-

MetaboliteLevels/Data/Algorithms/Definitions/Clusterers/Implementations/Legacy/LegacyDKMeansPPClusterer.cs

@@ -44,7 +44,7 @@ protected override IEnumerable<Cluster> Cluster( IntensityMatrix vmatrix, Distan
             // SEED GROUP
             GroupInfo groupInfo = (GroupInfo)tag.UntypedArgs.Parameters[3];
             // DO-K-MEANS?
-            bool doKMeans = (int)tag.UntypedArgs.Parameters[4] != 0;
+            bool doKMeans = (bool)tag.UntypedArgs.Parameters[4];
 
             // Create the seed cluster
             Cluster seedCluster = new Cluster("1", tag);
@@ -150,7 +150,7 @@ protected override AlgoParameterCollection CreateParamaterDesription()
                                                 new AlgoParameter("d", "Minimum distance between exemplars before no more are selected (use MIN for no limit)", AlgoParameterTypes.Double),
                                                 new AlgoParameter("seed.peak", "The peak to act as the first exemplar", AlgoParameterTypes.WeakRefPeak),
                                                 new AlgoParameter("seed.group", "The group to act as the first exemplar (only if one vector is generated per group, otherwise this is ignored)", AlgoParameterTypes.Group),
-                                                new AlgoParameter("use.kmeans", "Whether to perform k-means after the exemplars have been selected (0 = no, 1 = yes).", AlgoParameterTypes.Integer)
+                                                new AlgoParameter("use.kmeans", "Whether to perform k-means after the exemplars have been selected (0 = no, 1 = yes).", AlgoParameterTypes.Boolean)
                                               );
         }    
 

MetaboliteLevels/Data/Algorithms/General/EAlgoParameterType.cs

@@ -83,6 +83,7 @@ internal interface IAlgoParameterType
     internal static class AlgoParameterTypes
     {
         public static IAlgoParameterType Integer                       = new _Integer();
+        public static IAlgoParameterType Boolean                       = new _Boolean();
         public static IAlgoParameterType Double                        = new _Double();
         public static IAlgoParameterType WeakRefStatisticArray         = new _WeakRefStatisticArray();
         public static IAlgoParameterType WeakRefPeak                   = new _WeakRefPeak();
@@ -177,7 +178,62 @@ public string TryToString( object x )
             }
 
             internal abstract string OnTryToString( T x );
-        }        
+        }
+
+        private class _Boolean : _AlgoParameterType<bool>
+        {
+            public override IEnumerable<string> Aliases => new[] { "Boolean", "Bool" };
+
+            protected override object OnBrowse( Form owner, Core _core, object value )
+            {
+                MsgBoxButton[] btns =
+               {
+                    new MsgBoxButton( "YES", Resources.MnuUp, DialogResult.Yes ),
+                    new MsgBoxButton( "NO", Resources.MnuDown, DialogResult.No ),
+                    new MsgBoxButton( "Cancel", Resources.MnuCancel, DialogResult.Cancel )
+                };
+
+                switch (FrmMsgBox.Show( owner, "Select Value", null, "Select a value", Resources.MsgHelp, btns, DialogResult.Cancel, DialogResult.Cancel ))
+                {
+                    case DialogResult.Yes:
+                        return (object)true;
+
+                    case DialogResult.No:
+                        return (object)false;
+
+                    default:
+                        return null;
+                }
+            }
+
+            protected override object OnFromString( FromStringArgs args )
+            {
+                switch (args.Text.ToUpper())
+                {
+                    case "1":
+                    case "YES":
+                    case "Y":
+                    case "TRUE":
+                    case "T":
+                        return true;
+
+                    case "0":
+                    case "NO":
+                    case "N":
+                    case "FALSE":
+                    case "F":
+                        return false;
+
+                    default:
+                        return null;
+                }
+            }
+
+            internal override string OnTryToString( bool x )
+            {
+                return x ? "Yes" : "No";
+            }
+        }
 
         private class _Integer : _AlgoParameterType<int>
         {

MetaboliteLevels/Gui/Controls/Charts/ChartHelperForPeaks.cs

@@ -268,6 +268,14 @@ private void AddUpperAndLowerShade(
             }
         }
 
+        /// <summary>
+        /// Adds the mean and standard deviation lines to the plot.
+        /// </summary>
+        /// <param name="plot">Target plot</param>
+        /// <param name="o">Options</param>
+        /// <param name="observations">Set of observations</param>
+        /// <param name="peak">Peak being plotted</param>
+        /// <param name="groupLegends">Dictionary to get group legends from</param>
         private void AddMeanAndSdLines(
             MCharting.Plot plot,
             StylisedPeakOptions o,
@@ -331,8 +339,9 @@ private void AddMeanAndSdLines(
                 sMin.Style.DrawLines = new Pen( c, this._core.Options.LineWidth );
                 sMax.Style.DrawLines = new Pen( c, this._core.Options.LineWidth );
 
-                sMin.Style.DrawLines.DashStyle = DashStyle.Dot;
-                sMax.Style.DrawLines.DashStyle = DashStyle.Dot;
+                sMean.Style.DrawLines.DashStyle = DashStyle.Dash;
+                sMin.Style.DrawLines.DashStyle = DashStyle.Dash;
+                sMax.Style.DrawLines.DashStyle = DashStyle.Dash;
 
                 // Add the points
                 AddDataPoint( sMean, xLeft, yMean, @group );

MetaboliteLevels/Gui/Controls/EditableComboBox.cs

@@ -193,7 +193,7 @@ public bool Enabled
         {
             get
             {
-                return this.ComboBox.Enabled && this._button.Enabled;
+                return this.ComboBox.Enabled;
             }
             set
             {

MetaboliteLevels/Gui/Forms/Activities/FrmActDataLoad.cs

@@ -316,11 +316,13 @@ private static void Load_3_Adducts( FileLoadInfo dataInfo, List<Adduct> adducts,
 
                 if (fileName.StartsWith( "resx:\\\\" ))
                 {
-                    using (var s = Resx.Scripts.ResourceManager.GetStream( fileName.Substring( 7 ) ))
-                    {
-                        using (StreamReader sr = new StreamReader( s ))
+                    byte[] text = (byte[])Resx.Scripts.ResourceManager.GetObject( fileName.Substring( 7 ) );
+
+                    using (MemoryStream ms = new MemoryStream( text ))
+                    {
+                        using (StreamReader sr = new StreamReader( ms ))
                         {
-                            mat = reader.Read<string>( sr, fileName );
+                            mat = reader.Read<string>( sr, fileName );
                         }
                     }
                 }

MetaboliteLevels/Gui/Forms/Activities/FrmActPca.cs

@@ -14,6 +14,7 @@
 using MetaboliteLevels.Data.Session.General;
 using MetaboliteLevels.Data.Session.Main;
 using MetaboliteLevels.Gui.Controls.Lists;
+using MetaboliteLevels.Gui.Forms.Editing;
 using MetaboliteLevels.Gui.Forms.Selection;
 using MetaboliteLevels.Utilities;
 using MGui.Datatypes;
@@ -734,7 +735,9 @@ private void _btnColour_DropDownOpening(object sender, EventArgs e)
 
                 default:
                     throw new SwitchException(this.WhatPlotting);
-            }   
+            }
+
+            FrmEditColumns.Show( this, columns, selected );
 
             foreach (Column column in columns)
             {

MetaboliteLevels/Gui/Forms/Activities/FrmMain.cs

@@ -162,7 +162,7 @@ public FrmMain()
             this._btnSubAnnot.Tag = EVisualClass.Annotation;
             this._btnSubAss.Tag = EVisualClass.Assignment;
             this._btnSubComp.Tag = EVisualClass.Compound;
-            this._btnSubInfo.Tag = EVisualClass.SpecialMeta;
+            this._btnSubInfo.Tag = EVisualClass.SpecialAll;
             this._btnSubStat.Tag = EVisualClass.SpecialStatistic;
             this._btnSubPat.Tag = EVisualClass.Cluster;
             this._btnSubPeak.Tag = EVisualClass.Peak;

MetaboliteLevels/Gui/Forms/Editing/FrmDebug.cs

@@ -146,8 +146,15 @@ private void AddMethod( string p, MethodInvoker invoker, string description )
             lvi.SubItems[1].ForeColor = Color.Gray;
 
             this.listView1.Items.Add( lvi );
-        }                
-
+        }
+
+        [InList]
+        [Description( "Throws an unhandled exception (crashes the program)." )]
+        void unhandled_exception()
+        {
+            throw new InvalidOperationException( "This exception is intentionally unhandled." );
+        }
+
         [InList]
         [Description( "Creates a cluster from each of the pathways, allowing you to explore pathways as you do with clusters." )]
         void create_clusters_from_pathways()

MetaboliteLevels/Gui/Forms/Editing/FrmEditColumns.cs

@@ -19,9 +19,22 @@ internal partial class FrmEditColumns : Form
         private readonly HashSet<Column> _selected;
         private readonly HashSet<object> _view = new HashSet<object>();
 
+        public static Column Show( IWin32Window owner, IEnumerable<Column> available, Column selected )
+        {
+            using (FrmEditColumns frm = new FrmEditColumns( available, new[] { selected }, false ))
+            {
+                if (frm.ShowDialog( owner ) == DialogResult.OK)
+                {
+                    return frm._selected.FirstOrDefault();
+                }
+
+                return null;
+            }
+        }
+
         public static HashSet<Column> Show( IWin32Window owner, IEnumerable<Column> available, IEnumerable<Column> selected )
         {
-            using (FrmEditColumns frm = new FrmEditColumns( available, selected ))
+            using (FrmEditColumns frm = new FrmEditColumns( available, selected, true ))
             {
                 if (frm.ShowDialog( owner ) == DialogResult.OK)
                 {
@@ -32,7 +45,7 @@ public static HashSet<Column> Show( IWin32Window owner, IEnumerable<Column> avai
             }
         }
 
-        internal FrmEditColumns(IEnumerable<Column> available, IEnumerable<Column> selected )
+        internal FrmEditColumns(IEnumerable<Column> available, IEnumerable<Column> selected, bool multiSelect )
         {
             this.InitializeComponent();
             UiControls.SetIcon( this );
@@ -48,6 +61,8 @@ internal FrmEditColumns(IEnumerable<Column> available, IEnumerable<Column> selec
             this._chkDefault.ForeColor = ColumnManager.COLCOL_VISIBLE;
             this._chkFolders.ForeColor = ColumnManager.COLCOL_FOLDER;
 
+            this._multiSelect = multiSelect;              
+
             _view.AddRange( new[] { _chkMetaFields , _chkNormal , _chkStatistics, _chkDefault, _chkFolders } );
 
             ctlContextHelp1.Bind( this, ctlTitleBar1, null, CtlContextHelp.EFlags.None );
@@ -199,6 +214,7 @@ public void AllNodes( List<TreeNode> all, TreeNodeCollection col )
         }   
 
         bool _ignoreCheck = false;
+        private readonly bool _multiSelect;
 
         private void treeView1_AfterCheck( object sender, TreeViewEventArgs e )
         {
@@ -207,6 +223,20 @@ private void treeView1_AfterCheck( object sender, TreeViewEventArgs e )
                 return;
             }
 
+            if (!_multiSelect)
+            {
+                if (e.Node.Nodes.Count != 0)
+                {
+                    e.Node.Checked = false;
+                    return;
+                }
+
+                foreach (TreeNode node in  treeView1.GetAllNodes() )
+                {
+                    node.Checked = node == e.Node;
+                }      
+            }
+
             Column col = e.Node.Tag as Column;
 
             if (col != null)