/// <summary> /// Get the list, returns array of AssayIDs /// </summary> /// <returns></returns> /// public IList GetUnpivotedAssayResultsDataSource() { StreamReader sr; bool changed; int i1; if (AssayId != null) { return(AssayId); } // Read cache parameters changed = ServerFile.GetIfChanged(ServerCacheDir + "CacheParms.txt", ClientCacheDir + "CacheParms.txt"); sr = new StreamReader(ClientCacheDir + "CacheParms.txt"); string txt = sr.ReadLine(); ResultsRowCount = int.Parse(txt); sr.Close(); // Init Vo position tables TarFieldPositionMap = UnpivotedAssayResultFieldPositionMap.NewOriginalMap(); // used for fast indexing of value by col name QueryTable qt = Query.GetQueryTableByName(MultiDbAssayDataNames.CombinedNonSumTableName); if (qt != null) { TarFieldPositionMap.InitializeFromQueryTableVoPositions(qt, 0); } // Read in list of assay Ids AssayId = ReadUShortArray("AssayId.bin"); // read in the list of assay ids for starters return(AssayId); }
/// <summary> /// Summarize unpivoted unsummarized assay data by target /// </summary> /// <param name="parms"></param> /// <param name="qm2"></param> /// <returns></returns> public QueryManager SummarizeByTargetUnpivoted( TargetSummaryOptions summaryOptions, QueryManager qm2) { // This method takes an unpivoted input query, summarizes it according to the summarization parameters // and then formats the summarized data according to the specified output format. // If a targetMap is specified then then coordinates are included in the output, the summarization // level must be target, and the output format must be unpivoted. QueryTable qt, qt2; DataRowMx dr, dr2; DataRowAttributes dra; string cid = "", currentCid; int rti, rfi; AssayDict tad = TargetAssayDict; // be sure target assay dict has been loaded TargetAssaySummarizationLevel sumLevel = TargetAssaySummarizationLevel.Target; // target level SummarizationType sumMethod = summaryOptions.UseMeans ? SummarizationType.BioResponseMean : SummarizationType.MostPotent; OutputDest outputDest = OutputDest.WinForms; TargetMap targetMap = TargetMapDao.GetMapWithCoords(summaryOptions.TargetMapName); qt = Query.GetQueryTableByName(MultiDbAssayDataNames.CombinedNonSumTableName); if (qt == null) { throw new Exception("Query table not found: " + MultiDbAssayDataNames.CombinedNonSumTableName); } UnpivotedAssayResultFieldPositionMap voMap = UnpivotedAssayResultFieldPositionMap.NewOriginalMap(); // used for fast indexing of value by col name voMap.InitializeFromQueryTableVoPositions(qt, 0); if (qm2 == null) // need to create query manager? { qm2 = new QueryManager(); qm2 = InitializeSubqueryQm(MultiDbAssayDataNames.CombinedNonSumTableName); } Query q2 = qm2.Query; qt2 = q2.GetQueryTableByNameWithException(MultiDbAssayDataNames.BaseTableName); UnpivotedAssayResultFieldPositionMap voMap2 = UnpivotedAssayResultFieldPositionMap.NewOriginalMap(); // used for fast indexing of value by col name voMap2.InitializeFromQueryTableVoPositions(qt2, 0); // Summarize rows & store in DataSet qm2.DataTable.Clear(); Dictionary <string, object> includedTargets = null; if (summaryOptions.TargetsWithActivesOnly) { // scan data & make a list of targets to be included includedTargets = new Dictionary <string, object>(); // ... } List <UnpivotedAssayResult> tars = new List <UnpivotedAssayResult>(); // build list of TA rows here currentCid = ""; for (int dri = 0; dri <= DataTableMx.Rows.Count; dri++) { if (dri < DataTableMx.Rows.Count) { dr = DataTableMx.Rows[dri]; cid = dr[KeyValueVoPos] as string; dra = GetRowAttributes(dr); if (dra != null && dra.Filtered) { continue; } if (currentCid == "") { currentCid = cid; } } else { dr = null; } if (dr == null || cid != currentCid) { // summarize rows for current cid & add to new datatable if (tars.Count > 0) // { List <UnpivotedAssayResult> sumTars = TargetAssayUtil.SummarizeData( tars, sumLevel, sumMethod, true, NullValue.NullNumber, NullValue.NullNumber, targetMap); int voLength2 = qm2.DataTable.Columns.Count; foreach (UnpivotedAssayResult sumTar in sumTars) { object[] vo2 = sumTar.ToValueObject(voLength2, voMap2); dr2 = qm2.DataTable.NewRow(); dr2.ItemArrayRef = vo2; // copy ref for efficiency since vo won't be changed qm2.DataTable.Rows.Add(dr2); } } if (dr == null) { break; } tars.Clear(); currentCid = cid; } UnpivotedAssayResult tar = UnpivotedAssayResult.FromValueObjectNew(dr.ItemArray, voMap); tars.Add(tar); // store in form for summarization } qm2.DataTableManager.InitializeRowAttributes(); return(qm2); }
/// <summary> /// Join an unpivoted target-summarized table to itself /// </summary> public QueryManager BuildTargetTargetData( QueryManager qm2) { QueryTable qt, qt2; DataRowMx dr, dr2; DataRowAttributes dra, dra2; string cid = "", cid2 = "", currentCid, ttKey; int rti, rfi; qt = Query.GetQueryTableByNameWithException(MultiDbAssayDataNames.BaseTableName); // source table UnpivotedAssayResultFieldPositionMap voMap = UnpivotedAssayResultFieldPositionMap.NewOriginalMap(); // used for fast indexing of value by col name voMap.InitializeFromQueryTableVoPositions(qt, 0); if (qm2 == null || Math.Abs(1) == 1) // need to create query manager? (needs fixup) { qm2 = new QueryManager(); qm2 = InitializeSubqueryQm(MultiDbAssayDataNames.TargetTargetUnpivotedTableName); } Query q2 = qm2.Query; qt2 = q2.GetQueryTableByNameWithException(MultiDbAssayDataNames.TargetTargetUnpivotedTableName); // Join rows & store in DataSet qm2.DataTable.Clear(); Dictionary <string, int> ttDict = new Dictionary <string, int>(); // maps target pair to row Dictionary <string, List <string> > cidTargetDict = new Dictionary <string, List <string> >(); for (int dri = 0; dri < DataTableMx.Rows.Count; dri++) { // get list of targets for each cid dr = DataTableMx.Rows[dri]; cid = dr[KeyValueVoPos] as string; dra = GetRowAttributes(dr); if (dra != null && dra.Filtered) { continue; } object[] vo = dr.ItemArrayRef; if (!cidTargetDict.ContainsKey(cid)) { cidTargetDict[cid] = new List <string>(); } string target = AssayAttributes.GetStringVo(vo, voMap.TargetSymbol.Voi); cidTargetDict[cid].Add(target); } foreach (string cid0 in cidTargetDict.Keys) { // sum count for pair of targets List <string> targets = cidTargetDict[cid0]; for (int t1i = 0; t1i < targets.Count; t1i++) { string t1 = targets[t1i]; for (int t2i = t1i; t2i < targets.Count; t2i++) { string t2 = targets[t2i]; if (Lex.Lt(t1, t2)) { ttKey = t1 + '\t' + t2; } else { ttKey = t2 + '\t' + t1; } if (!ttDict.ContainsKey(ttKey)) { ttDict[ttKey] = 0; } ttDict[ttKey]++; } } } foreach (string ttkey0 in ttDict.Keys) { // build data rows string[] t1t2 = ttkey0.Split('\t'); string t1 = t1t2[0]; string t2 = t1t2[1]; int cpdCount = ttDict[ttkey0]; AddRow(qm2.DataTable, t1, t2, cpdCount); if (t2 != t1) { AddRow(qm2.DataTable, t2, t1, cpdCount); } } qm2.DataTableManager.InitializeRowAttributes(); return(qm2); }