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Rename variables and add dictionary words
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@alchemistmatt
alchemistmatt committed Feb 1, 2019
1 parent 7c42304 commit a4e6bcc
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Showing 38 changed files with 609 additions and 600 deletions.
9 changes: 9 additions & 0 deletions Inferno.sln.DotSettings
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@@ -0,0 +1,9 @@
<wpf:ResourceDictionary xml:space="preserve" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" xmlns:s="clr-namespace:System;assembly=mscorlib" xmlns:ss="urn:shemas-jetbrains-com:settings-storage-xaml" xmlns:wpf="http://schemas.microsoft.com/winfx/2006/xaml/presentation">
<s:Boolean x:Key="/Default/UserDictionary/Words/=dataset/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=datasets/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=Eset/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=Heatmap/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=loess/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=qrollup/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=Quantile/@EntryIndexedValue">True</s:Boolean>
<s:Boolean x:Key="/Default/UserDictionary/Words/=subnodes/@EntryIndexedValue">True</s:Boolean></wpf:ResourceDictionary>
150 changes: 75 additions & 75 deletions Inferno/Data/frmDAnTE.PreProcessMenu.cs
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14 changes: 7 additions & 7 deletions Inferno/Data/frmImputePar.cs
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Expand Up @@ -158,13 +158,13 @@ public Purgatorio.clsImputePar clsImputePar
{
get
{
mclsImputePar.mstrFiltCutoff = CutOff;
mclsImputePar.mstrmode = Mode;
mclsImputePar.mstrK = K;
mclsImputePar.mstrNPCs = nPCs;
mclsImputePar.mstrSVDth = SVDthres;
mclsImputePar.mstrMaxIter = MaxSteps;
mclsImputePar.mstrSubConst = Const;
mclsImputePar.mFiltCutoff = CutOff;
mclsImputePar.mImputationMode = Mode;
mclsImputePar.mK = K;
mclsImputePar.mNPCs = nPCs;
mclsImputePar.mSVDth = SVDthres;
mclsImputePar.mMaxIterations = MaxSteps;
mclsImputePar.mSubConst = Const;
mclsImputePar.FactorSelected = Factor;
mclsImputePar.mintFactorIndex = FactorIndex;
mclsImputePar.mblNoFill = NoFill;
Expand Down
48 changes: 24 additions & 24 deletions Inferno/DataIO/frmDAnTE.DataTypeSpecificMethods.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ namespace DAnTE.Inferno
public enum enmDataType
{
/// <summary>
/// Flat file of expression data
/// Flat file of expression data (expression set)
/// </summary>
ESET,

Expand Down Expand Up @@ -583,10 +583,10 @@ private bool OpenSession(string dataFilePath)
return false;
}

var rcmd = "load(file=\"" + dataFilePath.Replace("\\", "/") + "\")";
var rCmd = "load(file=\"" + dataFilePath.Replace("\\", "/") + "\")";
try
{
mRConnector.EvaluateNoReturn(rcmd);
mRConnector.EvaluateNoReturn(rCmd);
vars = mRConnector.GetSymbolAsStrings("vars");
mRConnector.EvaluateNoReturn("print(vars)");
}
Expand Down Expand Up @@ -788,14 +788,14 @@ private void AddDataNode(clsDatasetTreeNode dataNodeToAdd)
dataNodeToAdd.mTNode.ContextMenuStrip = mContextMenuTreeV;

if (dataNodeToAdd.mstrParentNode.Equals("DAnTE"))
ctltreeView.Nodes[0].Nodes.Add(dataNodeToAdd.mTNode);
ctlTreeView.Nodes[0].Nodes.Add(dataNodeToAdd.mTNode);
else
{
var parentNode = (mhtDatasets[dataNodeToAdd.mstrParentNode]).mTNode;
parentNode.Nodes.Add(dataNodeToAdd.mTNode);
}
ctltreeView.ExpandAll();
ctltreeView.SelectedNode = dataNodeToAdd.mTNode;
ctlTreeView.ExpandAll();
ctlTreeView.SelectedNode = dataNodeToAdd.mTNode;
statusBarPanelMsg.Text = dataNodeToAdd.mstrMessage;
statusBarPanelRowNum.Text = dataNodeToAdd.mDTable.Rows.Count + " Rows/" +
dataNodeToAdd.mDTable.Columns.Count + " Columns.";
Expand All @@ -804,7 +804,7 @@ private void AddDataNode(clsDatasetTreeNode dataNodeToAdd)
else
{
tn.Tag = dataNodeToAdd;
ctltreeView.SelectedNode = tn;
ctlTreeView.SelectedNode = tn;
NodeSelect(tn);
}
}
Expand Down Expand Up @@ -880,16 +880,16 @@ public string CorrespondingRdataset(string selected)
/// <returns></returns>
private string Vars2Save()
{
string rcmd = null;
string rCmd = null;
foreach (var item in mhtDatasets)
{
var datasetItem = item.Value;
if (!string.IsNullOrWhiteSpace(datasetItem.mstrRProtDatasetName))
rcmd += '"' + datasetItem.mstrRProtDatasetName + '"' + ",";
rCmd += '"' + datasetItem.mstrRProtDatasetName + '"' + ",";
else
rcmd += '"' + datasetItem.mstrRdatasetName + '"' + ",";
rCmd += '"' + datasetItem.mstrRdatasetName + '"' + ",";
}
return rcmd;
return rCmd;
}

/// <summary>
Expand All @@ -899,14 +899,14 @@ private string Vars2Save()
/// <returns></returns>
private string NumericVars()
{
string rcmd = null;
string rCmd = null;
foreach (var item in mhtDatasets)
{
var datasetItem = item.Value;
if (datasetItem.mblIsNumeric)
rcmd += '"' + datasetItem.mstrRdatasetName + '"' + ",";
rCmd += '"' + datasetItem.mstrRdatasetName + '"' + ",";
}
return rcmd;
return rCmd;
}

/// <summary>
Expand All @@ -928,7 +928,7 @@ private void RemoveNodeTree(TreeNode tn)

private TreeNode GetNode(string nodeText)
{
var allNodes = ctltreeView.Nodes[0].Nodes;
var allNodes = ctlTreeView.Nodes[0].Nodes;

foreach (TreeNode node in allNodes)
{
Expand All @@ -948,7 +948,7 @@ private TreeNode GetNode(string nodeText)
}

/// <summary>
/// Deleting each datatable.
/// Deleting each DataTable.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
Expand All @@ -968,18 +968,18 @@ private void DeleteCurrentNode()
{
if (mtabControlData.Controls.Count != 0)
{
var currNode = ctltreeView.SelectedNode;
var strSelectedNode = currNode.Text;
var currentNode = ctlTreeView.SelectedNode;
var strSelectedNode = currentNode.Text;

ctltreeView.Nodes.Remove(currNode);
RemoveNodeTree(currNode);
ctlTreeView.Nodes.Remove(currentNode);
RemoveNodeTree(currentNode);

if (ctltreeView.Nodes[0].Nodes.Count > 0)
if (ctlTreeView.Nodes[0].Nodes.Count > 0)
{
var idx = ctltreeView.Nodes[0].Nodes.Count;
ctltreeView.SelectedNode = ctltreeView.Nodes[0].Nodes[idx - 1];
var idx = ctlTreeView.Nodes[0].Nodes.Count;
ctlTreeView.SelectedNode = ctlTreeView.Nodes[0].Nodes[idx - 1];
}
if (ctltreeView.Nodes[0].Nodes.Count == 0)
if (ctlTreeView.Nodes[0].Nodes.Count == 0)
{
mtabControlData.Controls.RemoveAt(0);
Title = "Main";
Expand Down
6 changes: 3 additions & 3 deletions Inferno/DataIO/frmDAnTE.FileMenu.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,7 @@ private void SessionFileOpenFinalize(bool success, bool cancelled, string errorM
// Load succeeded (or an exception occurred)
if (success)
{
ctltreeView.Nodes[0].Nodes.Clear();
ctlTreeView.Nodes[0].Nodes.Clear();

foreach (var dataset in mhtDatasets)
{
Expand Down Expand Up @@ -468,7 +468,7 @@ private void menuItemSave_Click(object sender, EventArgs e)
{
try
{
var selectedNodeTag = (clsDatasetTreeNode)ctltreeView.SelectedNode.Tag;
var selectedNodeTag = (clsDatasetTreeNode)ctlTreeView.SelectedNode.Tag;

if (mtabControlData.Controls.Count != 0)
{
Expand Down Expand Up @@ -544,7 +544,7 @@ public bool OK2Exit()

private void mCtxtMenuSave_Click(object sender, EventArgs e)
{
var selectedTable = (clsDatasetTreeNode)ctltreeView.SelectedNode.Tag;
var selectedTable = (clsDatasetTreeNode)ctlTreeView.SelectedNode.Tag;

if (!mhtDatasets.ContainsKey("Protein Info"))
{
Expand Down
20 changes: 10 additions & 10 deletions Inferno/Explore/frmDAnTE.ExploreMenu.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,14 +19,14 @@ partial class frmDAnTE

private void menuItemPCAPlot_Click(object sender, EventArgs e)
{
var selectedNodeTag = (clsDatasetTreeNode)ctltreeView.SelectedNode.Tag;
var selectedNodeTag = (clsDatasetTreeNode)ctlTreeView.SelectedNode.Tag;

if (!ValidateNodeIsSelected(selectedNodeTag))
{
return;
}

if (!ValidateIsPlottable(selectedNodeTag, 2))
if (!ValidateIsPlotTable(selectedNodeTag, 2))
{
return;
}
Expand Down Expand Up @@ -75,7 +75,7 @@ public void PlotPCA(clsPCAplotPar mclsPCA)
if (frmPCA.ShowDialog() == DialogResult.OK)
{
mclsPCApar = frmPCA.clsPCApar;
var pcaPlots = new clsRplotData(mclsPCApar.Rcmd, "PCA");
var pcaPlots = new clsRplotData(mclsPCApar.RCommand, "PCA");

m_BackgroundWorker.RunWorkerAsync(pcaPlots);
mfrmShowProgress.Reset("Generating PCA Plots ...");
Expand All @@ -94,7 +94,7 @@ public void PlotPCA(clsPCAplotPar mclsPCA)

private void mnuItemHeatmap_Click(object sender, EventArgs e)
{
var selectedNodeTag = (clsDatasetTreeNode)ctltreeView.SelectedNode.Tag;
var selectedNodeTag = (clsDatasetTreeNode)ctlTreeView.SelectedNode.Tag;

if (!ValidateNodeIsSelected(selectedNodeTag))
{
Expand All @@ -103,7 +103,7 @@ private void mnuItemHeatmap_Click(object sender, EventArgs e)

maxRow = selectedNodeTag.mDTable.Rows.Count;

if (!ValidateIsPlottable(selectedNodeTag, 2))
if (!ValidateIsPlotTable(selectedNodeTag, 2))
{
return;
}
Expand Down Expand Up @@ -163,7 +163,7 @@ public void PlotHeatmap(clsHeatmapPar mclsHmapPar)
{
mclsHeatmapPar = frmHmapParams.clsHmapPar;
doClust = frmHmapParams.DoClust;
var heatmapPlot = new clsRplotData(mclsHeatmapPar.Rcmd, "Hmap");
var heatmapPlot = new clsRplotData(mclsHeatmapPar.RCommand, "Hmap");

Add2AnalysisHTable(mclsHeatmapPar, "Heatmap_Clustering");

Expand All @@ -183,14 +183,14 @@ public void PlotHeatmap(clsHeatmapPar mclsHmapPar)

private void mnuItemPatterns_Click(object sender, EventArgs e)
{
var selectedNodeTag = (clsDatasetTreeNode)ctltreeView.SelectedNode.Tag;
var selectedNodeTag = (clsDatasetTreeNode)ctlTreeView.SelectedNode.Tag;

if (!ValidateNodeIsSelected(selectedNodeTag))
{
return;
}

if (!ValidateIsPlottable(selectedNodeTag, 2))
if (!ValidateIsPlotTable(selectedNodeTag, 2))
{
return;
}
Expand Down Expand Up @@ -228,7 +228,7 @@ private void mnuItemPatterns_Click(object sender, EventArgs e)
mclsPatternPar = patternDefForm.clsPatternPar;
Add2AnalysisHTable(mclsPatternPar, "Pattern_Search");

m_BackgroundWorker.RunWorkerAsync(mclsPatternPar.Rcmd);
m_BackgroundWorker.RunWorkerAsync(mclsPatternPar.RCommand);
mfrmShowProgress.Reset("Pattern Searching ...");
mfrmShowProgress.ShowDialog();
}
Expand All @@ -253,7 +253,7 @@ private bool SearchPatterns()
var success = true;
try
{
mRConnector.EvaluateNoReturn(mclsPatternPar.Rcmd);
mRConnector.EvaluateNoReturn(mclsPatternPar.RCommand);
if (mRConnector.GetTableFromRmatrix("patternData"))
{
var patternTable = mRConnector.DataTable.Copy();
Expand Down

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