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 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);
}
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 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(";");
}
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 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;
}
