/// <summary>
/// Build the query that is executed to retrieve the summarized target data and optional structure data
/// </summary>
/// <returns></returns>
void BuildQuery(string title)
{
int qid = SS.I.ServicesIniFile.ReadInt("SpillTheBeansToolModelQuery", -1);
if (qid < 0)
{
throw new Exception("SpillTheBeansToolModelQuery not defined");
}
Query q = QbUtil.ReadQuery(qid);
if (q == null)
{
throw new Exception("Failed to read SpillTheBeansToolModelQuery: " + qid);
}
AssertMx.IsDefined(KeyQc?.Criteria, "KeyQc.Criteria");
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(KeyQc?.Criteria); // parse key criteria
KeyQc.CopyCriteriaToQueryKeyCritera(q);
Query = q; // save for later use
return;
}
/// <summary>
/// Execute query
/// </summary>
/// <param name="eqp"></param>
public override void ExecuteQuery(
ExecuteQueryParms eqp)
{
MetaTable mt;
MetaColumn mc;
Query q;
QueryTable qt;
QueryColumn qc;
ResultsPage rp;
ResultsViewProps view;
CompoundStructureActivityData cd1, cd2;
bool smallerIsbetter;
double r1, r2, r3, r4;
int di, di2, pdi, pdi2, i3;
string tok;
qt = eqp.QueryTable;
qc = qt.GetQueryColumnByNameWithException(SasMapParms.ParametersMetaColumnName);
AssertMx.IsDefined(qc.Criteria, qc.Label + " criteria not defined");
if (Lex.Eq(qc.Criteria, LastCriteriaString)) // if same criteria as last time then use existing data
{
VoListPos = -1; // init list position
return;
}
VoList = new List<object[]>();
VoListPos = -1; // init list position
LastCriteriaString = qc.Criteria;
ParsedSingleCriteria psc = ParsedSingleCriteria.Parse(qc);
SMP = SasMapParms.Deserialize(psc.Value);
mc = SMP.EndpointMc;
smallerIsbetter = mc.MultiPoint;
List<CompoundStructureActivityData> ds1 = ReadData(SMP); // read in the data to analyze
if (ds1 == null || ds1.Count == 0) return; // throw new QueryException("No data retrieved");
List<CompoundStructureActivityData> ds2 = ds1; // just one set for now
// Calculate difference or ratio coefficents for each pair
List<PairData> pd = new List<PairData>();
int minCoef = -1; // index of minimum coefficent selected so far
double molFactor = AssayAttributes.GetMolarConcFactor(SMP.EndpointMc);
for (di = 0; di < ds1.Count; di++)
{ // process all compounds in 1st set
// if (ds1[di].Nearest == 0) continue; // any data?
if (ds2 == ds1) di2 = di + 1; // only do lower rt diagonal if one dataset
else di2 = 0; // must do all compares, check for dups later
for ( /* start at di2 */; di2 < ds2.Count; di2++)
{
// if (ds2[di2].Nearest == 0) continue; // any data?
if (ds1[di].Cid == ds2[di2].Cid) continue; // avoid self compare
double sim = // similarity
CalculateSimilarity(ds1[di], ds2[di2]);
//if (sim==1.0 && !stereo) // eliminate stereo pairs if requested
// continue; // a more careful check may be needed
if (sim < SMP.MinimumSimilarity) continue; // below cutoff value?
double denom = 1 - sim; // denominator is 1 - sim
if (denom == 0) denom = .00000000001f; // avoid divide by zero
double actChange = 0;
if (smallerIsbetter && ds1[di].Activity < ds2[di2].Activity)
{
cd1 = ds1[di];
cd2 = ds2[di2];
}
else
{
cd1 = ds2[di2];
cd2 = ds1[di];
}
double a1 = cd1.Activity;
double a2 = cd2.Activity;
if (a1 == NullValue.NullNumber || a2 == NullValue.NullNumber)
actChange = 0;
else switch (SMP.ActDiffCalcType)
{
case ActDiffCalcType.SimpleDifference: // activity difference
{
actChange = a1 - a2;
break;
}
case ActDiffCalcType.NegativeLog:
{
actChange = -Math.Log10(a1) - -Math.Log10(a2);
break;
}
case ActDiffCalcType.MolarNegativeLog:
{
actChange = (-Math.Log10(a1 * molFactor)) - (-Math.Log10(a2 * molFactor));
break;
}
case ActDiffCalcType.Ratio: // activity ratio
{
r1 = a1;
if (r1 == 0) r1 = .00000000001f;
r2 = a2;
if (r2 == 0) r2 = .00000000001f;
r3 = r1 / r2;
r4 = r2 / r1;
actChange = r3;
if (SMP.UseAbsoluteValue && r4 > r3) // take the max value
actChange = r4;
break;
}
case ActDiffCalcType.Advanced:
{
throw new InvalidOperationException("SarMapCalcType.Advanced");
}
default:
throw new InvalidOperationException("SarMapCalcType: " + (int)SMP.ActDiffCalcType);
}
if (SMP.UseAbsoluteValue && SMP.ActDiffCalcType != ActDiffCalcType.Ratio)
actChange = Math.Abs(actChange);
double coef = actChange / denom;
if (pd.Count < SMP.MaxPairCount) // just add this pair to end
{
pdi = pd.Count;
pd.Add(new PairData());
}
else
{ // see if this value is greater than anything in list
if (minCoef < 0)
{ // find element with minimum coef
minCoef = 0;
for (i3 = 1; i3 < pd.Count; i3++)
{
if (pd[i3].Coef < pd[minCoef].Coef)
minCoef = i3;
}
}
if (coef <= pd[minCoef].Coef) continue; // if this one better?
//if (ds1 != ds2)
//{ // be sure not a duplicate of what we have in list
// for (i3 = 0; i3 < pd.Count; i3++)
// { // check for pair in list already
// if ((di == pd[i3].CD1 && di2 == pd[i3].CD2) ||
// (di == pd[i3].CD2 && di2 == pd[i3].CD1)) break;
// }
// if (i3 < pd.Count) continue; // continue to next pair if found
//}
pdi = minCoef; // replace this item
minCoef = -1; // reset to get new minimum next time
}
// Save data for the pair
pd[pdi].CD1 = cd1;
pd[pdi].CD2 = cd2;
pd[pdi].Sim = sim;
pd[pdi].ActChange = actChange;
pd[pdi].Coef = coef;
}
}
// Build the list of pair Vos
int voLen = qt.SetSimpleVoPositions();
PairData pdItem;
for (pdi = 1; pdi < pd.Count; pdi++) // sort from max to min coef value
{
pdItem = pd[pdi];
for (pdi2 = pdi - 1; pdi2 >= 0; pdi2--)
{
if (pdItem.Coef < pd[pdi2].Coef) break;
pd[pdi2 + 1] = pd[pdi2];
}
pd[pdi2 + 1] = pdItem;
}
for (pdi = 0; pdi < pd.Count; pdi++)
{
pdItem = pd[pdi];
cd1 = pdItem.CD1;
cd2 = pdItem.CD2;
object[] vo = new object[voLen];
VoArray.SetVo(qt, "PAIR_ID", vo, new NumberMx(pdi + 1));
VoArray.SetVo(qt, "COMPOUND1", vo, new StringMx(cd1.Cid));
VoArray.SetVo(qt, "STRUCTURE1", vo, cd1.Structure);
VoArray.SetVo(qt, "ACTIVITY1", vo, new NumberMx(cd1.Activity));
VoArray.SetVo(qt, "COMPOUND2", vo, new StringMx(cd2.Cid));
VoArray.SetVo(qt, "STRUCTURE2", vo, cd2.Structure);
VoArray.SetVo(qt, "ACTIVITY2", vo, new NumberMx(cd2.Activity));
VoArray.SetVo(qt, "SIMILARITY", vo, new NumberMx(pdItem.Sim));
VoArray.SetVo(qt, "ACTIVITY_DIFF", vo, new NumberMx(pdItem.ActChange));
VoArray.SetVo(qt, "ACT_SIM_COEF", vo, new NumberMx(pdItem.Coef));
VoList.Add(vo);
}
VoListPos = -1; // init list position
return;
}
/// <summary>
/// Setup the form for display
/// </summary>
/// <param name="cid"></param>
/// <param name="qm"></param>
/// <returns></returns>
bool SetupForm(
string cid,
QueryManager qm)
{
AssertMx.IsDefined(cid, "Compound Id (CorpId)");
SelectedCid = cid;
PreviousCid = cid;
RootTable = CompoundId.GetRootMetaTableFromCid(cid);
Qm = null; // no query context
SourceQuery = null;
CurrentBaseQueryCidHitList = null;
if (qm != null) // if querymanager defined then base the related data query on the "current" query
{
Qm = qm; // setup query context
SourceQuery = qm.Query;
RootTable = qm.Query.RootMetaTable;
if (qm.Query != null && qm.Query.Mode == QueryMode.Browse) // if browsing current base query results then get that cid list
{
CurrentBaseQueryCidHitList = Qm.DataTableManager.GetMostCompleteResultsKeyList();
}
}
//else throw new Exception("Parameters not defined");
//if (Lex.IsUndefined(SelectedCid) &&
// (Qm == null || Qm.MoleculeGrid == null || Qm.MoleculeGrid.Helpers == null))
// return false;
SetupCheckmarks();
// Current Cid
//if (Qm != null)
// SelectedCid = Qm.MoleculeGrid.Helpers.GetCidForSelectedCell();
SelectedCid = CompoundId.Format(SelectedCid);
CidCtl.Text = SelectedCid;
//CidCtl.Focus();
// Marked cid count
MarkedCidsList = null;
if (Qm?.MoleculeGrid != null)
{
CidList cl = Qm.MoleculeGrid.GetMarkedList();
if (cl != null)
{
MarkedCidsList = cl.ToStringList();
}
}
int selCnt = (MarkedCidsList != null ? MarkedCidsList.Count : 0);
MarkedCidsCheckEdit.Text = "Selected compound Ids (" + FormatCidListForDisplay(MarkedCidsList) + ")";
MarkedCidsCheckEdit.Enabled = (selCnt > 0);
if (selCnt == 0 && MarkedCidsCheckEdit.Checked)
{
CurrentCidCheckEdit.Checked = true;
}
// All Cid count
int allCnt = (CurrentBaseQueryCidHitList != null ? CurrentBaseQueryCidHitList.Count : 0);
AllCidsCheckEdit.Text = "All Ids in the current result set (" + FormatCidListForDisplay(CurrentBaseQueryCidHitList) + ")";
AllCidsCheckEdit.Enabled = (allCnt > 0);
if (selCnt == 0 && AllCidsCheckEdit.Checked)
{
CurrentCidCheckEdit.Checked = true;
}
// Structure
MoleculeMx cs = new MoleculeMx();
if (Lex.IsDefined(SelectedCid))
{
cs = MoleculeUtil.SelectMoleculeForCid(SelectedCid);
}
QueryMolCtl.SetupAndRenderMolecule(cs);
// MRU list
RenderMruList();
return(true);
}