public PatchPattern ToPatchPattern()
{
SpecialFunctions.CheckCondition(DisjunctAASetSequenceCollection.Count > 0); //!!!raise error
SpecialFunctions.CheckCondition(sbCurrentDisjunct.Count == 0); //!!!raise error
PatchPattern patchPattern = PatchPatternFactory.GetInstance(DisjunctAASetSequenceCollection.Keys);
return(patchPattern);
}
override public PatchPattern UnifyOnRightOrNull(int overlap, PatchPattern other)
{
SpecialFunctions.CheckCondition(overlap < CoreLength && overlap < other.CoreLength); //!!!raise error
SpecialFunctions.CheckCondition(other is PatchRegex); //!!!raise error
ArrayList rgrgOther = SplitRight((PatchRegex)other, overlap);
ArrayList rgrgMe = SplitLeft(overlap);
ArrayList rgOuts = new ArrayList();
foreach (PatchRegex[] rgOther in rgrgOther)
{
foreach (PatchRegex[] rgMe in rgrgMe)
{
PatchRegex unification = (PatchRegex)rgMe[0].UnifyOrNull(rgOther[1]);
if (unification != null)
{
PatchPattern patchPattern;
if (!unification.AnyFlanking())
{
patchPattern = Concatenate(rgOther[0], unification, rgMe[1]);
Debug.Assert(patchPattern != null);
}
else
{
patchPattern = ReunifyWithFlanking(rgOther[0], unification, rgMe[1]);
}
if (patchPattern != null)
{
rgOuts.Add(patchPattern);
}
if (rgOuts.Count >= DisjunctLimit)
{
goto SkipOutEarly;
}
}
}
}
SkipOutEarly :;
if (rgOuts.Count == 0)
{
return(null);
}
else if (rgOuts.Count == 1)
{
return((PatchPattern)rgOuts[0]);
}
else
{
return(MergePatchPatterns(rgOuts, PatchRegexFactory));
}
}
private static List <PatchPattern> PatchPatternCollection(Greedy greedy)
{
List <PatchPattern> rg = new List <PatchPattern>();
foreach (Component component in greedy.Components)
{
PatchPattern patchPattern = component.PatchPattern();
rg.Add(patchPattern);
}
return(rg);
}
/// <summary>
/// Example: Suppose "1" is "[TNMSQC]" and the patchPattern is "11T11" and the other pattern is "T1111Z"
/// then UnifyOrNull returns "T1T11Z" because that is the most general pattern
/// such that "11T11".IsMatch("T1T11Z") is true and "T1111Z".IsMatch("T1T11Z") is true.
/// Example: Suppose "1" is "[TNMSQC]" and the patchPattern is "11T11" and the other pattern is "A1111"
/// then UnifyOrNull returns null because there is no pattern X such that
/// such that "11T11".IsMatch(X) is true and "A1111".IsMatch(X) is true.
/// </summary>
override public PatchPattern UnifyOrNull(PatchPattern other)
{
SpecialFunctions.CheckCondition(CoreLength <= other.CoreLength); //!!!raise error
SpecialFunctions.CheckCondition(other is PatchString); //!!!raise error
if (other.ToString().IndexOf(String) >= 0)
{
return(other);
}
else
{
return(null);
}
}
private static List <PatchPattern> PatchPatternCollection(VaccineAsString vaccineUncompressed)
{
List <PatchPattern> rg = new List <PatchPattern>();
PatchPatternFactory aPatchPatternFactory = PatchPatternFactory.GetFactory("strings");
foreach (string componentAsString in vaccineUncompressed.NiceStringCollection())
{
PatchPattern patchPattern = aPatchPatternFactory.GetInstance(componentAsString);
rg.Add(patchPattern);
}
return(rg);
}
private Patch GetPatchFromCollection(PatchPattern patchPattern)
{
if (PatchPatternToPatch.ContainsKey(patchPattern))
{
return((Patch)PatchPatternToPatch[patchPattern]);
}
else
{
Patch aPatch = Patch.GetInstance(patchPattern, 0.0);
PatchPatternToPatch.Add(patchPattern, aPatch);
return(aPatch);
}
}
private void Add(Patch aPatch)
{
PatchPattern patchPattern = aPatch.PatchPattern();
if (PatchPatternToPatch.ContainsKey(patchPattern))
{
Patch previous = (Patch)PatchPatternToPatch[patchPattern];
previous.Weight += aPatch.Weight;
}
else
{
PatchPatternToPatch.Add(patchPattern, aPatch);
}
}
static private Move BestAbsorbedBy(Component component, Combinable combinable)
{
PatchPattern unification = component.PatchPattern().UnifyOrNull(combinable.PatchPattern());
if (unification != null)
{
Move bestMove = new MergeInPatch(component, combinable, unification);
return(bestMove);
}
else
{
return(null);
}
}
public override PatchPattern GetInstance(string expression)
{
if (Hashtable.ContainsKey(expression))
{
PatchPattern patchPattern = (PatchPattern)Hashtable[expression];
return(patchPattern);
}
else
{
PatchPattern patchPattern = PatchRegex.GetInstance(expression, this);
SpecialFunctions.CheckCondition(patchPattern.ToString() == expression, "PatchPattern expression is not in standard form."); //!!!raise error
Hashtable.Add(expression, patchPattern);
return(patchPattern);
}
}
public override PatchPattern GetInstance(string expression)
{
if (ExpressionToPatchPattern.ContainsKey(expression))
{
PatchPattern patchPattern = (PatchPattern)ExpressionToPatchPattern[expression];
return(patchPattern);
}
else
{
PatchPattern patchPattern = new PatchString(expression, this);
SpecialFunctions.CheckCondition(patchPattern.ToString() == expression, "PatchPattern expression is not in standard form."); //!!!raise error
ExpressionToPatchPattern.Add(expression, patchPattern);
return(patchPattern);
}
}
public override PatchPattern GetInstance(ICollection disjunctStringCollection)
{
PatchRegex patchRegex = PatchRegex.GetInstance(disjunctStringCollection, this);
if (Hashtable.ContainsKey(patchRegex.ToString()))
{
PatchPattern patchPattern = (PatchPattern)Hashtable[patchRegex.ToString()];
return(patchPattern);
}
else
{
PatchPattern patchPattern = patchRegex;
Hashtable.Add(patchPattern.ToString(), patchPattern);
return(patchPattern);
}
}
static private Move BestRightLeftOrNull(Component component, Combinable combinable, PatchPattern main, PatchPattern other)
{
int lengthOfShorter = Math.Min(main.CoreLength, other.CoreLength);
for (int overlap = lengthOfShorter - 1; overlap > 0; --overlap)
{
PatchPattern unification = other.UnifyOnRightOrNull(overlap, main);
if (unification != null)
{
Move aMove = new MergeInPatch(component, combinable, unification);
return(aMove);
}
}
return(null);
}
override public PatchPattern UnifyOnRightOrNull(int overlap, PatchPattern other)
{
SpecialFunctions.CheckCondition(overlap < CoreLength && overlap < other.CoreLength); //!!!raise error
SpecialFunctions.CheckCondition(other is PatchString); //!!!raise error
string[] rgsOther = SplitRight(other.ToString(), overlap);
string[] rgsMe = SplitLeft(String, overlap);
if (rgsOther[1] != rgsMe[0])
{
return(null);
}
string sUnification = rgsOther[0] + String;
PatchPattern patchPattern = PatchStringFactory.GetInstance(sUnification);
return(patchPattern);
}
static public PatchTable GetInstanceFromFile(PatchPatternFactory patchPatternFactory,
TextReader patchTableTextReader, string scorerName)
{
PatchTable patchTable = new PatchTable();
patchTable.PatchTableScorer = PatchTableScorer.GetInstance(scorerName);
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(patchTableTextReader, "Patch\tWeight", false))
{
PatchPattern patchPattern = patchPatternFactory.GetInstance(row["Patch"]);
double weight = double.Parse(row["Weight"]);
patchTable.SetMaxPatchLength(patchPattern);
Patch patch = Patch.GetInstance(patchPattern, weight);
patchTable.Add(patch);
}
patchTable.CreateSortedArrays();
return(patchTable);
}
static public PatchTable GetInstance(Dictionary <string, double> patchToWeight, string protein, string vaccineCriteriaName)
{
PatchTable patchTable = new PatchTable();
patchTable.PatchTableScorer = PatchTableScorer.GetInstance("normal");
PatchPatternFactory patchPatternFactory = PatchPatternFactory.GetFactory("strings");
patchTable.PatchPatternToPatch = new Dictionary <PatchPattern, Patch>();
foreach (KeyValuePair <string, double> patchAndWeight in patchToWeight)
{
string patchAsString = patchAndWeight.Key;
double weight = patchAndWeight.Value;
PatchPattern patchPattern = patchPatternFactory.GetInstance(patchAsString);
Patch aPatch = Patch.GetInstance(patchPattern, weight);
patchTable.Add(aPatch);
}
patchTable.CreateSortedArrays();
return(patchTable);
}
public MergeInPatch(Component component, Combinable combinable, PatchPattern unification)
{
string u = unification.ToString();
Debug.Assert(u[0] != '.' && u[u.Length - 1] != '.'); // real assert should have AASet.OptionalAny at start or end
Component = component;
Combinable = combinable;
Unification = unification;
if (combinable is Patch)
{
_LengthIncrease = unification.FullLength - component.FullLength;
Debug.Assert(_LengthIncrease >= 0); // real assert
_ScoreImprovement = combinable.Weight;
}
else
{
//!!!we don't distinish between a merge that reduces the length more or less
Debug.WriteLine("A merge of two components has been found");
_LengthIncrease = Unification.FullLength - (Component.FullLength + Combinable.FullLength);
Debug.Assert(_LengthIncrease < 0);
_ScoreImprovement = 0;
}
}
abstract public PatchPattern UnifyOnRightOrNull(int overlap, PatchPattern other);
abstract public PatchPattern UnifyOrNull(PatchPattern other);
public void ReplaceWithUnification(Combinable combinable, PatchPattern unification)
{
_patchPattern = unification;
Weight += combinable.Weight;
}
private void SetMaxPatchLength(PatchPattern patchPattern)
{
MaxPatchLength = Math.Max(MaxPatchLength, patchPattern.MaxLength);
}
public void AddComponent(PatchPattern patchPattern)
{
AddComponent(patchPattern.FullRealization());
}