/// <summary>
/// Load any target map info
/// </summary>
void LoadTargetMap()
{
try
{
Tso = TargetSummaryOptions.GetFromMdbAssayOptionsColumn(Qt);
if (Tso == null || Lex.IsNullOrEmpty(Tso.TargetMapName))
{
return;
}
TargetMap = TargetMapDao.GetMapByLabel(Tso.TargetMapName); // get the basics
TargetMap = TargetMapDao.GetMapWithCoords(TargetMap.Name); // get the coords
return;
}
catch (Exception ex) { return; } // just return if "none" or no longer exists
}
/// <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>
/// Selected a new target map
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void TargetMap_SelectedIndexChanged(object sender, EventArgs e)
{
if (InSetup)
{
return;
}
string newTargetMap = TargetMap.Text;
if (Lex.Eq(newTargetMap, "Retrieve KEGG Pathway...")) // lookup KEGG pathway
{
if (Math.Abs(1) == 1) // 2/1/2013, best available now e.g. http://www.kegg.jp/kegg-bin/show_pathway?hsa04010
{
MessageBoxMx.ShowError(@"Automated access to pathway maps is now available through subsciption only.");
return;
}
SetTargetMapText(SelectedTargetMap); // keep current map for now
string pathwayId = InputBoxMx.Show(
"Enter the KEGG pathway id (e.g. hsa00010) for the desired pathway. " +
"Pathway identifiers can be looked up at: " +
"<a href=\"http://www.genome.jp/kegg/pathway.html\" target=\"_blank\">http://www.genome.jp/kegg/pathway.html</a>",
"KEGG Pathway Identifier");
if (String.IsNullOrEmpty(pathwayId))
{
return;
}
try
{
Progress.Show("Retrieving KEGG information for pathway: " + pathwayId, UmlautMobius.String, false);
TargetMap tm = TargetMapDao.GetKeggPathway(pathwayId);
Progress.Hide();
if (!MapLabelDict.ContainsKey(tm.Label.ToUpper()))
{
MapLabelDict[tm.Label.ToUpper()] = null;
MapLabelList.Add(tm.Label);
UserMapNames.Add(tm.Name);
}
TargetMap.Properties.Items.Clear();
TargetMap.Properties.Items.AddRange(MapLabelList); // update list
SelectedTargetMap = tm.Label;
SetTargetMapText(SelectedTargetMap); // make current selection
}
catch (Exception ex)
{
string msg = ex.Message;
Progress.Hide();
MessageBoxMx.ShowError("Pathway not found");
return;
}
return;
}
else if (newTargetMap.StartsWith("---")) // divider selected, ignore
{
SetTargetMapText(SelectedTargetMap);
}
SetTargetMapText(newTargetMap); // new map selected
}
/// <summary>
/// Initialize form with map info
/// </summary>
/// <param name="tso"></param>
void InitializeTargetMapControl(TargetSummaryOptions tso)
{
MapLabelList = new List <string>();
MapLabelDict = new Dictionary <string, object>();
UserMapNames = new List <string>(); // pathways specific to this user
TargetMapNamesAndLabels = TargetMapDao.GetTargetNamesAndLabels(); // get full list of maps
List <string> commonMapNames = TargetMapDao.GetCommonMapNames(); // get common maps
foreach (string mapName in commonMapNames)
{
if (!TargetMapNamesAndLabels.ContainsKey(mapName))
{
continue;
}
string mapLabel = TargetMapNamesAndLabels[mapName];
MapLabelList.Add(mapLabel);
MapLabelDict[mapLabel.ToUpper()] = null;
}
if (tso.UserMapNames.Length > 0) // get user-specific pathways
{
List <string> sa = Csv.SplitCsvString(tso.UserMapNames);
foreach (string mapName0 in sa)
{
if (!TargetMapNamesAndLabels.ContainsKey(mapName0))
{
continue;
}
string mapLabel = TargetMapNamesAndLabels[mapName0];
if (MapLabelDict.ContainsKey(mapLabel.ToUpper()))
{
continue; // don't add if already have
}
MapLabelList.Add(mapLabel);
MapLabelDict[mapLabel.ToUpper()] = null;
UserMapNames.Add(mapName0);
}
}
Lex.SortList(MapLabelList);
MapLabelList.Add("None");
MapLabelList.Add("---------------");
MapLabelList.Add("Retrieve KEGG Pathway..."); // allow addition of new pathway
TargetMap.Properties.Items.Clear();
TargetMap.Properties.Items.AddRange(MapLabelList);
if (Lex.IsNullOrEmpty(tso.TargetMapName))
{
tso.TargetMapName = "General Multi-platform Dendogram";
}
SelectedTargetMap = tso.TargetMapName;
if (String.IsNullOrEmpty(SelectedTargetMap))
{
SelectedTargetMap = MapLabelList[0];
}
if (TargetMapNamesAndLabels.ContainsKey(SelectedTargetMap))
{
SelectedTargetMap = TargetMapNamesAndLabels[SelectedTargetMap];
}
TargetMap.Text = SelectedTargetMap;
Initialized = true;
}
