/// <summary>
/// General table / gene symbol query builder
/// </summary>
/// <param name="tableName"></param>
/// <param name="geneSymbol"></param>
/// <returns></returns>
public static Query BuildTargetAssayQuery(
string tableName,
string geneSymbol)
{
Query q = new Query();
MetaTable mt = MetaTableCollection.GetWithException(tableName);
QueryTable qt = new QueryTable(q, mt);
QueryColumn qc = qt.GetQueryColumnByNameWithException(MultiDbAssayDataNames.GeneSymbol);
qc.Criteria = MultiDbAssayDataNames.GeneSymbol + " = " + Lex.AddSingleQuotes(geneSymbol);
qc.CriteriaDisplay = "= " + geneSymbol;
if (qc.IsKey) // if key column store for that as well
{
q.KeyCriteria = " = " + Lex.AddSingleQuotes(geneSymbol);
q.KeyCriteriaDisplay = "= " + geneSymbol;
}
//qc = qt.GetQueryColumnByNameWithException("top_lvl_rslt");
//qc.Criteria = "top_lvl_rslt = 'Y'"; // only top level results
//qc.CriteriaDisplay = "= Y";
return(q);
}
/// <summary>
/// Build unpivoted subquery QueryManager including the DataTableManger,
/// ResultsFormat and ResultsFormatter.
/// Build empty DataTable
/// </summary>
/// <returns></returns>
QueryManager InitializeUnpivotedSubqueryQm()
{
Query q2 = null;
DataTableManager dtm2;
DataTableMx dt2;
ResultsFormat rf2;
ResultsFormatFactory rff;
ResultsFormatter rfmtr;
QueryTable qt;
MetaTable mt;
QueryManager qm2 = new QueryManager(); // build output query here
// Setup unpivoted output query
q2 = new Query(qm2);
mt = MetaTableCollection.GetWithException(MultiDbAssayDataNames.CombinedNonSumTableName);
qt = new QueryTable(q2, mt); // be sure proper cols are selected
dtm2 = new DataTableManager(qm2);
dt2 = DataTableManager.BuildDataTable(qm2);
rff = new ResultsFormatFactory(qm2, OutputDest.WinForms);
rff.Build();
rfmtr = new ResultsFormatter(qm2);
return(qm2);
}
/// <summary>
/// Edit the Cids criteris
/// </summary>
/// <returns></returns>
bool EditCids()
{
Query q;
QueryTable qt;
MetaTable mt;
QueryColumn qc;
mt = MetaTableCollection.GetWithException(Tso.GetSummarizedMetaTableName());
q = new Query();
qt = new QueryTable(q, mt);
qc = qt.KeyQueryColumn;
qc.Criteria = Cids.Text;
qc.CriteriaDisplay = Cids.Text;
if (!CriteriaEditor.GetCompoundIdCriteria(qc))
{
return(false);
}
if (qc.Criteria.StartsWith(" = ")) // make equality look nice
{
Cids.Text = qc.CriteriaDisplay;
}
else
{
Cids.Text = qc.Criteria;
}
return(true);
}
/// <summary>
/// Build summarization detail query
/// </summary>
/// <param name="mt"></param>
/// <param name="mc"></param>
/// <param name="level"></param>
/// <param name="linkInfo"></param>
/// <returns></returns>
public override Query GetDrilldownDetailQuery(
MetaTable mt,
MetaColumn mc,
int level,
string linkInfo)
{
QueryTable qt, qt2;
MetaTable mt2;
QueryColumn qc, qc2;
MetaColumn mc2;
string resultIdColName = "";
Query q = new Query();
// Summarized MdbAssay table drilling down to unsummarized MdbAssay table
if (UnpivotedAssayResult.IsSummarizedMdbAssayTable(mt.Name))
{
if (UnpivotedAssayResult.IsCombinedMdbAssayTable(mt.Name)) // multiple tables
{
mt2 = MetaTableCollection.GetWithException(MultiDbAssayDataNames.CombinedNonSumTableName);
resultIdColName = MultiDbAssayDataNames.SumResultId;
}
else // base unpivoted or pivoted by target
{
mt2 = MetaTableCollection.GetWithException(MultiDbAssayDataNames.BaseNonSumTableName);
resultIdColName = MultiDbAssayDataNames.BaseSumResultId;
}
qt = new QueryTable(q, mt2);
qc = qt.GetQueryColumnByNameWithException(resultIdColName);
qc.Criteria = resultIdColName + " = " + linkInfo;
return(q);
}
// Drilling down from old all_bioassay_unpivoted to specific source data
else if (Lex.Eq(mt.Name, UnpivotedAssayView.UnsummarizedMetaTableName))
{ // ResultId is formatted by the source with the first item being the source name
Match m = Regex.Match(linkInfo, @"(.*),(.*),(.*)", RegexOptions.IgnoreCase | RegexOptions.RightToLeft);
string mtName = m.Groups[1].Value;
string mcId = m.Groups[2].Value;
string linkInfo2 = m.Groups[3].Value;
mt2 = MetaTableCollection.GetWithException(mtName);
IMetaBroker imb = MetaBrokerUtil.GlobalBrokers[(int)mt2.MetaBrokerType];
q = imb.GetDrilldownDetailQuery(mt2, mcId, level, linkInfo2);
return(q);
}
else
{
throw new ArgumentException("Invalid tableName: " + mt.Name);
}
}
/// <summary>
/// Check that each of the numbers in the list exist in the database
/// </summary>
/// <param name="list">String form of list as entered by user</param>
/// <param name="rootTableName">Root table to check against</param>
/// <returns></returns>
public static string ValidateList(
string listText,
string rootTableName)
{
string cn, extCn, errorMsg;
int i1, i2;
if (String.IsNullOrEmpty(rootTableName))
{
return(null);
}
MetaTable rootTable = MetaTableCollection.GetWithException(rootTableName);
string[] cna = listText.Split(new Char[] { '\n', '\r', ' ' });
int t0 = TimeOfDay.Milliseconds();
for (i1 = 0; i1 < cna.Length; i1++)
{
if (i1 > 1000 || TimeOfDay.Milliseconds() - t0 > 3000)
{
return(null); // limit size & time of check
}
extCn = cna[i1].Trim();
if (extCn == "" || extCn.StartsWith("("))
{
continue;
}
i2 = extCn.IndexOf("("); // strip trailing text in parens
if (i2 > 0)
{
extCn = extCn.Substring(0, i2);
}
cn = CompoundId.BestMatch(extCn, rootTable);
if (cn == "")
{
cn = extCn; // nothing found, use original text
}
if (!CompoundIdUtil.Exists(cn, rootTable))
{
return(extCn);
}
}
return(null);
}
/// <summary>
/// Get query to select all data.
/// It consists of a single QueryTable with the CID and key table name
/// This keeps the initial query sent to the client small which helps
/// response time for users not on the same local network as the server.
/// </summary>
/// <param name="keyMtName"></param>
/// <param name="cn"></param>
/// <returns></returns>
public static Query GetSelectAllDataQuery(
string keyMtName,
string cn)
{
MetaTable mt = MetaTableCollection.GetWithException(MetaTable.AllDataQueryTable);
Query q = new Query();
QueryTable qt = new QueryTable(mt);
q.AddQueryTable(qt);
MetaTable keyMt = null;
if (Lex.IsDefined(keyMtName))
{
keyMt = MetaTableCollection.Get(keyMtName);
}
if (keyMt != null && keyMt.Root.IsUserDatabaseStructureTable) // if root metatable is user database then normalize based on key
{
keyMt = keyMt.Root; // be sure we have root
cn = CompoundId.Normalize(cn, keyMt);
}
else
{
cn = CompoundId.Normalize(cn);
keyMt = CompoundId.GetRootMetaTableFromCid(cn, keyMt);
keyMt = keyMt.Root; // be sure we have root (may not be structure table)
}
if (keyMt == null)
{
throw new Exception("Failed to identify key MetaTable");
}
q.KeyCriteria = q.KeyCriteriaDisplay = " = " + cn;
QueryColumn qc = qt.GetQueryColumnByNameWithException("root_table");
qc.Criteria = qc.CriteriaDisplay = qc.MetaColumn.Name + " = " + keyMt.Name;
return(q);
}
/// <summary>
/// Do Generic display of a list of structures
/// </summary>
/// <param name="title"></param>
/// <param name="cidLabel"></param>
/// <param name="structLabel"></param>
/// <param name="structures"></param>
public static void DisplayStructures(
string title,
string cidLabel,
string structLabel,
List <MoleculeMx> structures,
MoleculeGridPanel gridPanel,
bool embedDataInQuery)
{
QueryManager qm = null;
MetaTable mt = MetaTableCollection.GetWithException("Generic_Structure_Table");
mt.MetaBrokerType = MetaBrokerType.NoSql;
Query q = ToolHelper.InitEmbeddedDataToolQuery(mt);
QueryTable qt = q.Tables[0];
qt.Label = title;
qt.GetQueryColumnByName("CompoundId").Label = cidLabel;
qt.GetQueryColumnByName("Structure").Label = structLabel;
DataTableMx dt = q.ResultsDataTable as DataTableMx;
for (int mi = 0; mi < structures.Count; mi++)
{
MoleculeMx cs = structures[mi];
DataRowMx dr = dt.NewRow();
string cid = cs.Id;
if (Lex.IsUndefined(cid))
{
cid = (mi + 1).ToString();
}
dr[qt.Alias + ".CompoundId"] = new CompoundId(cid);
dr[qt.Alias + ".Structure"] = cs;
dt.Rows.Add(dr);
}
DisplayData(q, dt, gridPanel, embedDataInQuery);
return;
}
/// <summary>
/// Build query table for decomposition & add to query
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
Query q;
MetaTable mt;
MetaColumn mc;
QueryTable qt;
QueryColumn qc;
q = QbUtil.Query;
if (q == null || q.Tables.Count == 0)
{
MessageBoxMx.ShowError("No current query.");
return(DialogResult.None);
}
qt = q.GetQueryTableByName("Rgroup_Decomposition");
bool newTable = false;
if (qt == null)
{
mt = MetaTableCollection.GetWithException("Rgroup_Decomposition");
qt = new QueryTable(mt);
newTable = true;
}
qc = qt.GetQueryColumnByNameWithException("Core");
MoleculeMx core = new MoleculeMx(MoleculeFormat.Molfile, QueryMolCtl.MolfileString);
if (core.AtomCount == 0)
{
MessageBoxMx.ShowError("A Core structure with R-groups must be defined.");
return(DialogResult.None);
}
qc.MolString = core.GetMolfileString(); // put core structure into table criteria
qc.CriteriaDisplay = "Substructure search (SSS)";
qc.Criteria = "CORE SSS SQUERY";
if (!Structure.Checked && !Smiles.Checked && !Formula.Checked &&
!Weight.Checked && !Index.Checked)
{
MessageBoxMx.ShowError("At least one substituent display format must be selected.");
return(DialogResult.None);
}
qc = qt.GetQueryColumnByName("R1_Structure");
if (ShowCoreStructure.Checked)
{
qc.Label = "R-group, Core\tChime=" + core.GetChimeString(); // reference core in query col header label
qc.MetaColumn.Width = 25;
}
SetSelected(qt, "R1_Structure", Structure.Checked);
SetSelected(qt, "R1_Smiles", Smiles.Checked);
SetSelected(qt, "R1_Formula", Formula.Checked);
SetSelected(qt, "R1_Weight", Weight.Checked);
SetSelected(qt, "R1_SubstNo", Index.Checked);
string terminateOption = TerminateOption.Text;
qc = qt.GetQueryColumnByName("Terminate_Option");
if (qc != null && Lex.IsDefined(terminateOption))
{
qc.Criteria = qt.MetaTable.Name + " = " + Lex.AddSingleQuotes(terminateOption);
qc.CriteriaDisplay = "= " + Lex.AddSingleQuotes(terminateOption);
}
else
{
qc.Criteria = qc.CriteriaDisplay = ""; // not defined
}
if (newTable)
{
q.AddQueryTable(qt); // add to query if new
}
QbUtil.RenderQuery(); // show it
UsageDao.LogEvent("RgroupDecomposition");
return(DialogResult.OK);
}
/// <summary>
/// Build metatable for a Spotfire analysis link
/// </summary>
/// <param name="name"></param>
/// <returns></returns>
public MetaTable GetMetaTable(
string name)
{
UserObject uo;
SpotfireViewProps sl;
MetaTable mt, mt2;
MetaColumn mc;
int objectId;
string prefix = "spotfirelink_";
if (name.ToLower().IndexOf(prefix) != 0)
{
return(null);
}
string tok = name.Substring(prefix.Length); // get the object id
if (!int.TryParse(tok, out objectId))
{
return(null);
}
uo = UserObjectDao.Read(objectId);
if (uo == null)
{
return(null);
}
if (!Permissions.UserHasReadAccess(Security.UserName, uo))
{
return(null);
}
try
{
sl = SpotfireViewProps.Deserialize(uo.Content);
if (sl == null)
{
throw new Exception("Null Deserialize result for object " + uo.Id);
}
}
catch (Exception ex)
{
DebugLog.Message(ex);
return(null);
}
MetaTable root = MetaTableCollection.GetWithException(MetaTable.PrimaryRootTable);
mt = MetaTableCollection.GetWithException("SPOTFIRELINK_MODEL");
mt = mt.Clone(); // build metatable here
mt.Name = "SPOTFIRELINK_" + uo.Id;
mt.Code = uo.Content; // store serialized SpotfireLink content in Code field
mt.Parent = root;
mt.MetaBrokerType = MetaBrokerType.SpotfireLink;
mt.TableMap = root.TableMap; // allow searches on CorpId
mt.Label = uo.Name;
foreach (MetaColumn mc0 in mt.MetaColumns)
{
mc0.InitialSelection = ColumnSelectionEnum.Hidden;
}
foreach (SpotfireLinkParameter sp in sl.SpotfireLinkParameters.Values)
{
mc = mt.GetMetaColumnByName(sp.Name);
if (mc == null)
{
continue;
}
bool b = false;
bool.TryParse(sp.Value, out b);
mc.InitialSelection = b ? ColumnSelectionEnum.Selected : ColumnSelectionEnum.Hidden;
}
if (mt.KeyMetaColumn.InitialSelection != ColumnSelectionEnum.Selected)
{
mt.KeyMetaColumn.InitialSelection = ColumnSelectionEnum.Unselected;
}
mc = mt.GetMetaColumnByName("VISUALIZATION");
if (mc != null)
{
mc.InitialSelection = ColumnSelectionEnum.Selected;
}
SetAllInQueryInitialCriteria(mt, "invitro_assays", "invitro_assays_default_to_all", "in (ALL_ASSAY_INVITRO_ASSAYS_IN_THIS_QUERY)");
SetAllInQueryInitialCriteria(mt, "insilico_models", "insilico_models_default_to_all", "in (ALL_SPM_INSILICO_MODELS_IN_THIS_QUERY)");
return(mt);
}
/// <summary>
/// OK button clicked, process input
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
int rgCount; // number of Rgroups
List <Rgroup> rgList; // list of existing Rgroups
bool[] rgExists; // entry = true if rgroup exists in core
Rgroup rg;
bool oneD, twoD; // matrix dimensionality
List <string> keys = null;
Dictionary <string, List <QualifiedNumber> > mElem; // matrix element dictionary
List <RgroupSubstituent>[] rSubs; // substituents seen for each Rgroup
Query q, q0, q2;
QueryTable qt, qt2;
QueryColumn qc, qc2;
MetaTable mt, mt2;
MetaColumn mc, mc2;
DataTableMx dt;
DataRowMx dr;
DialogResult dlgRslt;
string tok;
int ri, rii, si, qti, qci, bi, bi2;
// Get core structure & list of R-groups
MoleculeMx core = new MoleculeMx(MoleculeFormat.Molfile, SQuery.MolfileString);
if (core.AtomCount == 0)
{
MessageBoxMx.ShowError("A Core structure with R-groups must be defined");
return(DialogResult.None);
}
if (!Structure.Checked && !Smiles.Checked && !Formula.Checked &&
!Weight.Checked && !Index.Checked)
{
MessageBoxMx.ShowError("At least one substituent display format must be selected.");
return(DialogResult.None);
}
mt = MetaTableCollection.GetWithException("Rgroup_Decomposition");
qt = new QueryTable(mt);
qc = qt.GetQueryColumnByNameWithException("Core");
qc.MolString = core.GetMolfileString(); // put core structure into table criteria
qc.CriteriaDisplay = "Substructure search (SSS)";
qc.Criteria = "CORE SSS SQUERY";
qc = qt.GetQueryColumnByNameWithException("R1_Structure");
if (ShowCoreStructure.Checked)
{
qc.Label = "R-group, Core\tChime=" + core.GetChimeString(); // reference core in query col header label
qc.MetaColumn.Width = 25;
}
RgroupDecomposition.SetSelected(qt, "R1_Structure", Structure.Checked); // select for retrieval if checked
RgroupDecomposition.SetSelected(qt, "R1_Smiles", Smiles.Checked);
RgroupDecomposition.SetSelected(qt, "R1_Formula", Formula.Checked);
RgroupDecomposition.SetSelected(qt, "R1_Weight", Weight.Checked);
RgroupDecomposition.SetSelected(qt, "R1_SubstNo", Index.Checked);
string terminateOption = "First mapping"; // terminate on first complete match
qc = qt.GetQueryColumnByNameWithException("Terminate_Option");
qc.Criteria = qt.MetaTable.Name + " = " + Lex.AddSingleQuotes(terminateOption);
qc.CriteriaDisplay = "= " + Lex.AddSingleQuotes(terminateOption);
QueryTable rgdQt = qt; // keep a ref to it
if (QbUtil.Query == null || QbUtil.Query.Tables.Count == 0)
{
MessageBoxMx.ShowError("No current query.");
return(DialogResult.None);
}
q0 = QbUtil.Query; // original query this analysis is based on
q = q0.Clone(); // make copy of source query we can modify
q.SingleStepExecution = false;
qti = 0;
while (qti < q.Tables.Count) // deselect query columns that we don't want
{
qt = q.Tables[qti];
if (Lex.Eq(qt.MetaTable.Name, "Rgroup_Decomposition"))
{ // remove any rgroup decomp table
qti++;
continue;
}
mt = qt.MetaTable;
if (mt.MultiPivot || // check for tables not allowed in underlying query
mt.MetaBrokerType == MetaBrokerType.CalcField || // (called ShouldPresearchAndTransform previously)
mt.MetaBrokerType == MetaBrokerType.MultiTable ||
mt.MetaBrokerType == MetaBrokerType.RgroupDecomp)
{
MessageBoxMx.ShowError("Multipivot/Rgroup table \"" + qt.ActiveLabel +
"\" can't be included in an underlying Rgroup Matrix query");
return(DialogResult.None);
}
for (qci = 0; qci < qt.QueryColumns.Count; qci++)
{
qc = qt.QueryColumns[qci];
if (qc.MetaColumn == null)
{
continue;
}
switch (qc.MetaColumn.DataType)
{
case MetaColumnType.CompoundId: // keep only these
case MetaColumnType.Integer:
case MetaColumnType.Number:
case MetaColumnType.QualifiedNo:
case MetaColumnType.String:
break;
default:
qc.Selected = false;
break;
}
}
qti++;
}
q.AddQueryTable(rgdQt); // Add Rgroup decom table to end of cloned source query
Progress.Show("Retrieving data...");
try
{
dlgRslt = ToolHelper.ExecuteQuery(ref q, out keys);
if (dlgRslt != DialogResult.OK)
{
return(dlgRslt);
}
}
catch (Exception ex)
{
MessageBoxMx.ShowError("Error executing query:\r\n" + ex.Message);
return(DialogResult.None);
}
if (keys == null || keys.Count == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No results were returned by the query.");
return(DialogResult.None);
}
// Scan modified query to get list of rgroup indexes that are present
rgExists = new bool[32];
rgList = new List <Rgroup>();
QueryTable rgQt = q.GetQueryTableByName("Rgroup_Decomposition");
foreach (QueryColumn qc0 in rgQt.QueryColumns)
{
mc = qc0.MetaColumn;
if (!(mc.Name.StartsWith("R") && mc.Name.EndsWith("_STRUCTURE") && qc0.Selected))
{
continue; // skip if not a selected Rgroup structure
}
int len = mc.Name.Length - ("R" + "_STRUCTURE").Length;
tok = mc.Name.Substring(1, len);
if (!int.TryParse(tok, out ri))
{
continue;
}
rgExists[ri - 1] = true;
rg = new Rgroup();
rg.RIndex = ri;
rg.VoPos = qc0.VoPosition;
rgList.Add(rg);
}
for (bi = 1; bi < rgList.Count; bi++)
{ // sort by increasing R index
rg = rgList[bi];
for (bi2 = bi - 1; bi2 >= 0; bi2--)
{
if (rg.RIndex >= rgList[bi2].RIndex)
{
break;
}
rgList[bi2 + 1] = rgList[bi2];
}
rgList[bi2 + 1] = rg;
}
rgCount = rgList.Count;
twoD = TwoD.Checked;
if (rgCount == 1)
{
twoD = false; // if only 1 rgroup can't do as 2d
}
oneD = !twoD;
// Read data into mElem and rgroup substituents into rSubs.
// Matrix mElem is keyed on [R1Smiles, R2Smiles,... RnSmiles, FieldName] for 1d and
// [R1Smiles, R2Smiles,... FieldName, RnSmiles] for 2d
QueryManager qm = q.QueryManager as QueryManager;
DataTableManager dtm = qm.DataTableManager;
dt = qm.DataTable;
mElem = new Dictionary <string, List <QualifiedNumber> >(); // matrix element dictionary
rSubs = new List <RgroupSubstituent> [32]; // list of substituents seen for each Rgroup
for (rii = 0; rii < rgCount; rii++) // alloc substituent list for rgroup
{
rSubs[rii] = new List <RgroupSubstituent>();
}
int rowCount = 0;
while (true)
{ // scan data accumulating rgroup substituents and data values
dr = dtm.FetchNextDataRow();
if (dr == null)
{
break;
}
rowCount++;
string cid = dr[dtm.KeyValueVoPos] as string;
string lastMapCid = "", rgroupKey = "", rgroupKeyLast = "";
int mapCount = 0;
for (rii = 0; rii < rgCount; rii++) // for
{
MoleculeMx rSub = dr[rgList[rii].VoPos] as MoleculeMx;
if (rSub == null || rSub.AtomCount == 0)
{
continue;
}
ri = rgList[rii].RIndex; // actual R index in query
int subIdx = RgroupSubstituent.Get(rSub, rSubs[rii]);
// if (ri == 1 && subIdx != 0) subIdx = subIdx; // debug
if (subIdx < 0)
{
continue;
}
string rKey = "R" + ri.ToString() + "_" + (subIdx + 1).ToString();
if (oneD || rii < rgCount - 1)
{
if (rgroupKey != "")
{
rgroupKey += "\t";
}
rgroupKey += rKey;
}
else
{
rgroupKeyLast = rKey;
}
lastMapCid = cid;
mapCount++;
}
if (lastMapCid == cid) // add the data if compound has a mapping
{
AccumulateMatrixElements(mElem, q, dr, rgroupKey, rgroupKeyLast, cid);
}
if (Progress.IsTimeToUpdate)
{
Progress.Show("Retrieving data: " + StringMx.FormatIntegerWithCommas(rowCount) + " rows...");
}
}
if (rowCount == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No data rows retrieved");
return(DialogResult.None);
}
if (twoD && (rSubs[rgCount - 1] == null || rSubs[rgCount - 1].Count == 0))
{ // if 2D be sure we have at least one substituent for the last Rgroup
Progress.Hide();
MessageBoxMx.ShowError("No substituents found for R" + rgCount.ToString());
return(DialogResult.None);
}
// Create a MetaTable & DataTable for matrix results
Progress.Show("Analyzing data...");
mt = new MetaTable(); // create output table
MatrixCount++;
mt.Name = "RGROUPMATRIX_" + MatrixCount;
mt.Label = "R-group Matrix " + MatrixCount;
mt.MetaBrokerType = MetaBrokerType.RgroupDecomp;
mc = // use sequence for key
mt.AddMetaColumn("RgroupMatrixId", "No.", MetaColumnType.Integer, ColumnSelectionEnum.Selected, 3);
mc.ClickFunction = "None"; // avoid hyperlink on this key
mc.IsKey = true;
int maxLeftR = rgCount;
if (twoD)
{
maxLeftR = rgCount - 1;
}
for (ri = 0; ri < maxLeftR; ri++)
{
string rStr = "R" + (ri + 1).ToString();
if (Structure.Checked)
{
mc = mt.AddMetaColumn(rStr + "Str", rStr, MetaColumnType.Structure, ColumnSelectionEnum.Selected, 12);
if (ri == 0 && ShowCoreStructure.Checked) // include core structure above R1 if requested
{
string chimeString = MoleculeMx.MolfileStringToSmilesString(SQuery.MolfileString);
mc.Label = "R1, Core\tChime=" + chimeString;
mc.Width = 25;
}
}
if (Smiles.Checked)
{
mc = mt.AddMetaColumn(rStr + "Smi", rStr + " Smiles", MetaColumnType.String, ColumnSelectionEnum.Selected, 12);
}
if (Formula.Checked)
{
mc = mt.AddMetaColumn(rStr + "Mf", rStr + " Formula", MetaColumnType.String, ColumnSelectionEnum.Selected, 8);
}
if (Weight.Checked)
{
mc = mt.AddMetaColumn(rStr + "MW", rStr + " Mol. Wt.", MetaColumnType.Number, ColumnSelectionEnum.Selected, 6, ColumnFormatEnum.Decimal, 2);
}
if (Index.Checked)
{
mc = mt.AddMetaColumn(rStr + "Index", rStr + " Subst. Idx.", MetaColumnType.Number, ColumnSelectionEnum.Selected, 4);
mc.Format = ColumnFormatEnum.Decimal;
}
}
mc = // add column to contain result type
mt.AddMetaColumn("ResultType", "Result Type", MetaColumnType.String, ColumnSelectionEnum.Selected, 12);
if (oneD) // add just 1 column to contain results
{
mc = mt.AddMetaColumn("Results", "Results", MetaColumnType.QualifiedNo, ColumnSelectionEnum.Selected, 12);
mc.MetaBrokerType = MetaBrokerType.RgroupDecomp; // broker to do special col handling for cond formtting
if (QbUtil.Query.UserObject.Id > 0)
{
mc.DetailsAvailable = true;
}
}
else // add col for each substituent for last rgroup
{
string rStr = "R" + rgCount.ToString();
for (si = 0; si < rSubs[rgCount - 1].Count; si++)
{
string cName = rStr + "_" + (si + 1).ToString();
string cLabel = cName.Replace("_", ".");
RgroupSubstituent rgs = rSubs[ri][si]; // get substituent info
if (Structure.Checked) // include structure
{
cLabel += "\tChime=" + rgs.Struct.GetChimeString();
}
else if (Smiles.Checked)
{
cLabel += " = " + rgs.Struct.GetSmilesString();
}
else if (Formula.Checked)
{
cLabel += " = " + rgs.Struct.MolFormula;
}
else if (Weight.Checked)
{
cLabel += " = " + rgs.Struct.MolWeight;
}
else if (Index.Checked)
{
cLabel += " = " + (si + 1).ToString();
}
mc = mt.AddMetaColumn(cName, cLabel, MetaColumnType.QualifiedNo, ColumnSelectionEnum.Selected, 12);
mc.MetaBrokerType = MetaBrokerType.RgroupDecomp;
if (QbUtil.Query.UserObject.Id > 0)
{
mc.DetailsAvailable = true;
}
}
}
MetaTableCollection.UpdateGlobally(mt); // add as a known metatable
if (mElem.Count == 0) // be sure we have a matrix
{
Progress.Hide();
MessageBoxMx.ShowError("No matrix can be created because insufficient data was found.");
return(DialogResult.None);
}
// Build the DataTable
Progress.Show("Building data table...");
q2 = new Query(); // build single-table query to hold matrix
qt2 = new QueryTable(q2, mt);
dt = DataTableManager.BuildDataTable(q2);
Dictionary <string, List <QualifiedNumber> > .KeyCollection kc = mElem.Keys;
string[] rgKeys = new string[mElem.Count];
kc.CopyTo(rgKeys, 0);
Array.Sort(rgKeys);
string[] rgKey = null, lastRgKey = null;
int rki = 0;
for (rki = 0; rki < rgKeys.Length; rki++)
{
rgKey = rgKeys[rki].Split('\t');
int riTop = rgCount + 1; // all r substituents & field name on left
if (twoD)
{
riTop = rgCount;
}
for (ri = 0; ri < riTop; ri++) // see if any changes in left side substituents or field name
{
if (lastRgKey == null || rgKey[ri] != lastRgKey[ri])
{
break;
}
}
if (ri < riTop || oneD) // if 2d then new row only if some change before last R
{
dr = dt.NewRow();
dt.Rows.Add(dr);
dr[dtm.KeyValueVoPos + 1] = new NumberMx(dt.Rows.Count); // integer row key
}
if (!HideRepeatingSubstituents.Checked)
{
ri = 0; // start at first if not hiding
}
lastRgKey = rgKey;
for (ri = ri; ri < riTop; ri++) // build row with these
{
string rgSub = rgKey[ri]; // get substituent id or table.column name
if (rgSub == "")
{
continue;
}
if (ri < riTop - 1)
{ // output substituent and/or smiles
string rStr = "R" + (ri + 1).ToString();
si = rgSub.IndexOf("_");
si = Int32.Parse(rgSub.Substring(si + 1)) - 1; // get substituent index
RgroupSubstituent rgs = rSubs[ri][si]; // get substituent info
if (Structure.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Str");
dr[QcToDcName(qc2)] = rgs.Struct;
}
if (Smiles.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Smi");
dr[QcToDcName(qc2)] = new StringMx(rgs.Struct.GetSmilesString());
}
if (Formula.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Mf");
dr[QcToDcName(qc2)] = new StringMx(rgs.Struct.MolFormula);
}
if (Weight.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Mw");
dr[QcToDcName(qc2)] = new NumberMx(rgs.Struct.MolWeight);
}
if (Index.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Index");
dr[QcToDcName(qc2)] = new NumberMx(si + 1);
}
}
else // output field name
{
string[] sa = rgSub.Split('.'); // get field name
qt = q.GetQueryTableByName(sa[0]);
qc = qt.GetQueryColumnByName(sa[1]);
string fieldName = qc.ActiveLabel;
if (q0.Tables.Count >= 3) // qualify by table if 3 or more tables in original query
{
fieldName = qt.ActiveLabel + " - " + fieldName;
}
qc2 = qt2.GetQueryColumnByName("ResultType");
dr[QcToDcName(qc2)] = new StringMx(fieldName);
}
}
// Output value
string cName;
if (oneD)
{
cName = "Results";
}
else
{
cName = rgKey[rgCount]; // get key for this substituent (e.g. R2_1)
}
if (Lex.IsUndefined(cName))
{
continue; // may be no substituent match
}
qc2 = qt2.GetQueryColumnByName(cName);
QualifiedNumber qn = SummarizeData(mElem[rgKeys[rki]]); // get summarized value
dr[QcToDcName(qc2)] = qn;
}
ToolHelper.DisplayData(q2, dt, true);
UsageDao.LogEvent("RgroupMatrix");
Progress.Hide();
return(DialogResult.OK);
}
/// <summary>
/// Setup/configure any needed secondary metabroker
/// </summary>
/// <param name="eqp"></param>
/// <param name="mpd"></param>
/// <param name="unpivotedTableIsFirst"></param>
void SetupSecondaryMetaBroker(
ExecuteQueryParms eqp,
MultiTablePivotBrokerTypeData mpd,
out bool unpivotedTableIsFirst)
{
QueryEngine qe2;
Query q2;
QueryTable qt2;
QueryColumn qc2;
MetaTable mt2;
string firstMtName = mpd.FirstTableName;
MetaTable firstMt = MetaTableCollection.GetWithException(firstMtName);
unpivotedTableIsFirst = UnpivotedAssayResult.IsUnpivotedSummarizedMdbAssayTable(firstMtName);
if (unpivotedTableIsFirst) // just use unpivoted table as is
{
SecondaryMetaBroker = this;
Eqp2 = eqp;
}
else // all pivoted tables, create secondary query on the summarized unpivoted table
{
if (SecondaryMetaBroker == null)
{
MultiDbAssayMetaBroker mb2 = SecondaryMetaBroker = new MultiDbAssayMetaBroker();
if (UnpivotedAssayResult.IsCombinedMdbAssayTable(firstMtName))
{
mt2 = MetaTableCollection.GetWithException(MultiDbAssayDataNames.CombinedTableName);
}
else
{
mt2 = MetaTableCollection.GetWithException(MultiDbAssayDataNames.BaseTableName);
}
q2 = new Query();
qt2 = new QueryTable(mt2);
qc2 = qt2.GetQueryColumnByNameWithException(MultiDbAssayDataNames.GeneSymbol);
if (mpd.TableCodeCsvList.Length != 0) // limit by codes
{
qc2.Criteria = qc2.CriteriaDisplay = MultiDbAssayDataNames.GeneSymbol + " in (" + mpd.TableCodeCsvList + ")";
}
q2.AddQueryTable(qt2);
qe2 = new QueryEngine();
qe2.Query = q2;
Eqp2 = new ExecuteQueryParms(qe2, qt2);
mb2.PrepareQuery(Eqp2);
mb2.Sql += " where " + qc2.Criteria;
}
Eqp2.SearchKeySubset = eqp.SearchKeySubset;
}
return;
}