/// <summary>
/// Set vo with specified QueryColumn name
/// </summary>
/// <param name="qt"></param>
/// <param name="colName"></param>
/// <param name="vo"></param>
/// <param name="voi"></param>
/// <param name="value"></param>
/// <param name="withException"></param>
public static void SetVo(
QueryTable qt,
string colName,
object[] vo,
object value)
{
bool withException = false; // always false for now
QueryColumn qc;
if (withException)
{
qc = qt.GetQueryColumnByNameWithException(colName);
}
else
{
qc = qt.GetQueryColumnByName(colName);
if (qc == null)
{
return;
}
}
int voPos = qc.VoPosition;
SetVo(vo, voPos, value);
return;
}
/// <summary>
/// Set QueryTable criteria values from TargetSummaryOptions
/// </summary>
/// <param name="TargetSumTable"></param>
public bool SetInQueryTable(
QueryTable targetSumTable)
{
QueryTable qt = targetSumTable;
if (qt == null)
{
return(false);
}
Query q = qt.Query;
QueryColumn qc = qt.GetQueryColumnByNameWithException(MultiDbAssayDataNames.MultiDbViewOptions);
if (qc == null)
{
return(false);
}
string tsoString = Serialize();
qc.Criteria = qc.MetaColumn.Name + " = " + Lex.AddSingleQuotes(tsoString);
qc.CriteriaDisplay = "Edit...";
qt.KeyQueryColumn.Criteria = CidCriteria; // keep in variable criteria form
SetListCriteriaForCol(qt, MultiDbAssayDataNames.GeneSymbol, TargetList);
SetListCriteriaForCol(qt, MultiDbAssayDataNames.GeneFamily, GeneFamilies);
return(true);
}
/// <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>
/// Initialize the chart
/// </summary>
DialogResult InitializeChart()
{
Qm1 = View.Qm; // assume chart initially pointing to root query manager
DialogResult dr = Qm1.DataTableManager.CompleteRetrieval();
if (dr == DialogResult.Cancel)
{
return(dr);
}
Qm2 = null; // nothing for new query yet
SummarizeDataUsingFormParameters(); // get initial summarized results & setup Qm2
View.BaseQuery = Qm2.Query; // link chart to new query & manager
QueryTable qt = Qm2.Query.Tables[0];
// Setup for unpivoted results
if (Qm2.DataTableManager.UnpivotedResults)
{
QueryColumn cidQc = qt.GetQueryColumnByNameWithException("CORP_ID");
View.YAxisMx.QueryColumn = cidQc;
QueryColumn assyNameQc = qt.GetQueryColumnByNameWithException("ASSY_NM");
View.XAxisMx.QueryColumn = assyNameQc;
View.XAxisMx.LabelAngle = -90; // vertical
QueryColumn rsltQc = qt.GetQueryColumnByNameWithException("RSLT_VAL");
View.MarkerColor.QueryColumn = rsltQc;
View.MarkerColor.FieldValueContainsColor = true;
View.UseExistingCondFormatting = true;
View.PivotedData = false;
}
// Setup for pivoted results
else
{
throw new NotImplementedException(); // todo
}
View.ConfigureRenderingControl(); // render
return(DialogResult.OK);
}
/// <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>
/// 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>
/// Create a new pivoted DataTable in the specified format from the existing unpivoted DataTable
/// </summary>
/// <param name="rows"></param>
/// <param name="pivotType"></param>
/// <param name="qt"></param>
/// <param name="newQuery"></param>
/// <param name="ResultKeys"></param>
void CreatePivotedTable(
DataSet rows,
TargetAssayPivotFormat pivotType,
QueryTable qt,
Query newQuery,
List <string> ResultKeys)
{
#if false
UnpivotedAssayResult rr;
QueryColumn qc, qc2;
MetaColumn mc, mc2;
string pivotValue;
int row, pivotPos, pos, colsPerPivotValue, qci, mci, pi, ri;
bool pivotByTarget = false, pivotByFamily = false, orderByFamily = false;
if (pivotType == TargetAssayPivotFormat.
{
pivotByTarget = true;
orderByFamily = // if gene family selected then order by it first before target
qt.GetQueryColumnByNameWithException("gene_fmly").Selected;
}
/// <summary>
/// Tools menu item click
/// Create a standalone SasMap analysis based on the current query and then run it
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public string Run(
string args)
{
QueryTable qt;
MetaTable mt;
QueryColumn qc;
int qid = SS.I.ServicesIniFile.ReadInt("SasMapToolModelQuery", 888070);
if (qid < 0)
{
throw new Exception("SasMapToolModelQuery not defined");
}
Query q = QbUtil.ReadQuery(qid);
if (q == null)
{
throw new Exception("Failed to read SasMapToolModelQuery: " + qid);
}
q.UserObject = new UserObject(UserObjectType.Query); // treat this as a new query
QueryTable sasQt = q.GetQueryTableByNameWithException(SasMapParms.MetaTableName);
SasQc = sasQt.GetQueryColumnByNameWithException(SasMapParms.ParametersMetaColumnName);
BaseQuery = GetBaseQuery();
if (BaseQuery == null || BaseQuery.Tables.Count == 0)
{
MessageBoxMx.ShowError("The current query must contain one or more data tables before a SasMap can be defined on the query");
return("");
}
Parms = LastParms;
qc = BaseQuery?.GetFirstKeyColumn();
qc = qc.Clone();
qc.CopyCriteriaFromQueryKeyCriteria(BaseQuery);
Parms.KeyCriteriaQc = qc;
Parms.EndpointMc = BaseQuery?.GetFirstResultColumnByPriority(true)?.MetaColumn; // pick the highest priority result column as the default endpoint
QbUtil.SetMode(QueryMode.Build); // be sure in build mode
DialogResult dr = Edit();
if (dr != DialogResult.OK)
{
return("");
}
StoreParmsInQueryColumnCriteria(Parms, SasQc);
// Add as a new query and run it
AnalysisCount++;
q.Name = "Structure-Activity Similarity Analysis " + AnalysisCount;
q.SingleStepExecution = true;
// Add the query to the QueryBuilder and run it
DelayedCallback.Schedule( // add and run the query after exiting this dialog
delegate(object state)
{
QbUtil.AddQuery(q);
QbUtil.SetCurrentQueryInstance(q); // set to new query
QbUtil.RenderQuery();
QueryExec.RunQuery(q, SS.I.DefaultQueryDest);
});
Progress.Hide();
return("");
}
/// <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>
/// Transform basic query to select all data for a compound number
/// </summary>
/// <param name="keyMt">Key metatable. If null then try to determine from key value</param>
/// <param name="cn"></param>
/// <returns></returns>
public static Query TransformSelectAllDataQuery(
Query originalQuery,
QueryTable qt0,
Query newQuery)
{
Query q2 = null;
MetaTable mt;
MetaColumn mc;
QueryTable qt;
QueryColumn qc;
MetaTreeNode mtn, tn;
qc = qt0.GetQueryColumnByNameWithException("root_table");
ParsedSingleCriteria psc = MqlUtil.ParseQueryColumnCriteria(qc);
if (psc == null || Lex.IsUndefined(psc.Value))
{
throw new UserQueryException("Root table not defined");
}
string keyMtName = psc.Value;
psc = MqlUtil.ParseSingleCriteria("cid " + originalQuery.KeyCriteria);
if (psc == null || Lex.IsUndefined(psc.Value))
{
throw new UserQueryException("Compound Id not defined");
}
string cn = psc.Value;
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");
}
string allTableName = keyMt.Name + "_AllData"; // see if specific all-data tree node
mtn = MetaTree.GetNode(allTableName);
if (mtn == null) // no special "_AllData" node, lookup in menu
{
foreach (MetaTreeNode parent in MetaTree.Nodes.Values)
{
foreach (MetaTreeNode child in parent.Nodes)
{
if (Lex.Eq(child.Target, keyMt.Name))
{
mtn = parent;
break;
}
}
}
IUserObjectTree iuot = InterfaceRefs.IUserObjectTree;
if (mtn == null && keyMt.IsUserDatabaseStructureTable && iuot != null) // see if user structure table & db
{
int userObjId = UserObject.ParseObjectIdFromInternalName(keyMt.Name);
string nodeItemId = "ANNOTATION_" + userObjId;
MetaTreeNode childMtn = iuot.GetUserObjectNodeBytarget(nodeItemId);
if (childMtn != null && childMtn.Parent.Type == MetaTreeNodeType.Database)
{
mtn = childMtn.Parent;
}
}
}
if (mtn == null)
{
return(null);
}
Query q = newQuery;
for (int i1 = 0; i1 < mtn.Nodes.Count; i1++)
{
tn = (MetaTreeNode)mtn.Nodes[i1];
if (!tn.IsDataTableType)
{
continue;
}
mt = MetaTableCollection.Get(tn.Target);
if (mt == null)
{
continue;
}
if (mt.Root.Name != keyMt.Name)
{
continue; // must have same root
}
if (mt.MultiPivot && !mt.UseSummarizedData && mt.SummarizedExists)
{
MetaTable mt2 = MetaTableCollection.Get(mt.Name + MetaTable.SummarySuffix);
if (mt2 != null)
{
mt = mt2;
}
}
//if (mt.RemapForRetrieval && mt.SummarizedExists) mt.UseSummarizedData = true; // get summarized multipivot data (not good, permanently changes the metatable)
qt = new QueryTable(mt);
// if (Lex.Eq(mt.Name, "all_star_pivoted") || Lex.Eq(mt.Name, "all_annotation_pivoted")) mt = mt // debug;
if (qt.SelectedCount > 0) // be sure something is selected
{
q.AddQueryTable(qt);
}
}
// See if a model query exists & use it or append to what we have already
string fileName = ServicesDirs.ModelQueriesDir + @"\" + allTableName + ".qry";
if (!ServerFile.GetLastWriteTime(fileName).Equals(DateTime.MinValue)) // model query file exist?
{
try
{
string query2String = FileUtil.ReadFile(fileName);
q2 = Query.Deserialize(query2String);
q.MergeSubqueries(q2); // just use subquery
}
catch (Exception ex) { ex = ex; }
}
q.SetupQueryPagesAndViews(ResultsViewType.HtmlTable); // be sure we have a default page & HTML view
// Set key criteria
q.KeyCriteria = " = " + cn;
// Review tables (debug)
//int tCnt = q.Tables.Count;
//string tls = q.TableListString;
//q.Tables.RemoveRange(23, 1);
//q.Tables.RemoveRange(27, q.Tables.Count - 27);
//q.Tables.RemoveRange(1, 25);
// Get list of any inaccessible tables & remove from query
q.InaccessableData = CheckDataSourceAccessibility(q);
if (q.InaccessableData != null)
{
foreach (string schema in q.InaccessableData.Keys)
{
foreach (string tName in q.InaccessableData[schema])
{
qt = q.GetQueryTableByName(tName);
if (qt != null && !qt.MetaTable.IsRootTable && q.Tables.Contains(qt))
{
q.RemoveQueryTable(qt);
}
}
}
//ShowUnavailableDataMessage(q);
q.InaccessableData = null;
}
UsageDao.LogEvent("QueryAllData", "");
//string mql = MqlUtil.ConvertQueryToMql(q); // debug
return(q);
}
/// <summary>
/// Handle a click on a link to a 3D structure & open in Vida
/// If clicked from an XtraGrid give the user a range of options for the data
/// to be exported. If clicked from a HTML page give limited options.
/// </summary>
/// <param name="mtName"></param>
/// <param name="mcName"></param>
/// <param name="url"></param>
public void ClickFunction(
string mtName,
string mcName,
string url)
{
ResultsFormatter fmtr = null;
ResultsField rfld = null;
//DataRowMx dr;
StringMx sx;
StreamWriter sw;
int markedCount = 0;
string densityMapUrl = null;
string target = null;
_currentMetaTable = mtName;
_currentPdbColumnName = mcName;
IncludeElectronDensityPyMol.Checked = false;
MetaTable mt = MetaTableCollection.Get(mtName);
if (mt == null)
{
return;
}
MetaColumn mc = mt.GetMetaColumnByName(mcName);
if (mc == null)
{
return;
}
_xRay2Request = Lex.Contains(mtName, "XRay2"); // newer XRay2 database table?
_urlFileName = Path.GetFileName(url); // extract file name from url
QueryManager qm = ClickFunctions.CurrentClickQueryManager;
if (qm != null)
{
Query q = qm.Query;
ResultsFormat rf = qm.ResultsFormat;
fmtr = qm.ResultsFormatter;
rfld = rf.GetResultsField(mc);
if (rfld == null)
{
return;
}
QueryTable qt = q.GetQueryTableByNameWithException(mtName);
_qcProtein = qt.GetQueryColumnByNameWithException(mcName);
if (_xRay2Request) // newer XRay2 database
{
string mapUrl = "";
if (mcName == "ALIGNED_SPLIT_COMPLEX_URL")
{
mapUrl = "ALIGNED_SPLIT_MAP_URL";
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL")
{
mapUrl = "ALIGNED_FULL_MAP_URL";
}
else if (mcName == "ORIGINAL_PDB_URL")
{
mapUrl = "ORIGINAL_MAP_URL";
} //{ mapUrl = "ORIGINAL_MAP_URL"; }
_qcDensity = qt.GetQueryColumnByName(mapUrl); //("ALIGNED_SPLIT_MAP_URL");
if (_qcDensity != null && !_qcDensity.Selected)
{
_qcDensity = null;
}
_qcTarget = qt.GetQueryColumnByName("primary_gene_name_alias");
if (_qcTarget != null && !_qcTarget.Selected)
{
_qcTarget = null;
}
}
if (_qcDensity != null)
{
// if there is a density map url located in the density column, enable the PyMol CheckEdit
DataRowMx dr = qm.DataTable.Rows[qm.MoleculeGrid.LastMouseDownCellInfo.DataRowIndex];
densityMapUrl = Lex.ToString(dr[_qcDensity.VoPosition]);
}
else
{
// user did not select the map column, try to retrieve the XRay1 or Xray2 density map url fromt he metatable
densityMapUrl = _xRay2Request ? GetXray2DensityMapUrl(url, qt.MetaTable.Name, mcName) : GetXray1DensityMapUrl(url, qt.MetaTable.Name);
}
// default checkbox to false so user does not load electron density maps everytime, since these take
// extra time to load.
IncludeElectronDensityPyMol.Checked = false;
IncludeElectronDensityPyMol.Enabled = !string.IsNullOrEmpty(densityMapUrl);
if (_qcProtein == null && _qcDensity == null)
{
throw new Exception("Neither the PDB nor the MAP column is selected in the query");
}
markedCount = fmtr.MarkedRowCount;
int unmarkedCount = fmtr.UnmarkedRowCount;
if (markedCount == 0 || unmarkedCount == 0) // if no specific selection assume user wants single structure
{
ExportSingle.Checked = true;
FileName.Text = _urlFileName;
}
else
{
ExportMarked.Checked = true; // assume wants marked structures
}
ExportMarked.Enabled = true;
}
else // simple setup for click from HTML display
{
ExportSingle.Checked = true;
ExportMarked.Enabled = false;
FileName.Text = _urlFileName;
densityMapUrl = GetXray2DensityMapUrl(url, _currentMetaTable, mcName);
target = GetTarget(url, _currentMetaTable, mcName);
////IncludeProtein.Enabled = IncludeElectronDensityEnabled = false;
////if (Lex.Eq(mcName, "bsl_xray_cmplx_url"))
//// IncludeProtein.Checked = true;
////else if (Lex.Eq(mcName, "bsl_xray_edensity_url"))
//// IncludeElectronDensityChecked = true;
}
if (mcName == "ALIGNED_SPLIT_MAP_URL" || mcName == "ALIGNED_FULL_MAP_URL" || mcName == "ORIGINAL_MAP_URL") // not viewable fileds
{
DisablePymol();
DisableMoe();
ExportToFile.Enabled = ExportToFile.Checked = true;
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL" || mcName == "ORIGINAL_PDB_URL" || mcName == "ALIGNED_SPLIT_COMPLEX_URL") // viewable by PyMol
{
EnableMoe();
EnablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
else //everything else should be viewable by MOE
{
EnableMoe();
DisablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
DialogResult dlgRslt = ShowDialog(SessionManager.ActiveForm);
if (dlgRslt == DialogResult.Cancel)
{
return;
}
bool exportSingle = ExportSingle.Checked;
bool exportMarked = !exportSingle;
if (!IncludeElectronDensityPyMol.Checked)
{
densityMapUrl = null;
}
if (exportMarked) // see if reasonable count if exporting marked rows
{
string msg;
if (markedCount == 0)
{
msg = "No rows have been marked for export";
MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
if (markedCount > 10)
{
msg =
markedCount + " structures have been selected out export.\n" +
"Are you sure these are the structures you want to export?";
dlgRslt = MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dlgRslt != DialogResult.Yes)
{
return;
}
}
}
// Export to PyMol (Schrodinger) - Collab with Paul Sprengeler and Ken Schwinn
// Relavant Files:
// 1. Plugin: CorpView.py (in Mobius config dir)
// 2. Script: CorpView.pml - Runs the plugin and then passes in the .csv file (in Mobius config dir)
// Expected content (note: <csv-file-name> gets replaced):
// import pymol
// pluginLocation = 'C:\Progra~1\PyMOL\PyMOL\modules\pmg_tk\startup\CorpView.py'
// cmd.do('run ' + pluginLocation)
// cmd.do('lv_create_environment')
// cmd.do('lv_import_mobius <csv-file-name>')
// cmd.do('lv_destroy_environment')
// 3. Csv file: PyMolBatchLoad.csv - Csv file in format expected by plugin (in Mobius temp dir)
if (ExportToPyMol.Checked)
{
ExportToPyMolMethod(url, densityMapUrl, target, qm);
}
else if (ExportToMOE.Checked) // Export to MOE
{
ExportToMOEMethod(url, qm, fmtr, rfld);
}
else
{
ExportToFilesMethod(url, qm, fmtr, rfld);
}
}
/// <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;
}
