public static void LoadGenome()
{
try{
ProgramState.LoadedGenome = false;
ProgramState.GenomeLoadLock = false;
UpdateLog("Loading Genome..", true);
if (AppSettings.Loading.GEN_LINE_BREAK.Item)
{
Genome.LoadGenomeReturnSeq(genomeFileName);
}
else
{
Genome.LoadGenomeLongSeq(genomeFileName);
}
RankSplit.GetMethodsFromGenomeInstance();
UpdateLog("Loaded " + Genome.ShortFileName + " into memory..", true);
ProgramState.LoadedGenome = true;
ProgramState.GenomeLoadLock = true;
}
catch (Exception e) {
MainWindow.GenerateMessageWindow(e.Message);
ProgramState.GenomeLoadLock = true;
}
}
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);
}
}
public static void Assemble()
{
Genome = new Genome();
ProgramState.Init();
AppSettings.Assemble();
RankSplit.Assemble();
FPKMFileNames = new List <string> ();
BAMFileNames = new List <string> ();
VariantFileNames = new List <string> ();
TypeDict = new ElementTypeDictionary();
Samples = new Dictionary <string, BioSample> ();
BioSample.ResetStaticLoader();
GeneToScaffDict = new Dictionary <string, string> ();
RegionToScaffDict = new Dictionary <string, string> ();
RSPToMergeSeries = new List <Series> ();
StatsTester.Assemble();
}
public void UpdateRankSplit()
{
if (ProgramState.LoadedSamples)
{
ClearComboBox(rspTextOutputCombo);
ClearComboBox(rspSequenceCombo);
ClearComboBox(rspMethodCombo);
ClearComboBox(rspGraphicalOutputCombo);
ClearComboBox(rspSampleCombo);
ClearComboBox(rspSequenceForCombo);
RankSplitMethods = RankSplit.GetRelevantMethods();
RankSplitGraphOut = RankSplit.GetRelevantOutputGraph();
RankSplitTextOut = RankSplit.GetRelevantOutputText();
RankSplitSamples = RankSplit.GetRelevantSamples();
RankSplitGraphToTypes = RankSplit.GetGraphTypes();
RankSplitGraphDesc = RankSplit.GetRelevantGraphTypes();
List <string> seqFet = RankSplit.GetRelevantFeatures();
foreach (KeyValuePair <string, BioSample> kvp in RankSplitSamples)
{
rspSampleCombo.AppendText(kvp.Key);
}
foreach (KeyValuePair <string, RankMethod> kvp in RankSplitMethods)
{
rspMethodCombo.AppendText(kvp.Key);
}
foreach (KeyValuePair <string, OutputMethGraph> kvp in RankSplitGraphOut)
{
rspGraphicalOutputCombo.AppendText(kvp.Key);
}
foreach (KeyValuePair <string, OutputMethText> kvp in RankSplitTextOut)
{
rspTextOutputCombo.AppendText(kvp.Key);
}
foreach (string st in seqFet)
{
rspSequenceCombo.AppendText(st);
}
foreach (string st in seqFet)
{
rspSequenceForCombo.AppendText(st);
}
}
}
protected void RSPOnGraphComboChange(object sender, EventArgs e)
{
if (rspGraphicalOutputCombo.ActiveText.Length > 3)
{
ClearComboBox(rspGraphTypeCombo);
OutputMethGraph omg = RankSplitGraphOut [rspGraphicalOutputCombo.ActiveText];
List <GraphType> tys = RankSplitGraphToTypes [omg];
List <string> descs = RankSplit.GraphTypesToStrings(tys);
foreach (string gt in descs)
{
rspGraphTypeCombo.AppendText(gt);
}
}
}
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);
}