/// <summary>
/// Initialize with associated command line control
/// </summary>
/// <param name="commandLineControl"></param>
public static QuickSearchPopup Initialize(
MRUEdit commandLineControl,
Form parentForm,
ContentsTreeControl contentstree)
{
QuickSearchPopup qsp = null;
AssertMx.IsNotNull(commandLineControl, "CommandLineControl");
AssertMx.IsNotNull(parentForm, "ParentForm");
foreach (Control c in parentForm.Controls) // see if already exists
{
if (c is QuickSearchPopup)
{
qsp = c as QuickSearchPopup;
break;
}
}
bool newPopup = false;
if (qsp == null) // need to create new popup in parent form
{
qsp = new QuickSearchPopup();
parentForm.Controls.Add(qsp);
newPopup = true;
}
qsp.Initialize2(commandLineControl, parentForm, contentstree, newPopup);
return(qsp);
}
/// <summary>
/// Ignore criteria because they are used as parameters for formatting Rgroup table
/// not as search criteria.
/// </summary>
/// <param name="mt"></param>
/// <returns></returns>
public override bool IgnoreCriteria(
MetaTable mt)
{
AssertMx.IsNotNull(SpecificBroker, "SpecificBroker");
return(SpecificBroker.IgnoreCriteria(mt));
}
/// <summary>
/// NextRow - Return the next matching row value object
/// </summary>
/// <returns></returns>
public override Object[] NextRow()
{
AssertMx.IsNotNull(SpecificBroker, "SpecificBroker");
Object[] row = SpecificBroker.NextRow();
return(row);
}
/// <summary>
/// Execute a chunk of JavaScript, wait for completion & return response
/// </summary>
/// <param name="script"></param>
public static object ExecuteScript(
KekuleJsWinFormsBrowserMsft KekuleJsBrowser,
string script)
{
//if (DebugMx.True) return new JavascriptResponse(); // disable - debug
Stopwatch sw = Stopwatch.StartNew();
if (KekuleJsBrowser?.Browser?.Document == null)
{
AssertMx.IsNotNull(KekuleJsBrowser?.Browser?.Document, "KekuleJsBrowser?.Browser?.Document");
}
WebBrowser browser = KekuleJsBrowser.Browser;
if (Debug)
{
DebugLog.Message("Script: " + script + KekuleJsBrowser.IdText);
}
object result = browser.Document.InvokeScript("execScript", new Object[] { script, "JavaScript" });
if (Debug)
{
DebugLog.StopwatchMessage("Script complete, Time: ", sw);
}
return(result);
}
internal void SetupColumnsTab()
{
QueryColumn qc = null;
ColumnMapMsx map = null;
AssertMx.IsNotNull(SVP, "ViewManager");
//AssertMx.IsNotNull(SVP.BaseQuery, "ViewQuery");
//ColumnsTabSourceQueryControl.Setup(SVM.SVP.DataMap);
// Id column
//IdColumnQc = CurrentMap.ColumnMapCollection.GetQueryColumnForSpotfireColumnName(V.IdColumnName);
//if (IdColumnQc == null)
//{
// IdColumnQc = SVP.BaseQuery.GetFirstMatchingQueryColumn(MetaColumnType.CompoundId, mustBeSelected: true);
//}
//IdColumnSelector.Setup(SVP, IdColumnQc, EditValueChanged);
// Focus Column
//FocusColumnQc = CurrentMap.ColumnMapCollection.GetQueryColumnForSpotfireColumnName(V.FocusColumnName);
//if (FocusColumnQc == null)
//{
// FocusColumnQc = SVP.BaseQuery.GetFirstMatchingQueryColumn(MetaColumnType.Structure, mustBeSelected: true);
//}
//FocusColumnSelector.Setup(SVP, FocusColumnQc, EditValueChanged);
// Horizontal & vertical chart setups
SetupCondFormatRulesFromColorCodingItems(HorizontalGradientBarChartControl, V.SelectedColumns, CondFormatStyle.ColorScale);
SetupCondFormatRulesFromColorCodingItems(VerticalBarChartControl, V.FeatureColumns, CondFormatStyle.ColorSet);
return;
}
/// <summary>
/// Do a quick validation on a node to be sure the key document links are defined
/// </summary>
public void ValidateNode()
{
AssertMx.IsNotNull(App, "App");
AssertMx.IsNotNull(App?.Document, "App.Document");
AssertMx.IsNotNull(App?.Document?.DataManager, "App.Document.DataManager");
AssertMx.IsNotNull(App?.Document?.DataManager?.TableCollection, "App.Document.TableCollection");
AssertMx.IsNotNull(App?.Document?.Pages, "App.Document.Pages");
}
/// <summary>
/// GetFormValues
/// </summary>
/// <param name="tso"></param>
/// <returns></returns>
public bool GetFormValues(
QueryColumn tso)
{
QueryColumn qc = QueryColumn;
AssertMx.IsNotNull(qc, "QueryColumn");
return(true);
}
/// <summary>
/// Setup the control for specified view
/// </summary>
/// <param name="view"></param>
public void Setup(
DataTableMapMsx dataTableMap,
EventHandler callerEditValueChangedEventHandler = null)
{
InSetup = true;
DataTableMap = dataTableMap;
CallerEditValueChangedHandler = callerEditValueChangedEventHandler;
QueryTablesComboBox.Text = "";
QueryTablesComboBox.SelectedItem = null;
ComboBoxItemCollection items = QueryTablesComboBox.Properties.Items;
items.Clear();
QueryTablesComboBox.Text = "";
AssertMx.IsNotNull(Query, "Query");
foreach (QueryTable qtEnum in Query.Tables)
{
items.Add(new ComboBoxItem(new LabeledUiItem(qtEnum.ActiveLabel, qtEnum)));
}
items.Add(AllTablesItem);
items.Add(NoTablesItem);
QueryTable qt = DataTableMap?.QueryTable;
if (dataTableMap.IsMappedToSingleQueryTable)
{
QueryTablesComboBox.Text = qt.ActiveLabel;
QueryTablesComboBox.SelectedItem = new LabeledUiItem(qt.ActiveLabel, qt);
}
else if (dataTableMap.IsMappedToAllQueryTables) // if cols are mapped assume all tables
{
QueryTablesComboBox.Text = AllTablesItem.Label;
QueryTablesComboBox.SelectedItem = AllTablesItem;
}
else // not mapped to any tables
{
QueryTablesComboBox.Text = NoTablesItem.Label;
QueryTablesComboBox.SelectedItem = NoTablesItem;
}
InSetup = false;
return;
}
/// <summary>
/// Build query to get summarization detail for RgroupMatrix data element
/// </summary>
/// <param name="mt"></param>
/// <param name="mc"></param>
/// <param name="resultId">act_code.compound_id</param>
/// <returns></returns>
public override Query GetDrilldownDetailQuery(
MetaTable mt,
MetaColumn mc,
int level,
string resultId)
{
AssertMx.IsNotNull(SpecificBroker, "SpecificBroker");
Query q = SpecificBroker.GetDrilldownDetailQuery(mt, mc, level, resultId);
return(q);
}
/// CopyCriteriaToKeyQueryCritera (Query.KeyCriteria has precedence over QC.Critera)
public void CopyCriteriaToQueryKeyCritera(
Query query)
{
AssertMx.IsNotNull(query, "Query");
string criteria = Criteria;
string colName = MetaColumnName + " "; // prepend metacolumn name if not done yet
if (Lex.StartsWith(criteria, colName)) // remove col name
{
criteria = criteria.Substring(colName.Length);
}
query.KeyCriteria = criteria;
query.KeyCriteriaDisplay = CriteriaDisplay;
return;
}
/// <summary>
/// Adding a new SasMap view to an existing query
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public DialogResult ShowInitialViewSetupDialog(
QueryColumn sasQc,
Query baseQuery)
{
MetaTable mt;
QueryColumn qc = null;
DialogResult dr;
AssertMx.IsNotNull(sasQc, "SasQc");
AssertMx.IsNotNull(SasQuery, "SasMapQuery");
SasQc = sasQc;
BaseQuery = baseQuery;
Parms = GetParmsFromQueryColumnCriteria(SasQc);
qc = BaseQuery?.GetFirstKeyColumn();
if (qc == null)
{
qc = QueryTable.GetDefaultRootQueryTable()?.KeyQueryColumn;
}
qc = qc.Clone();
Parms.KeyCriteriaQc = qc; // assign QC with undefined criteria
QueryManager refQm = (baseQuery.QueryManager as QueryManager);
List <string> resultsKeys = refQm?.DataTableManager?.ResultsKeys;
if (resultsKeys != null && resultsKeys.Count > 0)
{
string listText = Csv.JoinCsvString(resultsKeys);
qc.CriteriaDisplay = CidList.FormatAbbreviatedCidListForDisplay(qc, listText);
qc.Criteria = qc.MetaColumn.Name + " IN (" + listText + ")";
}
Parms.EndpointMc = BaseQuery?.GetFirstResultColumnByPriority(true)?.MetaColumn; // pick the highest priority result column as the default endpoint
dr = Edit();
if (dr == DialogResult.OK)
{
StoreParmsInQueryColumnCriteria(Parms, SasQc);
}
return(dr);
}
/// <summary>
/// CopyCriteriaFromKeyQueryCritera - Query.KeyCriteria has precedence over QC.Critera
/// </summary>
public void CopyCriteriaFromQueryKeyCriteria(
Query query)
{
AssertMx.IsNotNull(query, "Query");
Criteria = query.KeyCriteria;
CriteriaDisplay = query.KeyCriteriaDisplay;
if (Lex.IsUndefined(Criteria))
{
return; // undefined
}
string colName = MetaColumnName + " "; // prepend metacolumn name if not done yet
if (!Lex.StartsWith(Criteria, colName))
{
Criteria = colName + Criteria;
}
return;
}
/// <summary>
/// Invoke the editor
/// </summary>
/// <param name="qc">QueryColumn to edit</param>
/// <returns></returns>
public static bool Edit(
QueryColumn qc)
{
AssertMx.IsNotNull(qc, "qc");
if (Instance == null)
{
Instance = new CriteriaCompoundId();
}
new JupyterGuiConverter().ConvertFormOrUserControl(Instance);
if (qc.IsKey) // if key col be sure qc is in sync with Query.KeyCriteria
{
qc.CopyCriteriaFromQueryKeyCriteria();
}
if (qc.Criteria.Trim().StartsWith("=") && qc.MetaColumn != null)
{
qc.Criteria = qc.MetaColumnName + " " + qc.Criteria;
}
Instance.Qc = qc;
Instance.Setup(qc);
DialogResult dr = Instance.ShowDialog(SessionManager.ActiveForm);
if (dr == DialogResult.OK)
{
if (qc.IsKey) // if key col then update Query.KeyCriteria
{
qc.CopyCriteriaToQueryKeyCritera();
}
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Edit the Cids criteris
/// </summary>
/// <returns></returns>
bool EditCids()
{
QueryColumn qc = QueryColumn;
AssertMx.IsNotNull(qc, "QueryColumn");
if (!CriteriaEditor.GetCompoundIdCriteria(qc))
{
return(false);
}
if (Lex.IsDefined(qc.CriteriaDisplay))
{
Cids.Text = qc.CriteriaDisplay;
}
else
{
Cids.Text = qc.Criteria;
}
return(true);
}
/// <summary>
/// Search a single file
/// </summary>
void SearchSingleFile(int fi)
{
StructSearchMatch sm = null;
AssertMx.IsNotNull(FpDao, "FpDao");
List <StructSearchMatch> matchList = FileMatchLists[fi];
AssertMx.IsNotNull(matchList, "matchList");
OpenBitSet queryObs = new OpenBitSet(QueryFpLongArray, QueryFpLongArray.Length);
AssertMx.IsNotNull(queryObs, "queryObs");
OpenBitSet dbObs = new OpenBitSet(QueryFpLongArray, QueryFpLongArray.Length); // gets set to DB fp for intersect
AssertMx.IsNotNull(dbObs, "dbObs");
FileStream fs = FileStreamReaders[fi];
AssertMx.IsNotNull(fs, "fs");
ReadFingerprintRecArgs a = new ReadFingerprintRecArgs();
a.Initialize(fs, QueryFpLongArray.Length);
try
{
while (true)
{
bool readOk = FpDao.ReadRawFingerprintRec(a);
if (!readOk)
{
break;
}
//if (IsSrcCidMatch("03435269", a)) a = a; // debug
dbObs.Bits = a.fingerprint;
dbObs.Intersect(queryObs);
int commonCnt = (int)dbObs.Cardinality();
float simScore = commonCnt / (float)(a.cardinality + QueryFpCardinality - commonCnt);
if (simScore >= MinimumSimilarity)
{
sm = ReadFingerprintRec_To_StructSearchMatch(a);
sm.SearchType = StructureSearchType.MolSim;
sm.MatchScore = simScore;
matchList.Add(sm);
}
}
}
catch (Exception ex)
{
string msg = ex.Message;
msg += string.Format("\r\nfi: {0}, fs.Name: {1}, sm: {2}", fi, fs.Name, sm != null ? sm.Serialize() : "");
DebugLog.Message(DebugLog.FormatExceptionMessage(ex, msg));
throw new Exception(msg, ex);
}
return;
}
public static bool Edit(
QueryColumn qc)
{
AssertMx.IsNotNull(qc, "qc");
MetaColumn mc = qc.MetaColumn;
if (Instance == null)
{
Instance = new CriteriaYesNo();
}
new JupyterGuiConverter().ConvertFormOrUserControl(Instance);
Instance.Text = "Search criteria for " + qc.ActiveLabel;
Instance.Prompt.Text = "Select a search option for " + qc.ActiveLabel + " from the list below.";
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(qc.Criteria);
if (psc == null)
{
psc = new ParsedSingleCriteria(); // no criteria
}
if (Lex.Eq(psc.Value, "Y"))
{
Instance.YesCheckEdit.Checked = true;
}
else if (Lex.Eq(psc.Value, "N"))
{
Instance.NoCheckEdit.Checked = true;
}
else
{
Instance.None.Checked = true;
}
DialogResult dr = Instance.ShowDialog(SessionManager.ActiveForm);
if (dr == DialogResult.OK)
{
if (Instance.YesCheckEdit.Checked)
{
qc.CriteriaDisplay = "= Y";
qc.Criteria = mc.Name + " = 'Y'";
}
else if (Instance.NoCheckEdit.Checked)
{
qc.CriteriaDisplay = "= N";
qc.Criteria = mc.Name + " = 'N'";
}
else if (Instance.None.Checked)
{
qc.CriteriaDisplay = "";
qc.Criteria = "";
}
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Try to get the row at the given index from the buffer or cache
/// </summary>
/// <param name="ri"></param>
/// <returns></returns>
///
public object[] GetRow(
int ri)
{
object[] vo = null;
if (ri < 0 || ri >= TotalRowCount)
{
string msg = string.Format("Row {0} not in cache or buffer (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count);
throw new InvalidDataException(msg);
}
// See if in buffer
if (ri >= RowsWrittenToCache)
{
vo = (object[])RowBuffer[ri - RowsWrittenToCache];
if (DebugCaching)
{
DebugLog.Message(string.Format("Row: {0} in Buffer (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count));
}
return(vo);
}
// Get from cache
if (ri < CacheReaderPosition + 1) // if already read past this then close current cursor
{
CloseCacheReader();
}
if (CacheReader == null) // need to open reader?
{
AssertMx.IsNotNull(CacheWriter, "CacheWriter");
AssertMx.IsTrue(File.Exists(CacheFilePath), "CacheFilePath doesn't exist");
FileStream fs = File.Open(CacheFilePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
CacheReader = new BinaryReader(fs);
CacheReaderPosition = -1;
if (DebugCaching)
{
DebugLog.Message("Opening cache reader");
}
}
while (CacheReaderPosition + 1 <= ri) // read rows until we get the one we want
{
vo = VoArray.ReadBinaryVoArray(CacheReader, VoaLength);
CacheReaderPosition++;
}
CacheReaderPosition = ri;
if (DebugCaching)
{
DebugLog.Message(string.Format("Row: {0} in Cache (cacheSize: {1}, bufferSize: {2})", ri, RowsWrittenToCache, RowBuffer.Count));
}
return(vo);
}
/// <summary>
/// Read input data from database
/// </summary>
/// <param name="smp">
/// <returns></returns>
List<CompoundStructureActivityData> ReadData(
SasMapParms smp)
{
MetaColumn activityMc = smp.EndpointMc;
QueryColumn keyCriteriaQc = smp.KeyCriteriaQc;
AssertMx.IsNotNull(activityMc, "mc");
AssertMx.IsNotNull(keyCriteriaQc, "keyCriteriaQc");
MetaTable mt, mt2;
MetaColumn mc2 = null;
Query q = new Query();
mt = activityMc.MetaTable;
QueryTable qt = new QueryTable(mt);
if (mt.SummarizedExists && !mt.UseSummarizedData)
{ // retrieve summarized data if exists
mt2 = MetaTableCollection.Get(mt.Name + MetaTable.SummarySuffix);
if (mt2 != null)
{
mc2 = mt2.GetMetaColumnByName(activityMc.Name);
if (mc2 == null) mc2 = mt2.GetMetaColumnByLabel(activityMc.Label);
}
if (mc2 != null) // same column available in summarized?
{
mt = mt2;
activityMc = mc2;
}
}
SMP.KeyCriteriaQc.CopyCriteriaToQueryKeyCritera(q);
q.KeyCriteriaDisplay = SMP.KeyCriteriaQc.CriteriaDisplay;
qt.SelectKeyOnly();
QueryColumn qc = qt.GetQueryColumnByName(activityMc.Name);
qc.Selected = true;
q.AddQueryTable(qt);
QueryEngine qe = new QueryEngine();
List<string> keyList = qe.ExecuteQuery(q); // note that keylist may be empty if single-step query
HashSet<string> keySet = new HashSet<string>(StringComparer.OrdinalIgnoreCase);
List<CompoundStructureActivityData> data = new List<CompoundStructureActivityData>();
int rowCount = 0;
while (true)
{
object[] vo = qe.NextRow();
if (vo == null) break;
CompoundStructureActivityData cd = new CompoundStructureActivityData();
string cid = (string)vo[0];
cd.Cid = cid;
keySet.Add(cid); // accumulate keys
object val = vo[2];
if (NullValue.IsNull(val)) continue;
if (val is double)
cd.Activity = (double)val;
else if (val is Int32)
cd.Activity = (Int32)val;
else if (val is NumberMx)
{
NumberMx nex = val as NumberMx;
cd.Activity = nex.Value;
}
else if (val is QualifiedNumber)
{
QualifiedNumber qn = val as QualifiedNumber;
cd.Activity = qn.NumberValue;
//if (qn.Qualifier != null && qn.Qualifier != "" && qn.Qualifier != "=")
// continue; // (don't want to do this since may filter out good data (e.g. IC50 <0.0001))
}
else continue;
if (cd.Activity == NullValue.NullNumber) continue;
data.Add(cd);
rowCount++;
}
// Retrieve structures
keyList = new List<string>(keySet);
Dictionary<string, MoleculeMx> csDict = MoleculeUtil.SelectMoleculesForCidList(keyList, qt.MetaTable); // get the structures in a single step
// Add structures and build/store fingerprints to data
DebugLog.Message("========== Fingerprints ============");
foreach (CompoundStructureActivityData cd in data)
{
if (!csDict.ContainsKey(cd.Cid) || csDict[cd.Cid] == null) continue;
if (cd.Cid == "111" || cd.Cid == "222") csDict = csDict; // debug
MoleculeMx cs = csDict[cd.Cid];
cd.Structure = cs;
FingerprintType fpType = FingerprintType.Circular;
int fpSubtype = -1;
if (SMP.SimilarityType == SimilaritySearchType.ECFP4) // some issue with ECFP4?
{
fpType = FingerprintType.Circular;
fpSubtype = CircularFingerprintType.ECFP4;
}
else if (SMP.SimilarityType == SimilaritySearchType.Normal)
{
fpType = FingerprintType.MACCS;
}
cd.BitsetFingerprint = cs.BuildBitSetFingerprint(fpType, fpSubtype);
if (cd.BitsetFingerprint == null) continue; // couldn't build fingerprint (e.g. no structure)
if (Debug) DebugLog.Message(cd.Cid + ": " + Lex.Join(CdkMolUtil.GetBitSet(cd.BitsetFingerprint), ", "));
}
return data;
}
/// <summary>
/// Close broker & release resources
/// </summary>
public override void Close()
{
AssertMx.IsNotNull(SpecificBroker, "SpecificBroker");
SpecificBroker.Close();
}
