode = diagramNodeFactory.NewNode("", HasseNode.HasseNodeTypes.ROOT,"");
            HasseDiagramNodes.Add("{}", RootNode);
        }
Ejemplo n.º 59
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 public HasseNode AddNode(HasseNode newNode)
 {
     addNode(newNode, null, null);
     InsertFragmentsInQueue();
     return newNode;
 }
Ejemplo n.º 60
0
        public static HasseNodeCollection FindLub(HasseNode ReferenceNode, HasseNodeCollection AllNodes)
        {
            bool dbg = Convert.ToBoolean(DEBUGLEVEL & LOG_DEBUG_MAKE_LUB);
            HasseNodeCollection lub = new HasseNodeCollection();
            //List<string> ToBeRemoved = new List<string>();
            HashSet<string> ToBeRemoved = new HashSet<string>();
            foreach (HasseNode Node in AllNodes.Values)
            {
                if (!ToBeRemoved.Contains(Node.KeyString))
                {
                    System.Diagnostics.Debug.WriteLineIf(dbg, "test if " + Node.KeyString + " is larger than " + ReferenceNode.KeyString);

                    // debug:
                    //HasseNode[] subobj = ReferenceNode.getElementarySubobjects().Values.ToArray();
                    //if (!Node.HasElements(subobj) &&
                    //    (Node.IsLargerThan(ReferenceNode)))
                    //{
                    //    System.Diagnostics.Debugger.Break();
                    //}

                    if ( Node.IsLargerThan(ReferenceNode))
                    {
                        System.Diagnostics.Debug.WriteLineIf(dbg, " yes - is lub candidate, delete above...");
                        lub.Add(Node.KeyString, Node);
                        FindNodesAbove(Node, ToBeRemoved, 0);
                    }
                    /*
                     else if (ReferenceNode.IsLargerThan(Node))
                    {
                        DeleteNodesBelow(Node, ToBeRemoved, 0);
                    }
                     */
                    else ToBeRemoved.Add(Node.KeyString);

                }
            }

            foreach (string key in ToBeRemoved)
            {
                lub.Remove(key);
            }

            return (lub);
        }