added first trial of reading cdxml files instead of image files for d…

…isplaying lipid precursor / fragment structures
lifs-tools · Oct 6, 2023 · d49e145 · d49e145
1 parent 2437ac6
commit d49e145
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Showing 7 changed files with 577 additions and 23 deletions.
diff --git a/LipidCreator/CreatorGUI.Designer.cs b/LipidCreator/CreatorGUI.Designer.cs
diff --git a/LipidCreator/CreatorGUI.cs b/LipidCreator/CreatorGUI.cs
@@ -38,6 +38,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 using log4net;
 using System.ComponentModel;
 using System.Diagnostics;
+using System.Drawing.Drawing2D;
 using ExtensionMethods;
 
 namespace LipidCreator
@@ -143,7 +144,7 @@ public CreatorGUI(string _inputParameters)
                         }
                     }
                 }
-                tabList = new ArrayList(new TabPage[] {homeTab, glycerolipidsTab, phospholipidsTab, sphingolipidsTab, sterollipidsTab, mediatorlipidsTab});
+                tabList = new ArrayList(new TabPage[] {homeTab, glycerolipidsTab, phospholipidsTab, sphingolipidsTab, sterollipidsTab, mediatorlipidsTab, quicksearchTab});
                 if (!lipidCreatorInitError) tutorial = new Tutorial(this);
 
                 Rectangle r = Screen.FromControl(this).Bounds;
@@ -246,8 +247,7 @@ public CreatorGUI(string _inputParameters)
 
 
 
-
-
+
 
         public void resetLipidCreatorMenu(Object sender, EventArgs e)
         {
@@ -258,6 +258,30 @@ public void resetLipidCreatorMenu(Object sender, EventArgs e)
 
 
 
+        public void parseXML(XElement element, List<XElement> nodes, List<XElement> edges)
+        {
+            foreach (var fragment in element.Elements().Where(el => el.Name.LocalName.Equals("fragment")))
+            {
+                foreach (var node in fragment.Elements().Where(el => el.Name.LocalName.Equals("n")))
+                {
+                    nodes.Add(node);
+                    parseXML(node, nodes, edges);
+                }
+                foreach (var node in fragment.Elements().Where(el => el.Name.LocalName.Equals("b")))
+                {
+                    edges.Add(node);
+                }
+                foreach (var node in fragment.Elements().Where(el => el.Name.LocalName.Equals("graphic")))
+                {
+                    nodes.Add(node);
+                }
+            }
+        }
+
+
+
+
+
 
 
         public void statisticsMenu(Object sender, EventArgs e)
@@ -392,7 +416,8 @@ public void resetAllLipids()
                                                       new Phospholipid(lipidCreator),
                                                       new Sphingolipid(lipidCreator),
                                                       new Sterol(lipidCreator),
-                                                      new Mediator(lipidCreator)});
+                                                      new Mediator(lipidCreator),
+                                                      null});
         }
 
 

diff --git a/LipidCreator/LipidCreator.cs b/LipidCreator/LipidCreator.cs
@@ -143,7 +143,7 @@ public class LipidCreator : IDisposable
         public static PlatformID LC_OS;
         public ArrayList registeredLipids;
         public Dictionary<ulong, Lipid> registeredLipidDictionary;
-        public IDictionary<string, IDictionary<bool, IDictionary<string, MS2Fragment>>> allFragments; // lipid class -> positive charge -> fragment name -> fragment
+        public IDictionary<string, IDictionary<bool, IDictionary<string, MS2Fragment>>> allFragments; // lipid class -> positive/negative charge -> fragment name -> fragment
         public IDictionary<int, ArrayList> categoryToClass;
         public IDictionary<string, Precursor> headgroups;
         public DataTable transitionList;
@@ -775,7 +775,7 @@ public LipidCreator(string pipe, bool firstInit = false)
                     log.Info("Opening connection to Skyline through pipe " + pipe);
                     client.Connect();
                     log.Info("Connected to Skyline through pipe " + pipe);
-                    while (client.NumberOfServerInstances>0)
+                    while (client.NumberOfServerInstances > 0)
                     {
                         log.Debug("Checking Skyline pipe connection!");
                         var nServers = client.NumberOfServerInstances;

diff --git a/LipidCreator/LipidsInterList.cs b/LipidCreator/LipidsInterList.cs
@@ -30,6 +30,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 using System.Drawing;
 using System.IO;
 using System.Windows.Forms;
+using System.Globalization;
 
 
 namespace LipidCreator
@@ -53,10 +54,12 @@ public LipidsInterList (CreatorGUI _creatorGUI, ArrayList _returnValues)
             precursorDataTable.Columns[1].DataType = typeof(string);
             precursorDataTable.Columns.Add(new DataColumn("Adduct"));
             precursorDataTable.Columns[2].DataType = typeof(string);
-            precursorDataTable.Columns.Add(new DataColumn("Category"));
+            precursorDataTable.Columns.Add(new DataColumn("Precursor Ion m/z"));
             precursorDataTable.Columns[3].DataType = typeof(string);
+            precursorDataTable.Columns.Add(new DataColumn("Category"));
+            precursorDataTable.Columns[4].DataType = typeof(string);
             precursorDataTable.Columns.Add(new DataColumn("reference"));
-            precursorDataTable.Columns[4].DataType = typeof(PrecursorData);
+            precursorDataTable.Columns[5].DataType = typeof(PrecursorData);
 
             InitializeComponent ();
 
@@ -66,6 +69,7 @@ public LipidsInterList (CreatorGUI _creatorGUI, ArrayList _returnValues)
                 row["Keep"] = precursorData.precursorSelected;
                 row["Precursor name"] = precursorData.precursorName;
                 row["Adduct"] = precursorData.precursorAdductFormula;
+                row["Precursor Ion m/z"] = string.Format(CultureInfo.InvariantCulture, "{0:N4}", precursorData.precursorM_Z).Replace(",", "");
                 row["Category"] = precursorData.lipidCategory.ToString();
                 row["reference"] = precursorData;
                 precursorDataTable.Rows.Add(row);
@@ -82,17 +86,21 @@ public LipidsInterList (CreatorGUI _creatorGUI, ArrayList _returnValues)
 
         private void precursorGridViewDataBindingComplete(object sender, DataGridViewBindingCompleteEventArgs e)
         {
+            dataGridViewPrecursors.Columns[0].ReadOnly = true;
             dataGridViewPrecursors.Columns[0].Width = 50;
             dataGridViewPrecursors.Columns[0].SortMode = DataGridViewColumnSortMode.Automatic;
-            dataGridViewPrecursors.Columns[1].Width = (int)Math.Floor(dataGridViewPrecursors.Size.Width * 0.4);
+            dataGridViewPrecursors.Columns[1].Width = (int)Math.Floor(dataGridViewPrecursors.Size.Width * 0.3);
             dataGridViewPrecursors.Columns[1].ReadOnly = true;
             dataGridViewPrecursors.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.None;
-            dataGridViewPrecursors.Columns[2].Width = (int)Math.Floor(dataGridViewPrecursors.Size.Width * 0.2);
+            dataGridViewPrecursors.Columns[2].Width = (int)Math.Floor(dataGridViewPrecursors.Size.Width * 0.20);
             dataGridViewPrecursors.Columns[2].ReadOnly = true;
             dataGridViewPrecursors.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.None;
+            dataGridViewPrecursors.Columns[3].Width = (int)Math.Floor(dataGridViewPrecursors.Size.Width * 0.15);
             dataGridViewPrecursors.Columns[3].ReadOnly = true;
-            dataGridViewPrecursors.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
-            dataGridViewPrecursors.Columns[4].Visible = false;
+            dataGridViewPrecursors.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.None;
+            dataGridViewPrecursors.Columns[4].ReadOnly = true;
+            dataGridViewPrecursors.Columns[4].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
+            dataGridViewPrecursors.Columns[5].Visible = false;
 
         }
 

diff --git a/LipidCreator/LipidsReview.Designer.cs b/LipidCreator/LipidsReview.Designer.cs
diff --git a/LipidCreator/MS2Form.Designer.cs b/LipidCreator/MS2Form.Designer.cs