private void AssignAction(int state, int token, ParserAction action)
{
int cell = ParserAction.Encode(action);
int currentCell = actionTable.Get(state, token);
if (currentCell == 0)
{
actionTable.Set(state, token, cell);
}
else if (currentCell != cell)
{
int resolvedCell;
if (!TryResolveShiftReduce(currentCell, cell, token, out resolvedCell))
{
RequiresGlr = true;
ParserConflictInfo conflict;
var key = new TransitionKey(state, token);
if (!transitionToConflict.TryGetValue(key, out conflict))
{
conflict = new ParserConflictInfo(state, token);
transitionToConflict[key] = conflict;
conflict.AddAction(currentCell);
}
if (!conflict.Actions.Contains(action))
{
conflict.AddAction(action);
}
}
actionTable.Set(state, token, resolvedCell);
}
}
// private methods
private TransitionKey GetKey(TEnum from, TEnum to)
{
int ifrom = EnumInt32ToInt.Convert(from);
int ito = EnumInt32ToInt.Convert(to);
var key = new TransitionKey(ifrom, ito);
return(key);
}
public StateNode NextState(TransitionKey tk, bool fAdd)
{
StateNode state = null;
if (_mpchstate.ContainsKey(tk))
{
state = _mpchstate[tk];
}
else if (fAdd)
{
state = new StateNode();
_mpchstate.Add(tk, state);
}
return(state);
}
private TrieNode GetOrCreateNextState(TrieNode node, char c)
{
TransitionTarget transitionTarget;
var transition = new TransitionKey(node.NodeId, c);
if (!transitions.TryGetValue(transition, out transitionTarget))
{
var newNode = AddNode(node, c);
// Creating new outgoing edge and store character corresponding to
// existing outgoing edge (this way outgoing edges for single vertex form a linked list)
transitionTarget = new TransitionTarget(newNode.NodeId, node.FirstOutgointChar);
// Updating reference to top of linked list of
node.UpdateOutgoingChar(c);
transitions.Add(transition, transitionTarget);
return(newNode);
}
return(nodes[transitionTarget.NextNodeId]);
}
private TrieNode GetNextState(TrieNode node, char c)
{
TransitionTarget transitionTarget;
var transition = new TransitionKey(node.NodeId, c);
if (transitions.TryGetValue(transition, out transitionTarget))
{
return(nodes[transitionTarget.NextNodeId]);
}
foreach (var n in TraversePrefixes(node))
{
transition = new TransitionKey(n.NodeId, c);
if (transitions.TryGetValue(transition, out transitionTarget))
{
return(nodes[transitionTarget.NextNodeId]);
}
}
return(null);
}
public float? CalcTransitionRatio(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, IsotopeLabelType labelTypeNum, IsotopeLabelType labelTypeDenom)
{
// Avoid 1.0 ratios for self-to-self
if (ReferenceEquals(labelTypeNum, labelTypeDenom))
return null;
float areaNum, areaDenom;
var key = nodeTran.Key(nodeGroup);
var keyNum = new TransitionKey(nodeGroup, key, labelTypeNum);
var keyDenom = new TransitionKey(nodeGroup, key, labelTypeDenom);
if (!TranAreas.TryGetValue(keyNum, out areaNum) ||
!TranAreas.TryGetValue(keyDenom, out areaDenom))
return null;
return areaNum/areaDenom;
}
public float? CalcTransitionGlobalRatio(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, IsotopeLabelType labelType)
{
if (GlobalStandardArea == 0)
return null;
float areaNum;
var keyNum = new TransitionKey(nodeGroup, nodeTran.Key(nodeGroup), labelType);
if (!TranAreas.TryGetValue(keyNum, out areaNum))
return null;
return (float) (areaNum / GlobalStandardArea);
}
public void AddChromInfo(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, TransitionChromInfo info)
{
if (info.IsEmpty)
return;
var key = new TransitionKey(nodeGroup, nodeTran.Key(nodeGroup), nodeGroup.TransitionGroup.LabelType);
if (TranAreas.ContainsKey(key))
throw new InvalidDataException(String.Format(Resources.PeptideChromInfoCalculator_AddChromInfo_Duplicate_transition___0___found_for_peak_areas, nodeTran.Transition));
TranAreas.Add(key, info.Area);
}
private bool Equals(TransitionKey other)
{
return Equals(other._ionType, _ionType) &&
Equals(_customIonEquivalenceTestValue, other._customIonEquivalenceTestValue) &&
other._ionOrdinal == _ionOrdinal &&
other._massIndex == _massIndex &&
Equals(other._decoyMassShift, _decoyMassShift) &&
other._charge == _charge &&
other._precursorCharge == _precursorCharge &&
Equals(other._losses, _losses) &&
Equals(other._labelType, _labelType);
}
public TransitionKey(TransitionKey key, IsotopeLabelType labelType)
{
_ionType = key._ionType;
_customIonEquivalenceTestValue = key._customIonEquivalenceTestValue;
_ionOrdinal = key._ionOrdinal;
_massIndex = key._massIndex;
_decoyMassShift = key._decoyMassShift;
_charge = key._charge;
_precursorCharge = key._precursorCharge;
_losses = key._losses;
_labelType = labelType;
}
//// Given a transition key, find the next state. Optionally,
//// add a new state when the key isn't yet a valid transition
//// for this state.
//public StateNode NextState(TransitionKey tk, bool fAdd)
//{
// StateNode state;
// try
// {
// state = _mpchstate[tk];
// }
// catch (KeyNotFoundException)
// {
// state = null;
// }
// if (state == null && fAdd)
// {
// state = new StateNode();
// _mpchstate.Add(tk, state);
// }
// return state;
//}
// Remove a given transition to another state from this state
public void RemoveLink(TransitionKey tk)
{
_mpchstate.Remove(tk);
}
