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);
}
}
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(";");
}
public override bool GetMaxCommonFragments(
HasseNode Node1, HasseNode Node2,
bool dbg, HasseFragmentInsertionQueue NewFragmentList,
int MinimumOverlap)
{
return(ChemObject.GetMaxCommonFragments(this, Node1, Node2, dbg, NewFragmentList, MinimumOverlap));
}
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;
}
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);
}
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);
}
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 ();
}
public override string[] GetDifferenceString(HasseNode LargerNode)
{
if (this.NodeType == HasseNodeTypes.ROOT)
{
return(new string[] { }); //TODO - is this right?
}
return(ChemObject.GetDifferenceString(LargerNode));
}
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);
}
}
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);
}
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);
}
private bool ExistsEdge(HasseNode N1, HasseNode N2)
{
foreach (HasseEdge E in N1.EdgesToCovering)
{
if (E.UpperNode == N2)
{
return(true);
}
}
return(false);
}
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);
}
}
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);
}
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);
}
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);
}
}
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);
}
}
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);
}
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);
}
}
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);
}
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));
}
// 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");
}
}
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));
}
// ==========================================
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);
}
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");
}
}
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);
}
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);
}
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);
}
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);
}
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);
}
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);
}
public void AddLinkedNode(HasseNode LinkedNode)
{
linkedNodes.Add(LinkedNode);
}
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(";");
}
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);
}
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);
}
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);
}
public abstract string[] GetDifferenceString(HasseNode LargerNode);
// public abstract int elementCount(); public abstract bool IsLargerThan(HasseNode smallobj);
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);
}
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;
}
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);
}
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);
}
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);
}
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();
}
}
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);
}
// Implement IComparable CompareTo method - provide default sort order.
int IComparable.CompareTo(object node)
{
HasseNode Node = (HasseNode)node;
return(String.Compare(this.KeyString, Node.KeyString));
}
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);
}
}
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);
}
private bool ExistsEdge(HasseNode N1, HasseNode N2)
{
foreach (HasseEdge E in N1.EdgesToCovering)
{
if (E.UpperNode == N2)
{
return true;
}
}
return false;
}
public abstract bool GetMaxCommonFragments(HasseNode Node1, HasseNode Node2, bool dbg, HasseFragmentInsertionQueue NewFragmentList, int MinimumOverlap);
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;
}
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;
}
// ==========================================
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 HasseNode AddNode(HasseNode newNode)
{
addNode(newNode, null, null);
InsertFragmentsInQueue();
return newNode;
}
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);
}