protected void OnRankSplitProcess(object sender, EventArgs e)
{
try{
ParameterizedThreadStart prams = new ParameterizedThreadStart(RankSplit.ProcessRequest);
Thread o = new Thread(prams);
RankSplitInfo rsi = GatherRankSplitInfo(true);
o.Start((object)rsi);
}
catch (Exception ex)
{
MainData.ShowMessageWindow(ex.Message, false);
}
}
protected void OnRankSplitSaveGo(object sender, EventArgs e)
{
try{
ParameterizedThreadStart prams = new ParameterizedThreadStart(RankSplit.ProcessRequest);
Thread o = new Thread(prams);
RankSplitInfo rsi = GatherRankSplitInfo(false);
if (RankSplit.PickFileName(out RankSplit.LastFileName))
{
o.Start((object)rsi);
}
}
catch (Exception ex)
{
MainData.ShowMessageWindow(ex.Message, false);
}
}
private static Dictionary <string, List <T> > ProcessRSplitContainer <T>(RSplitContainer <T> rspc, RankSplitInfo rsi,
Dictionary <string, double> rDict, Dictionary <string, T> outDict, bool seqMatch)
{
if (rsi.doSubSet && rsi.SubSetType == SubSetMethod.Previous)
{
rspc.AddIDFilterList(rsi.oldIDlist);
}
rspc.MergeDictosToList(rDict, outDict, false, seqMatch);
if (rsi.doSubSet && rsi.SubSetType == SubSetMethod.Current)
{
return(rspc.GetDivisionDict(rsi.SplitCount, rsi.subCurMainRank, rsi.subCurSplitCount));
}
else
{
return(rspc.GetDivisionDict(rsi.SplitCount));
}
}
public static void ProcessRequest(object TheInfo)
{
try
{
RankSplitInfo info = TheInfo as RankSplitInfo;
string fName = LastFileName;
bool keepGoing = true;
bool seqMatch = false;
RankMethodSubSequence = info.SeqDiv;
OutputMethodSubSequence = info.SeqDivOut;
if (RankMethodSubSequence == SubSequenceDivision.Normalised)
{
RankStartDiv = info.divStart;
RankEndDiv = info.divEnd;
}
if (OutputMethodSubSequence == SubSequenceDivision.Normalised)
{
OutputStartDiv = info.divStartOut;
OutputEndDiv = info.divEndOut;
}
if (RankMethodSubSequence == SubSequenceDivision.AbsoluteBases)
{
RankBaseCount = info.baseCount;
RankFromStart = info.fromStart;
}
if (OutputMethodSubSequence == SubSequenceDivision.AbsoluteBases)
{
OutputFromStart = info.fromStartOut;
OutputBaseCount = info.baseCountOut;
}
if (info.GraphingType == GraphType.Image && OutputMethodSubSequence != SubSequenceDivision.AbsoluteBases)
{
OutputMethodSubSequence = SubSequenceDivision.AbsoluteBases;
OutputFromStart = !AppSettings.Output.DEFAULT_IMG_FROMEND.Item;
OutputBaseCount = AppSettings.Output.DEFAULT_IMG_BASES.Item;
}
if (info.sample != "All")
{
SampleToUse = info.sample;
UseSample = true;
}
else
{
UseSample = false;
}
if (info.SeqFeature == info.SeqFeature2)
{
seqMatch = true;
}
else
{
seqMatch = false;
}
if (keepGoing)
{
RSplitContainer <string> rspcString = new RSplitContainer <string> ("none", false);
RSplitContainer <double> rspcDouble = new RSplitContainer <double> (0, false);
RSplitContainer <List <double> > rspcListDouble = new RSplitContainer <List <double> > (null, true);
Dictionary <string, double> rankDict = Methods [info.RMethod].Invoke(info.SeqFeature);
Dictionary <string, string> baseDict;
Dictionary <string, double> singleDict;
Dictionary <string, List <double> > listDict;
if (info.doGraph == false)
{
switch (info.Text)
{
case OutputMethText.BlastID:
baseDict = MainData.Genome.RSPOUTBlastHitID(info.SeqFeature);
rspcString.MergeDictosToList(rankDict, baseDict, true, seqMatch);
ProcessingClass.WriteDataFile(fName, rspcString.GetData(false));
break;
case OutputMethText.BaseSeq:
baseDict = MainData.Genome.RSPOUTBaseSeq(info.SeqFeature);
rspcString.MergeDictosToList(rankDict, baseDict, false, seqMatch);
ProcessingClass.WriteDataFile(fName, rspcString.GetData(false));
break;
case OutputMethText.FastaBase:
baseDict = MainData.Genome.RSPOUTBaseSeq(info.SeqFeature);
rspcString.MergeDictosToList(rankDict, baseDict, false, seqMatch);
rspcString.WriteFastaFile(fName);
break;
case OutputMethText.SeqNames:
baseDict = MainData.Genome.RSPOUTReadName(info.SeqFeature);
rspcString.MergeDictosToList(rankDict, baseDict, false, seqMatch);
ProcessingClass.WriteDataFile(fName, rspcString.GetData(false));
break;
default:
break;
}
}
else
{
string yLab; string xLab;
SetLabels(info.Graph, info.GraphingType, out xLab, out yLab);
string title = info.SeqFeature + " ";
if (info.doSubSeq)
{
title += "from ";
if (info.SeqDiv == SubSequenceDivision.AbsoluteBases)
{
title += info.baseCount + " ";
if (info.fromStart)
{
title += "from start ";
}
else
{
title += "to end ";
}
}
else
{
title += "division " + info.divStart + "/20 to " + info.divEnd + "/20 ";
}
}
title += "ranked by " + MethodDesc [info.RMethod] + " and split into " + info.SplitCount + " groups";
Dictionary <string, List <double> > procCont;
Dictionary <string, List <List <double> > > procContList;
switch (info.Graph)
{
case OutputMethGraph.Expr:
singleDict = MainData.Genome.RSPOUTExprValue(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
if (info.GraphingType == GraphType.Histo)
{
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else
{
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
break;
case OutputMethGraph.ExprNorm:
singleDict = MainData.Genome.RSPOUTExprNorm(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
if (info.GraphingType == GraphType.Histo)
{
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else
{
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
break;
case OutputMethGraph.ExprVar:
singleDict = MainData.Genome.RSPOUTExprRange(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
if (info.GraphingType == GraphType.Histo)
{
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else
{
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
break;
case OutputMethGraph.MethyCov:
if (info.GraphingType == GraphType.Spatial)
{
listDict = MainData.Genome.RSPOUTMethylCoverageDivision(info.SeqFeature2);
procContList = ProcessRSplitContainer <List <double> > (rspcListDouble, info, rankDict, listDict, seqMatch);
if (info.SeqDivOut != SubSequenceDivision.AbsoluteBases)
{
MainData.MakeMultiBayesRankGraph(procContList, GraphWindow.Global, xLab, yLab, title, rspcListDouble, info.MergeGraphs);
}
else
{
MainData.MakeMultiBayesBaseRankGraph(procContList, GraphWindow.Global, xLab, yLab, title, info.fromStartOut, rspcListDouble, info.MergeGraphs);
}
}
else if (info.GraphingType == GraphType.Means)
{
singleDict = MainData.Genome.RSPOUTQuantMethyCov(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else if (info.GraphingType == GraphType.Image)
{
//TODO: Make the image!
}
break;
case OutputMethGraph.MethyDepthCov:
if (info.GraphingType == GraphType.Spatial)
{
listDict = MainData.Genome.RSPOUTMethylCoverageDepthDivision(info.SeqFeature2);
procContList = ProcessRSplitContainer <List <double> > (rspcListDouble, info, rankDict, listDict, seqMatch);
if (info.SeqDivOut != SubSequenceDivision.AbsoluteBases)
{
MainData.MakeMultiBayesRankGraph(procContList, GraphWindow.Global, xLab, yLab, title, rspcListDouble, info.MergeGraphs);
}
else
{
MainData.MakeMultiBayesBaseRankGraph(procContList, GraphWindow.Global, xLab, yLab, title, info.fromStartOut, rspcListDouble, info.MergeGraphs);
}
}
else if (info.GraphingType == GraphType.Means)
{
singleDict = MainData.Genome.RSPOUTQuantMethyDepthCov(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else if (info.GraphingType == GraphType.Histo)
{
singleDict = MainData.Genome.RSPOUTMethylDepthTotal(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else if (info.GraphingType == GraphType.Image)
{
listDict = MainData.Genome.RSPOUTMethylCoverageDepthDivision(info.SeqFeature2);
procContList = ProcessRSplitContainer <List <double> > (rspcListDouble, info, rankDict, listDict, seqMatch);
MainData.MakeRegionChangeMap(procContList, rspcListDouble, info.MergeGraphs);
}
break;
case OutputMethGraph.BlastE:
singleDict = MainData.Genome.RSPBlastEValue(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
if (info.GraphingType == GraphType.Means)
{
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else
{
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
break;
case OutputMethGraph.BlastID:
singleDict = MainData.Genome.RSPBlastPercID(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
if (info.GraphingType == GraphType.Means)
{
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else
{
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
break;
case OutputMethGraph.Variant:
singleDict = MainData.Genome.RSPOUTQuantVar(info.SeqFeature2);
procCont = ProcessRSplitContainer <double> (rspcDouble, info, rankDict, singleDict, seqMatch);
if (info.GraphingType == GraphType.Means)
{
MainData.MakeRankLineGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
else
{
MainData.MakeMultiHistoRankGraph(procCont, GraphWindow.Global, xLab, yLab, title, rspcDouble, info.MergeGraphs);
}
break;
default:
break;
}
}
}
}
catch (Exception e)
{
MainData.ShowMessageWindow(e.Message, true);
}
}
protected RankSplitInfo GatherRankSplitInfo(bool isGraph)
{
RankMethod m;
OutputMethGraph omg;
OutputMethText omt;
GraphType gt;
string feature;
string feature2;
try{
m = RankSplitMethods [rspMethodCombo.ActiveText];
omg = OutputMethGraph.Expr;
omt = OutputMethText.BaseSeq;
gt = RankSplitGraphDesc[rspGraphTypeCombo.ActiveText];
if (isGraph)
{
omg = RankSplitGraphOut [rspGraphicalOutputCombo.ActiveText];
}
else
{
omt = RankSplitTextOut [rspTextOutputCombo.ActiveText];
}
}
catch (Exception e) {
throw new Exception("You need to select an option from the combo menu!");
}
feature = rspSequenceCombo.ActiveText;
feature2 = rspSequenceForCombo.ActiveText;
bool seqFeaturePass = false;
bool seqFeature2Pass = false;
foreach (string st in RankSplit.GetRelevantFeatures())
{
if (st == feature)
{
seqFeaturePass = true;
}
if (st == feature2)
{
seqFeature2Pass = true;
}
}
if (!seqFeaturePass || !seqFeature2Pass)
{
throw new Exception("You need to choose two features to look at\n they can be the same!");
}
RankSplitInfo rsi;
if (!rspSubDivideCheck.Active)
{
if (isGraph)
{
rsi = new RankSplitInfo(m, omg, feature);
}
else
{
rsi = new RankSplitInfo(m, omt, feature);
}
}
else
{
if (rspBaseCountRadio.Active)
{
int bases;
if (!int.TryParse(rspNoBaseEntry.Text, out bases))
{
throw new Exception("Input -> Unable To Parse Base Count!");
}
if (bases > 5000)
{
throw new Exception("Input -> Maximum Number of bases is 5000!");
}
bool doStart = true;
if (rspToEndRadio.Active)
{
doStart = false;
}
if (isGraph)
{
rsi = new RankSplitInfo(m, omg, feature, bases, doStart);
}
else
{
rsi = new RankSplitInfo(m, omt, feature, bases, doStart);
}
}
else
{
int stDiv; int edDiv;
if (!int.TryParse(rspStartDivEntry.Text, out stDiv))
{
throw new Exception("Input -> Unable to Parse Start Division!");
}
if (!int.TryParse(rspEndDivEntry.Text, out edDiv))
{
throw new Exception("Input -> Unable to Parse End Division!");
}
if (stDiv >= edDiv)
{
throw new Exception("Input -> Start division must be smaller than end!");
}
if (stDiv > 20 || edDiv > 20)
{
throw new Exception("Input -> Division limit is 20.");
}
if (isGraph)
{
rsi = new RankSplitInfo(m, omg, feature, stDiv, edDiv);
}
else
{
rsi = new RankSplitInfo(m, omt, feature, stDiv, edDiv);
}
}
}
rsi.SeqFeature2 = feature2;
rsi.GraphingType = gt;
if (rspSubDivideCheck2.Active)
{
rsi.doSubSeqOut = true;
if (rspPickNormaliseRadio2.Active)
{
rsi.SeqDivOut = SubSequenceDivision.Normalised;
int stDiv2;
int edDiv2;
if (!int.TryParse(rspStartDivEntry2.Text, out stDiv2))
{
throw new Exception("Output -> Unable to Parse Start Division!");
}
if (!int.TryParse(rspEndDivEntry2.Text, out edDiv2))
{
throw new Exception("Output -> Unable to Parse End Division!");
}
if (stDiv2 >= edDiv2)
{
throw new Exception("Output -> Start division must be smaller than end!");
}
if (stDiv2 > 20 || edDiv2 > 20)
{
throw new Exception("Output -> Division limit is 20.");
}
rsi.divStartOut = stDiv2;
rsi.divEndOut = edDiv2;
}
else
{
rsi.SeqDivOut = SubSequenceDivision.AbsoluteBases;
int bases2;
if (!int.TryParse(rspNoBaseEntry2.Text, out bases2))
{
throw new Exception("Output -> Unable To Parse Base Count!");
}
if (bases2 > 5000)
{
throw new Exception("Output -> Maximum Number of bases is 5000!");
}
bool doStart2 = true;
if (rspToEndRadio2.Active)
{
doStart2 = false;
}
rsi.baseCountOut = bases2;
rsi.fromStartOut = doStart2;
}
}
int splitInt;
if (!int.TryParse(rspRankDivEntry.Text, out splitInt))
{
throw new Exception("Rank Division - please enter a positive integer.");
}
rsi.SplitCount = splitInt;
if (rspDoSubDivCheck.Active)
{
rsi.doSubSet = true;
if (rspSubDivNextRadio.Active)
{
rsi.SubSetType = SubSetMethod.Current;
int mainRank; int splitRank;
if (!int.TryParse(rspSubTakeGroupEntry.Text, out mainRank))
{
throw new Exception("Unable to parse Sub-Set 'take group' entry, please enter a positive integer.");
}
if (!int.TryParse(rspSubAndSplitEntry.Text, out splitRank))
{
throw new Exception("Unable to parse Sub-Set 'and split' entry, please enter a positive integer.");
}
if (mainRank > rsi.SplitCount)
{
throw new Exception("'Take Group' value must be lower than or equal to the split count.");
}
else if (mainRank < 1)
{
throw new Exception("'Take Group' value too low, please enter a positive integer.");
}
if (splitRank < 1)
{
throw new Exception("'And Split' value too low, please enter a positive integer.");
}
rsi.subCurMainRank = mainRank;
rsi.subCurSplitCount = splitRank;
}
else
{
rsi.SubSetType = SubSetMethod.Previous;
int fromGroup; int toGroup;
if (!int.TryParse(rspSubFromGroupEntry.Text, out fromGroup))
{
throw new Exception("Unable to parse Sub-Set 'from group' entry, please enter a positive integer.");
}
if (!int.TryParse(rspSubToGroupEntry.Text, out toGroup))
{
throw new Exception("Unable to parse Sub-Set 'to group' entry, please enter a positive integer.");
}
if (fromGroup > OldRSPSize)
{
throw new Exception("'From Group' must be lower than or equal to the previous Split-Count");
}
if (toGroup > OldRSPSize)
{
throw new Exception("'To Group' must be lower than or equal to the previous Split-Count");
}
if (toGroup < fromGroup)
{
throw new Exception("'To Group' should be higher than or equal to 'From Group'");
}
rsi.subOldEndRank = toGroup;
rsi.subOldStartRank = fromGroup;
rsi.oldIDlist = RSPGetOldIDList(fromGroup, toGroup);
}
}
else
{
rsi.doSubSet = false;
rsi.SubSetType = SubSetMethod.None;
}
if (rspMergeGraphCheck.Active)
{
rsi.MergeGraphs = true;
}
else
{
rsi.MergeGraphs = false;
}
try {
rsi.sample = rspSampleCombo.ActiveText;
}
catch (Exception e) {
throw new Exception("You need to select one or all samples from the drop-down menu!");
}
OldRSPSize = rsi.SplitCount;
rspMergeGraphCheck.Active = false;
return(rsi);
}